Bacterial Endophytes

Endophytic fungi are ubiquitous organisms found in the plants, residing intercellular or intracellular, at least for a portion of their lives without causing apparent symptoms of infection. Almost all plants are known to harbor endophytes. The choice of the plant to be used for exploring endophytes for bioactives is important. Therefore, medicinal plants which are known to be used since centuries as an alternative source of medicine, are a valuable source for bioprospecting endophytes. Nevertheless, due to many reasons there is a dire need for novel resources
for novel drugs which can be an answer to many deadly diseases. It is in this context that the present review was
envisaged. The review reveals the importance of endophytic fungi from medicinal plants as a source of bioactive and chemically novel compounds. The bioactive metabolites produced by endophytic fungi originate from different biosynthetic pathways and belong to diverse structural groups such as terpenoids, steroids, quinones, phenols, coumarins etc. Endophytes therefore, represent a chemical reservoir for
new compounds such as, anticancer, immunomodulatory,
antioxidant, antiparasitic, antiviral, antitubercular, insecticidal etc. for use in the pharmaceutical and agrochemical industries. Although, efforts have been made to accommodate as many examples as possible but the depth of the subject is so vast that it cannot be covered in one single review. This in itself speaks of the fact that endophytic fungi from medicinal plants is indeed a treasure worth searching. In the present review only some selected examples have been covered.

A fundamental issue in biology is the question of how bacteria initiate
and maintain pathogenic relationships with eukaryotic hosts. Despite
billions of years of coexistence, far less is known about bacterial/fungal
interactions than the equivalent associations formed by either of these
types of microorganisms with higher eukaryotes. This review highlights
recent research advances in the field of bacterial/fungal interactions, and
provides examples of the various forms such interactions may assume,
ranging from simple antagonism and parasitism to more intimate associations
of pathogenesis and endosymbiosis. Information derived from
the associations of bacteria and fungi in the context of natural and agronomic
ecosystems is emphasized, including interactions observed from
biological control systems, endosymbiotic relationships, diseases of cultivated
mushrooms, and model systems that expand our understanding
of human disease. The benefits of studying these systems at the molecular
level are also emphasized.

Eksplorasi bakteri endofit sebagai agen biokontrol dan pemacu pertumbuhan tanaman tomat telah banyak dilakukan. Isolat tunggal bakteri endofit diketahui berpotensi sebagai agen biokontrol dan pemacu pertumbuhan tanaman, namun sampai saat ini masih sangat sedikit informasi mengenai isolat konsorsium bakteri endofit terutama dari tanaman kehutanan. Tanaman kehutanan diduga memiliki keragaman mikroba endofit yang tinggi karena berada di ekosistem yang belum bayak mengalami modifikasi, oleh karena itu diperlukan isolasi dan uji potensi konsorsium bakteri endofit asal tanaman kehutanan. Isolasi dilakukan dari bagian akar tanaman pada medium tryptone soya agar (TSA) 20%. Isolat yang didapat diuji hipersensitif untuk mendapatkan bakteri non-patogen. Isolat yang lulus seleksi diuji kemampuannya untuk meningkatkan pertumbuhan bibit tomat dengan cara merendam benih tomat pada suspensi bakteri endofit yang telah dibiakkan dalam medium tryptone soya broth (TSB). Pengujian selanjutnya adalah mengukur kemampuan bakteri endofit dalam menekan pertumbuhan Fusarium oxysporum dan Sclerotium rolfsii secara in vitro. Berdasarkan uji yang dilakukan diperoleh 5 isolat konsorsium bakteri endofit mampu menekan pertumbuhan F. oysporum dan S. rolfsii secara in vitro, dan 1 isolat mampu memacu pertumbuhan tanaman tomat.

Kata Kunci: agen antagonis, Fusarium oxysporum, plant growth promotor, Sclerotium rolfsii

The main objective of this study is: Effect of two treatment of bacterial endophytes strains Azotobacter chrocooccum (E1) and Pseudomonas sp. (E2) individually whether as grains soaking and foliar application on some physiological parameters of two wheat plants (Triticum aestivum L.) cultivars (Sakha 93 and Gmiza 9) grown under three levels of irrigation water deficit stress 75, 50 and 25 % field capacity. The tested physiological parameters were chlorophyll pigment (chl. a, b and total) contents, relative water content (RWC), leaf water content (LWC), leaf water deficit (LWD), proline content and some major  essential elements (NPK) contents. Negative impacts were obtained in the tested wheat cultivars grown under the different irrigation water deficit. Application of Azotobacter chrocooccum (E1) and Pseudomonas sp. (E2) strains individually were carried out by spray foliar and grains soaking treatments increased the tested physiological parameters for two cultivars compared with untreated plant, which can overcome the negative effects of drought stress.

Analysis of implications of past and future work
-Location of medicinal and native plants according to Dr. Gary Strobel’s rationale for plant selection in areas of high biodiversity.
-Anti tumor and antimicrobial activities of endophytes.
-Isolation and characterization of bioactive compounds exhibiting antimicrobial activity.
-Application into pharmaceutical industry to produce eco-friendly, efficient, pure source of beneficial bioactive compounds (such as Lobeline, Berberine, etc.).
-Further research and consequent application to agricultural industry to provide heat, drought, ice, and pest tolerant endophyte blends for soil application.
-Understanding natural symbiosis and beneficial relationships between plants and endophytes for better understanding of micro ecosystems and the greater challenge of the preservation of biodiversity.

Background

Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant–microbe interactions.

Results

An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to α, β, γ-Proteobacteria,Actinobacteria and Firmicutes.Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female–male flower ratio.

Conclusion

The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria–plant interaction may significantly contribute to Jatropha’s tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant’s nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.

Electronic supplementary material

The online version of this article (doi:10.1186/s13068-015-0404-y) contains supplementary material, which is available to authorized users.

Keywords: Culturable endophyte, Nitrogen fixation, Methylobacterium, Jatropha curcas L., Biofuel

Pot experiments were carried out during successive winter season of 2010/2011 in the greenhouse conditions at the Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University. The aim of this study was designed to investigate the effect of two treatments of bacterial endophytes strains Azotobacter chrocoocum (E1) and Pseudomonas fluorescens. (E2) individually whether as grains soaking and foliar application on anatomical features of two wheat plants (Triticum aestivum L.) cultivars (Sakha 93 and Gmiza 9) grown under three levels of irrigation water deficit stress (drought) 75, 50 and 25% field capacity (FC). Wheat stem and flag leaf anatomical parameters were take into account were vascular bundle dimensions, xylem vessel diameters as well as epidermis tissue thickness. Moreover, mesophyll tissue thickness values in flag leaf were calculated. The obtained results that, irrigation water deficit levels (75, 50 and 25% FC) treatments decreased revealed the values of the anatomical parameters such as thickness of epidermis, ground, mesophyll and phloem tissues, diameter of xylem vessel, and dimensions of vascular bundles of the tested wheat cultivars. While, treating wheat plants with Azotobacter chrocoocum (E1) and Pseudomonas sp. (E2) significantly increased the values of the tested anatomical characters. This study suggests that the effects of the tested bacterial endophytes treatments act as protective factors against irrigation water deficit and can improve water bio-productivity.

Endophytic bacterial consortia assist plant growth by various secretions in a mutualistic relationship. Studies deciphering such relationships may be meaningful as they explore novel alternatives for agricultural chemical inputs which would otherwise pollute the nature. Hence, an attempt was made to examine the plant-growth-promoting (PGP) potentials of leaf bacterial endophytes from selected medicinal herbs and also their potential to impede the growth of leaf spot disease pathogen Pithomyces atro-olivaceous isolated from Arachis hypogaea L. A total of 10 distinct bacterial morphotypes were isolated from medicinal herbs such as Catharanthus roseus, Phyllanthus amarus, and Ocimum tenuiflorum. All the endophytes were screened for plant-growth-promoting traits and observed to secrete Ammonia (NH 3) (at 90%), Lipases (at 90%), Proteases (at 60%), Siderophores (at 40%), Amylases (at 20%), Chitinases (at 40%), Hydrogen Cyanide (HCN) (at 70%), Indole 3-Acetic Acid (IAA) (at 70%), Cellulases (at 40%), and Phosphate solubilisation (at 10%), followed by antifungal activity against Pithomyces atro-olivaceous (at 10%). We observed Rothia spp., Staphylococcus spp., Lactobacillus sp., Micrococcus sp., Bacillus sp., Propionibacterium spp., and Actinobaculum sp. as leaf endophytes based on biochemistry and the potent isolate was identified as Staphylococcus hominis subsp. novobiosepticus strain KE6 based on 16S gene sequence homology. A marked increase in the total amount of chlorophyll, sugars and protein content, biomass yield and vegetative growth parameters were observed upon 30 days' post inoculation through induced cuts in mature groundnut leaves and the outcomes were statistically analyzed and

Nickel (Ni) bioavailable fraction in the soil is of utmost importance because of its involvement in plant growth and environmental feedbacks. High concentrations of Ni in the soil environment, especially in the root zone, may retard plant growth that ultimately results in reduced plant biomass and yield. However, endophytic microorganisms have great potential to reduce the toxicity of Ni, especially when applied together with zeolite. The present research work was conducted to evaluate the potential effects of an endophytic bacterium Caulobacter sp. MN13 in combination with zeolite on the physiology, growth, quality, and yield of sesame plant under normal and Ni stressed soil conditions through possible reduction of Ni uptake. Surface sterilized sesame seeds were sown in pots filled with artificially Ni contaminated soil amended with zeolite. Results revealed that plant agronomic attributes such as shoot root dry weight, total number of pods, and 1000-grains weight were increased by 41, 45, 54, and 65%, respectively, over control treatment, with combined application of bacteria and zeolite in Ni contaminated soil. In comparison to control, the gaseous exchange parameters (CO2 assimilation rate, transpiration rate, stomatal-sub-stomatal conductance, chlorophyll content, and vapor pressure) were significantly enhanced by co-application of bacteria and zeolite ranging from 20 to 49% under Ni stress. Moreover, the combined utilization of bacteria and zeolite considerably improved water relations of sesame plant, in terms of relative water content (RWC) and relative membrane permeability (RMP) along with improvement in biochemical components (protein, ash, crude fiber, fat), and micronutrients in normal as well as in Ni contaminated soil. Moreover, the same treatment modulated the Ni-stress in plants through improvement in antioxidant enzymes (AEs) activities along with improved Ni concentration in the soil and different plant tissues. Correlation and principal component analysis (PCA) further revealed that combined application of metal-tolerant bacterium Caulobacter sp. MN13 and zeolite is the most influential strategy in alleviating Ni-induced stress and subsequent improvement in growth, yield, and physio-biochemical attributes of sesame plant.

ABSTRAK – Telah dilakukan penelitian tentang aktivitas antioksidan metabolit sekunder bakteri endofit yang diisolasi dari rimpang jahe merah (zingiber officinale linn. var rubrum). Penelitian ini bertujuan untuk memperoleh isolat bakteri endofit yang bersimbiosis dengan rimpang jahe merah, memperoleh data aktivitas antioksidan dengan metode DPPH dan mengetahui informasi mengenai kandungan kimia metabolit sekunder bakteri endofit. Metode yang digunakan pada penelitian ini adalah surface sterilization dan spreading pada media YMA dilanjutkan dengan uji aktivitas antioksidan dengan metode peredaman radikal DPPH dan penapisan fitokimia. Tahapan penelitian ini meliputi isolasi bakteri endofit yang bersimbiosis dengan rimpang jahe, produksi metabolit sekunder isolat bakteri endofit, uji aktivitas antioksidan dan penapisan fitokimia. Penelitian ini menghasilkan tiga isolat bakteri endofit yaitu isolat J 1 , isolat J 2 dan isolat J 3 yang memiliki morfologi sel berbeda serta memiliki aktivitas antioksidan yang paling efektif pada konsentrasi 31,25 ppm dengan nilai % inhibisi pada isolat J 1 , J 2 dan J 3 berturut-turut sebesar 22,71% ; 20,86% dan 13,08% dan semua metabolit sekunder isolat bakteri endofit memiliki kandungan flavanoid dan saponin. Kata kunci: Bakteri endofit, Antioksidan, jahe merah (Zingiber officinale Linn. Var rubrum) ABSTRACT-This research has been done about Antioxidant Activity Of Secondary Metabolites Of Endophytic Bacteria Isolated From Rhizome Red Ginger (Zingiber officinale Linn. Var rubrum). The aim of this research is to obtain isolates of endophytic bacteria in symbiosis with red ginger rhizome, obtain data antioxidant activity by DPPH method and find out information about the chemical content of secondary metabolites of endophytic bacteria. The method used in this study are surface sterilization and spreading on YMA medium followed by antioxidant activity is analyzed by using DPPH radical scavenging method and phytochemical screening. This study resulted in three isolates of endophytic bacteria isolates namely J 1 , J 2 isolates and isolates J 3 which has a different cell morphology as well as having the most effective antioxidant activity at concentrations of 31.25 ppm with values% inhibition on isolates J 1 , J 2 and J 3 , respectively for 22,71%; 20.86% and 13.08% and all the secondary metabolites of endophytic bacterial isolates contain flavonoids and saponins.

Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.

Metal-hyperaccumulating plants, which are hypothesized to use metals for defence against pests and pathogens, provide a unique context in which to study plant – pathogen coevolution. Previously, we demonstrated that the high concentrations of zinc found in leaves of the hyperaccumulator Noccaea caerulescens provide protection against bacterial pathogens, with a potential trade-off between metal-based and pathogen-induced defences. We speculated that an evolutionary arms race between zinc-based defences in N. caerulescens and zinc tolerance in pathogens might have driven the development of the hyperaccumulation phenotype. Here, we investigate the possibility of local adaptation by bacteria to the zinc-rich environment of N. caerulescens leaves and show that leaves sampled from the contaminated surroundings of a former mine site harboured endophytes with greater zinc tolerance than those within plants of an artificially created hyperaccumulat-ing population. Experimental manipulation of zinc concentrations in plants of this artificial population influenced the zinc tolerance of recovered endo-phytes. In laboratory experiments, only endophytic bacteria isolated from plants of the natural population were able to grow to high population densities in any N. caerulescens plants. These findings suggest that long-term coexistence with zinc-hyperaccumulating plants leads to local adaptation by endophytic bacteria to the environment within their leaves.

Nickel (Ni) bioavailable fraction in the soil is of utmost importance because of its involvement in plant growth and environmental feedbacks. High concentrations of Ni in the soil environment, especially in the root zone, may retard plant growth that ultimately results in reduced plant biomass and yield. However, endophytic microorganisms have great potential to reduce the toxicity of Ni, especially when applied together with zeolite. The present research work was conducted to evaluate the potential effects of an endophytic bacterium Caulobacter sp. MN13 in combination with zeolite on the physiology, growth, quality, and yield of sesame plant under normal and Ni stressed soil conditions through possible reduction of Ni uptake. Surface sterilized sesame seeds were sown in pots filled with artificially Ni contaminated soil amended with zeolite. Results revealed that plant agronomic attributes such as shoot root dry weight, total number of pods, and 1000-grains weight were increased by...

Even though beneficial plant–microbe relationships have been studied for over one century, the recognition of a complex microbiome inhabiting the plant is relatively recent and reveals new opportunities for manipulating plant growth and health. Endophytes, commonly defined as non-pathogenic microorganisms inhabiting the plant interior, constitute an important component of the plant microbiome. Specifically, bacterial endophytes gained research interest only in the past decades, due to their role in plant-growth promotion and their potential use in agriculture. New research is continuously published in this topic, with increasing sophistication provided by new technologies such as omics. For this reason, this chapter aimed to summarize current knowledge on bacterial endophytes focusing on three major aspects: (1) current knowledge on their bacterial endophytic diversity and regulation by plant and soil factors, (2) functional aspects of bacterial endophytes and available tools to stu...

Explant oxidative browning and necrosis of Camellia sinensis var. sinensis is a severe problem in tissue culture, often associated with the exuded phenolic compounds and microbial contamination from the explants. In this study, 2-aminoindane-2-phosphonic acid (AIP), an inhibitor of the polyphenol production-required enzyme phenylalanine ammonia lyase (PAL), and different antibiotics were tested to control tea explant necrosis and browning. These compounds were supplemented in the regular plant growth medium together with 6-benzylaminopurine and thidiazuron at different concentrations. Our data indicated that application of 2 µM of AIP was able to effectively inhibit callus browning, significantly reduce EGC abundance, and greatly improve callus induction and growth. Moreover, the use of 150 mg/L of timentin and 30 mg/L gentamycin resulted in an effective elimination of the surface and endophytic microbes associated with explants of C. sinensis var. sinensis. Our study revealed that the inhibition of PAL using AIP combined with the two tested antibiotics could open up new doors to control oxidative tissue browning and endophyte contamination in tissue culture for tea genetic manipulation. Keywords 2-Aminoindane-2-phosphonic acid (AIP) · Bacterial endophytes · Phenolic compounds · Phenylalanine ammonia lyase (PAL)

Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars-Pionero 2010 FL and DANAC SD20A-extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and. We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize tog...

Endophytic bacteria have been recognised as a microorganism that has an important role as the producer of bioactive compounds. In the literature, endophytic bacteria from Noni fruits (Morinda citrifolia l.) with their antioxidant activities have been rarely studied. This research aimed at isolating endophytic bacteria associated with Noni fruits to investigate their antioxidant activity, to identify potential endophytic bacteria with16s rRNA and to detect bioactive compounds. Based on morphological characteristics of bacterial colonies, six endophytic bacteria were isolates from Noni fruits. The isolates were observed and evaluated in terms of their antioxidant activities using 1,1-Diphenyl-2-picryl-hydrazyl radical scavenging activity. Results of this study discovered supernatant from isolate ACP3 to have the highest 1,1-Diphenyl-2-picryl-hydrazyl free-radical scavenging activity up to 68.90%. In addition, molecular identification conducted by poly chain reaction amplification on 16S rRNA gene showed isolate ACP3 belong to Staphylococcus sp. with 100% sequence similarities. Looking at GCMS analysis, ethyl acetate fraction from the secondary metabolites of isolate ACP3 contained pyrazine alkaloids, which have been known as a bioactive compound. Based on these results, the ACP3 strain was considered as a good and sustainable resource for natural antioxidants.

Chapter 10 of the book: Endophytes: Biology and Biotechnology, Volume 1
Maheshwari, Dinesh K. (Ed.) - Springer ( http://www.springer.com/la/book/9783319665405 ).

Associations between microorganisms and botanical species play an important role in the ability of plants to survive and thrive in diverse environments, by better facing unfavorable climatic and edaphic conditions or by determining either a greater vegetative development or possibly the resistance to diseases and pests. In this article, we focus on the relationship between grapevine (Vitis vinifera) and its endophytic plant growth-promoting bacteria (PGPB), i.e., the endophytes that stimulate and facilitate grapevine growth. Most previous studies have considered the ability of such microbes to help plants draw nutrients from the soil or to counter the effect of phytopathogens. Here, we discuss recent studies concerning the infection process, the spatiotemporal localization of endophytic PGPB in grapevine, and particularly their contribution to plant growth and defense against pathogens in this important fruit crop.

Endophytic bacteria have been recognised as a microorganism that has an important role as the producer of bioactive compounds. In the literature, endophytic bacteria from Noni fruits (Morinda citrifolia l.) with their antioxidant activities have been rarely studied. This research aimed at isolating endophytic bacteria associated with Noni fruits to investigate their antioxidant activity, to identify potential endophytic bacteria with16s rRNA and to detect bioactive compounds. Based on morphological characteristics of bacterial colonies, six endophytic bacteria were isolates from Noni fruits. The isolates were observed and evaluated in terms of their antioxidant activities using 1,1-Diphenyl-2-picryl-hydrazyl radical scavenging activity. Results of this study discovered supernatant from isolate ACP3 to have the highest 1,1-Diphenyl-2-picryl-hydrazyl free-radical scavenging activity up to 68.90%. In addition, molecular identification conducted by poly chain reaction amplification on 1...

Piper nigrum, commonly known as black pepper, is one of the most important spice crops with high demand by the world market. However, diseases like foot rot and stem blight cause by Phytophthora capsici have become the important production constraints in black pepper industry. The frequent application of toxic fungicides to counter the diseases in pepper plantations has raised certain environmental issues. In order to mitigate the use of fungicides, biological approach to control P. capsici has been suggested. In this study, endophytic bacteria were isolated from six P. nigrum roots and screened for in vitro antagonistic activity against P. capsici through dual culture, mycelial growth, spore germination and double plate assay. The antagonism testing involved the secretion of volatile and diffusible bioactive compounds by the endophytic bacteria. Out of 19 isolates tested, two isolates DB(2)7 and SB(2)6 produced volatile bioactive compounds and these two isolates showed highest antagonism against P. capsici mycelia with the percentage of inhibition up to 47.63% and 43.33%, respectively. Diffusible compounds from isolates DB(2)7, DB(2)9 and SB(2)6 produced clear zones in spore germination test with radii measurements of 10.0-17.0 mm. Three isolates with promising antifungal activity were further characterised through 16S rDNA sequencing. The analysis of their sequences via National Center for Biotechnology Information (NCBI) suggests close identity towards Enterobacter cancerogenus, Enterobacter cloacae and Enterobacter asburiae. This research study demonstrated that these endophytic bacteria isolates are potentially to be used as biocontrol agent in pepper cultivation.

The effects of salt stress on endophytic prokaryotic communities in plants are largely unknown, and the distribution patterns of bacterial and archaeal endophytes in different tissues of a plant species are rarely compared. We investigated the endophytic bacterial and archaeal communities in roots, stems and leaves of the common reed, Phragmites australis, collected from three tidal zones along a salinity gradient, using terminal restriction fragment (T-RF) length polymorphism analysis of the 16S rRNA genes. The results showed that the bacterial diversity in the roots was significantly higher than that in the leaves, whereas similar archaeal diversity was revealed for either plant tissues or tidal zones. Network analysis revealed that T-RFs were grouped largely by tissue, and the major groups were generally linked by a few common T-RFs. Unique T-RFs in roots were mainly present in plants growing in the supratidal zone, but unique T-RFs in stems and leaves were mainly present in those from the middle and high tidal zones. Non-metric multidimensional scaling ordination and analysis of similarity revealed that bacterial communities were significantly different among tissues (P < 0.05), but similar among tidal zones (P = 0.49). However, the archaeal communities differed among tidal zones (P < 0.05), but were similar among tissues (P = 0.89). This study indicates that: (1) the endophytic archaeal communities are influenced more significantly than the endophytic bacterial communities by soil salinity, and (2) the differential distribution patterns of bacterial and archaeal endophytes in plant tissues along a salinity gradient imply that these two groups play different roles in coastal hydrophytes.