Composition Of Endophytic Bacterial Communities Research Articles

The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles.

Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

Endophytic Bacteria in Ricinus communis L.: Diversity of Bacterial Community, Plant−Growth Promoting Traits of the Isolates and Its Effect on Cu and Cd Speciation in Soil

Ricinus communis L. shows certain tolerance to and good accumulation ability with heavy metals. Endophytic bacteria−enhanced phytoremediation is an effective method to improve heavy metal extraction efficiency. Here, for better application of castor in phytoremediation, the Illumina high−throughput sequencing was carried out to reveal the endophytic bacterial community in the tissues of castor grown in two locations, and traditional microbial cultivation was used to isolate endophytic bacteria from castor. The dominant bacterial phyla were Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes and Acidobacteria, and Proteobacteria was absolutely dominate in all castor tissues. There were significant differences in the composition of endophytic bacterial communities between castor grown in two sites, with obvious variation in the relative abundance of the dominant phylum. The samples from two sites also had their own unique dominant bacterial genera. The analysis of alpha diversity illustrated that the diversity and species richness of endophytic bacteria community in different parts of castor sampled in Tonglushan mining area were lower than those in Gangxia village, Yangxin county. In total, there were 44 endophytic bacteria strains isolated from the tissues of castor, of which 42 strains possessed three or more growth−promoting properties. Most of these isolates were tolerant to Cu or Cd to varying degrees. Eight isolates were selected for further Cu mobilization and soil incubation experiments. Strains TR8, TR18, TR21, YL1, YS3 and YS5 could well solubilize Cu2(OH)2CO3 in medium. Strain YS3 had the best effect on increasing soil DTPA−Cu and DTPA−Cd contents by 8.4% and 6.9%, respectively. Inoculated endophytic isolates were conducive to the conversion of heavy metal forms from insoluble to relatively unstable, and could increase available phosphate content in soil (10.8–29.2%). Therefore, the plant growth−promoting endophytes screened from castor have great application prospects and can provide important support for the microbial−assisted phytoremediation of heavy metal−contaminated soil.

Root endophytic bacterial community composition of Aconitum carmichaelii debx. from three main producing areas in China.

Aconitum carmichaelii Debx. is famous for the bioactive aconitum alkaloids as traditional Chinese medicine. Endophytic bacteria play vital roles in plant growth, health, and the production of secondary metabolites such as alkaloids. In this study, we employed 16 S rRNA amplicon high-throughput sequencing to determine the root endophytic bacterial community of A. carmichaelii Debx. collected from three main producing areas including the geo-authentic area in China, high performance liquid chromatography to measure the contents of six bioactive alkaloids and correlation analysis to explore the relationship among environmental factors, alkaloids contents, and endophytic bacterial community. The results indicated that the root core microbiota of A. carmichaelii Debx. was dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Root endophytic bacterial community in the geo-authentic area was distinct from the other two regions. Soil nitrogen contents, organic matter, and temperature were the main factors contributing to the endophytic bacterial community structure. Significant correlation was found between alkaloids contents and some bacterial genera. Particularly, the abundance of Lactobacillus was positively correlated with the contents of benzoyl-mesaconitine and benzoyl-aconine. This study provided the first insight into the root endophytic bacterial community composition of A. carmichaelii Debx., and can direct further isolation of functional bacterial strains.

Effect of long-term fertilization on bacterial communities in wheat endosphere

Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we investigated endophytic bacterial communities in wheat leaves and roots under different long-term fertilization regimes, including NPK chemical fertilizer and NPK chemical fertilizer combined with wheat straw, pig manure, or cow manure. Endophytic bacterial community composition considerably differed in leaves and roots. Although different fertilization treatments did not affect the endophytic bacterial species richness or phylogenetic diversity in either leaves or roots, the community composition was significantly altered, particularly in roots. The endophytic bacterial co-occurrence network in leaves was more complex and stable than that in roots. Furthermore, many of the keystone species that were identified by their topological positions in the co-occurrence networks of leaves and roots were involved in plant growth and fitness. The total relative abundance of keystone species was the highest in the NPK plus cow manure treatment in both leaves and roots. Overall, our results suggest that different fertilization regimes can strongly affect endophytic bacterial communities, and the combination of NPK fertilizer and cow manure promoted the relative abundance of the key endophytic bacterial microbiota in both leaves and roots, which might be beneficial for plants in agroecosystems.

Root-Associated Endophytic Bacterial Community Composition of Asparagus officinalis of Three Different Varieties.

The online version contains supplementary material available at (10.1007/s12088-021-00926-6) contains supplementary material, which is available to authorized users.

Endogenous bacterial community structure of Pinus massoniana with differing resistance to pine wilt disease

Summary Pine wilt disease (PWD) is a devastating pine disease caused by Bursaphelenchus xylophilus and its main host in China is Pinus massoniana. The relationship between endophytic bacteria and disease resistance in P. massoniana remains unclear. In this paper, the leaves, roots, stems and treetops of different disease-resistant P. massoniana were studied as the research objective and Illumina MiSeq sequencing was used to analyse whether there were significant differences in the composition and diversity of endophytic bacterial communities between different disease-resistant P. massoniana. The results showed that at the genus level there were no obvious differences in the composition of the endophytic bacterial community of different disease-resistant P. massoniana in the leaves, but there were obvious differences in the roots, stems and treetops. The richness and diversity of endophytic bacteria in P. massoniana had no significant impact on its disease resistance, whilst the structure of endophytic bacterial community in stems and treetops may be related to its disease resistance.

The Dynamics of Endophytic Bacterial Community Structure in Rice Roots under Different Field Management Systems

The structure of endophytic bacteria is important to plant health and stress tolerance, but little is known about the impacts of farming systems on temporal changes in diversity of endophytic bacteria. In this study, we investigated the endophytic microbiome in rice roots under organic and conventional farming systems at the seedling and tillering stages over two consecutive cropping seasons using 16S rRNA gene sequencing. Although the composition of the microbiome was significantly influenced by a field management system, growth stage, and interaction between the two factors, the growth stage alone explained more than 40% of variance. Soil pH and organic matter content also partially influenced the endophytic bacterial community composition. In addition, through indicator species analysis and the functional profiles predicted by phylogenetic analysis, we revealed the selection force of rice roots at the tillering stage to recruit endophytes, which are beneficial to plant growth. In summary, our data show that the dynamics of rice root bacterial composition are mainly influenced by the plant growth stage. Our findings offer new insights regarding the control of the root microbiome by host plants and the influence of farming systems.

Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year

BackgroundThe dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites.ResultsIn this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1–3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1–3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium.ConclusionsThis study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna.

The rapid developments in the next-generation sequencing methods in the recent years have provided a wealth of information on the community structures and functions of endophytic bacteria. However, the assembly processes of these communities in different plant tissues are still currently poorly understood, especially in wild plants in natural settings. The aim of this study was to compare the composition of endophytic bacterial communities in leaves and roots of arcto-alpine pioneer plant Oxyria digyna, and investigate, how plant tissue (leaf or root) or plant origin affect the community assembly. To address this, we planted micropropagated O. digyna plants with low bacterial load (bait plants) in experimental site with native O. digyna population, in the Low Arctic. The endophytic bacterial community structures in the leaves and roots of the bait plants were analyzed after one growing season and one year in the field, and compared to those of the wild plants growing at the same site. 16S rRNA gene targeted sequencing revealed that endophytic communities in the roots were more diverse than in the leaves, and the diversity in the bait plants increased in the field, and was highest in the wild plants. Both tissue type and plant group had strong impact on the endophytic bacterial community structures. Firmicutes were highly abundant in the leaf communities of both plant types. Proteobacteria and Bacteroidetes were more abundant in the roots, albeit with different relative abundances in different plant groups. The community structures in the bait plants changed in the field over time, and increasingly resembled the wild plant endophytic communities. This was due to the changes in the relative abundances of several bacterial taxa, as well as species acquisition in the field, but with no species turnover. Several OTUs that were acquired by the bait plants in the field and represent phosphate solubilizing and diazotrophic bacterial taxa, suggesting major role in nutrient acquisition of these bacteria for this nonmycorrhizal plant, thriving in the nutrient poor arctic soils.

Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot

BackgroundSeeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems.ResultsFrom seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. Alpha diversity indices showed significant differences in observed OTU richness (P≤0.05) across genotypes. Significant differences were also found between the individual hills of a rice genotype. PCoA analysis exhibited three separate clusters and revealed the clusters separated based on genotype, while agroecosystem showed a minimal effect on the variation of seed microbiota (adonis, R2=0.07, P=0.024). Interestingly, animal gut resident bacteria such as Bifidobacterium, Faecalibacterium, Lactobacillus, etc. were found in abundance as members of the seed microbiota.ConclusionOverall, our study demonstrates, indigenous rice genotypes of north-east India have a unique blend of endophytic bacteria in their mature seeds. While there are notable variations among plants of the same genotype, we found similarities among genotypes cultivated in completely different environmental conditions. The beta diversity variations across the seven rice genotypes were significantly shaped by their genotype rather than their agroecosystems.

Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments

Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis.

Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China.

Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.

Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines

Super hybrid rice is one of the important research achievements in the field of rice super-high yield breeding in China. Compared with general high-yield rice, the yield potential of super hybrid rice is relatively high, and the average yields per hectare can exceed 10.5 t. This study aimed to study the endophytic bacterial community among a super hybrid rice combination and its parental lines and to reveal the potential relationship and association of endophytic bacteria between rice genotypes and their genetic relevance. In this research, through high-throughput sequencing based on Illumina Hiseq 2500 platform, the seeds of super hybrid rice variety ‘Shenliangyou 5814’ (sample C) and its parental lines ‘Y58S’ (sample M) and ‘C4114’ (sample F) independently cultivated by China were used as plant materials to study their endophytic bacterial structure and diversity. The number of OTUs for sample M, F and C was 327, 288 and 283 respectively, and among them 218 endophytic OTUs coexisted in the 3 samples. Pantoea (18.6–31.1%) was the first dominant groups shared in all three samples, and other dominant shared groups belonged to Methylobacterium (4.48%~17.65%), Sphingomonas (4.0%~11.4%), Rhizobium (5.69–8.78%), Microbacterium (3.85%~9.41%) and Pseudomonas (4.13%~5.68%). Although Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS) analysis showed that there were obvious differences in endophytic bacterial community composition and structure among the 3 samples, the dominant endophytic bacterial genus sample C and its parental lines remained consistency. This study would provide scientific clues for the future research on the vertical transmission of endophytes between rice generations.

Bacterial communities of three plant species from Pb-Zn contaminated sites and plant-growth promotional benefits of endophytic Microbacterium sp. (strain BXGe71).

The endophytic bacterial community of two hyperaccumulators (Arabis alpine, Dysphania ambrosioides) and Veronica ciliate was investigated by Illumina sequencing technology. In addition, the culturable endophytic bacteria (EB) were isolated and their plant-growth promotion capabilities were studied. A dataset consisting of 221,075 filtered high-quality and classifiable unique 16S rDNA gene tags, and an average of 36,846 tags with a mean length of 464-bp for each sample was generated. In total, 10801 different operational taxonomic units (OTUs) were detected, belonging to 18 bacterial phyla, 41 classes, 91 orders, 135 families, and 215 genera. Pseudomonas was the most dominant genus in both shoots and roots of the two hyperaccumulators, making up 81.56% and 81.13%, 41.60% and 77.06% of the total number of OTUs, respectively. However, both Chao 1 and Shannon indices of EB of the two hyperaccumulators were significantly lower than those of V. ciliate (P <. 05), except the Shannon index of D. ambrosioides shoots. The endophytic bacterial community of roots and shoots of A. alpine showed greater similarity with that of D. ambrosioides roots (12 km away), and clustered to one group in dendrogram, in clear contrast to that of V. ciliate, which grew closer to A. alpine (60 m away). Combining results of soil and plant analyses, we suggest that the soil properties, especially heavy metal concentration, may influence the plants endophytic bacterial community composition. Pot experiments showed that the strain BXGe71 (Microbacterium sp.) from A. alpine significantly enhanced host plants' growth under multi-heavy metal (HM) stress (P < .05, t-test).

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage.

Micropropagation has been applied in the recovery and rejuvenation of adult trees, which is achieved by various subcultures in the multiplication phase. This strategy has brought questions about the endophytic microbiota associated with these plants along its manipulation. Therefore, the aim of this study was to evaluate the composition of the endophytic bacterial communities associated with two explants sources [the canopy branches (CB) and the trunk base of the tree (TB)] under prolonged in vitro cultivation. In addition we analyzed the bacterial community dynamic along the subcultures in different micropropagation phases. Bacterial DNA was extracted from samples of mini-stumps (in vivo) from CB and TB and in micro-stumps produced by in vitro cultivations of these explants sources--both originated from one single matrix plant of Eucalyptus benthamii. In vitro establishment occurred in two dates and the evaluation of endophytic bacterial communities was made in vivo and in vitro samples (on 10th, 13th and 16th subcultures), when elongated shoots and roots were analyzed. Analysis was performed by PCR-DGGE based on the V6 region of ribosomal gene 16S rDNA. Bands profiles showed differences in communities between in vivo and in vitro samples, and also distinctions of communities assessed in the subcultures, elongated and rooted samples. Distinctions in the composition of endophytic bacterial communities were greater in CB micro-stumps. These results indicate a differential colonization of explants by endophytic bacteria, with predominance of common (ever-present) endophytes in TB samples and casual, here named opportunistic, in CB samples.

Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability

To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture.

Analysis of endophytic bacterial community composition by 16S rDNA clone library in Achnatherum inebrians

The endophytic bacterial diversity of drunken horse grass (DHG) (Achnatherum inebrians) growing in native habitat station in Xinjiang Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of DHG, a pair of bacterial PCR primers was selected to specifically amplify bacterial 16S rDNA sequences directly from DHG root tissues. Among 249 positive clones in the 16S rDNA library of endophytes, 57 OTUs were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Flavobacteria, Actinobacteria, Sphingobacteria, and uncultured bacteria. The dominant group was Proteobacteria, whie the most numerous genus was Bacillus. More than 8.00% of the total clones showed a high similarity to uncultured bacteria, suggesting that nonculturable bacteria make a significant part of DHG endophytic bacterial community. To our knowledge, this is the first report that endophytic bacteria associated with DHG are revealed by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in DHG.

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process.

BackgroundEndophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic.ResultsFour healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality.ConclusionResults indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.

파이로시퀀싱을 이용한 비료 장기 연용지의 벼 뿌리 내생세균의 군집 분석

화학비료의 장기 시용이 벼 내생 세균 군집에 미치는 영향을 조사하기 위해서 국립농업과학원의 장기 비료 연용 포장에서 재배한 벼 뿌리의 내생균의 군집을 파이로시퀀싱 기법으로 분석하였다. 3요소구 (APK)와 무비구 (NF) 시료에서 직접 DNA를 추출하여 세균에 특이적인 barcode PCR을 수행한 후 454 파이로시퀀싱을 하였다. 두 시료 (3요소구, 무비구)에서 1,900개의 염기서열을 얻었으며, 각각 177개와 72개의 OTU로 분류하였다. 두 시료는 22개의 OTU를 공유하였으며, 이들 OTU는 두 시료에서 모두 우점하였다. 특히 Pseudomonas속에 속하는 OTU의 비율이 매우 높았다. 문 (phylum) 수준에서 우점하는 내생균은 두 시료 모두 Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Actinobacteria 등 이었다. 처리구별로 계산한 다양성 지수는 3요소구 시료에서 더 높았다. 본 연구를 통해 장기간 비료 시용은 식물체내 존재하는 내생균 군집 구조에 영향을 주며, 벼 뿌리의 내생 세균의 군집 다양성을 증가시키는 것을 알 수 있었다. Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.