Endophytic Bacteria Community Research Articles

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Melatonin alleviates cadmium toxicity by regulating root endophytic bacteria community structure and metabolite composition in apple.

The level of cadmium (Cd) accumulation in orchard soils is increasing, and excess Cd will cause serious damage to plants. Melatonin is a potent natural antioxidant and has a potential role in alleviating Cd stress. This study aimed to investigate the effects of exogenous melatonin on a root endophyte bacteria community and metabolite composition under Cd stress. The results showed that melatonin significantly scavenged the reactive oxygen species and restored the photosynthetic system (manifested by the improved photosynthetic parameters, total chlorophyll content and the chlorophyll fluorescence parameters (Fv/Fm)), increased the activity of antioxidant enzymes (the activities of catalase, superoxide dismutase, peroxidase and ascorbate oxidase) and reduced the concentration of Cd in the roots and leaves of apple plants. High-throughput sequencing showed that melatonin increased the endophytic bacterial community richness significantly and changed the community structure under Cd stress. The abundance of some potentially beneficial endophytic bacteria (Ohtaekwangia, Streptomyces, Tabrizicola and Azovibrio) increased significantly, indicating that the plants may absorb potentially beneficial microorganisms to resist Cd stress. The metabolomics results showed that melatonin significantly changed the composition of root metabolites, and the relative abundance of some metabolites decreased, suggesting that melatonin may resist Cd stress by depleting root metabolites. In addition, co-occurrence network analysis indicated that some potentially beneficial endophytes may be influenced by specific metabolites. These results provide a theoretical basis for studying the effects of melatonin on the endophytic bacterial community and metabolic composition in apple plants.

Diversity analysis of Populus euphratica endophytic bacteria in Tarim River Basin, China.

The bacterial diversity in Populus euphratica stem storage liquid samples grown in Shaya County and Yuli County of the Tarim River Basin was investigated. A culture-dependent (dilution spread plate method) and culture-independent method (PCR-RFLP technique) were used to identify the endophytic bacteria community structure and composition in P. euphratica in Tarim River Basin. Sixty-six bacterial strains were isolated from P. euphratica stem storage liquid samples on three agar media. The 16S rDNA gene was amplified and sequenced using bacterial universal primers. Phylogenetic analysis showed that the 66 strains belonged to three phyla (Firmicutes, Actinomycetes, and Gamma-Proteobacteria) and included 16 genera and 29 species. Among them, Pseudomonas (27.27%) and Bacillus (19.69%) were the dominant isolates. CGM-17 was a potentially new species of Pantoea. Restriction fragment length polymorphism of 16S rDNA gene amplified by polymerase chain reaction (PCR-RFLP) revealed 48 operational taxonomic units (OTUs). Phylogenetic analysis indicated that the 48 OTUs belonged to Firmicutes, Actinobacteria, Proteobacteria (α-, β-, γ-subgroup), Bacteroidetes, and Verrucomicrobia. Gamma-Proteobacteria was the dominant group, similarly to the culture-dependent method, accounting for 53% of the entire bacterial clone library. Our results indicate that P. euphratica endophytic bacteria diversity in the Tarim River Basin was rich, and the resources of endophytic bacteria were high. They provide valuable reference data and species resources for screening indigenous and functional strains of endophytic bacteria in P. euphratica.

Endophytic Bacteria Isolated from Tea Leaves (Camellia sinensis var. assamica) Enhanced Plant-Growth-Promoting Activity

Tea (Camellia sinensis var. assamica) is a traditional and economically important non-alcoholic beverage-producing plant grown in large plantations in the northern region of Thailand and has a diverse community of endophytic bacteria. In this study, a total of 70 bacterial isolates were isolated from healthy asymptomatic samples of tea leaves from five different tea gardens in Chiang Mai, Thailand. Based on 16S rDNA sequence analysis, these bacterial isolates were taxonomically grouped into 11 different genera, namely Bacillus, Curtobacterium, Enterobacter Microbacterium, Moraxella, Neobacillus, Priestia, Pseudarthrobacter, Pseudomonas, Sporosarcina, and Staphylococcus. All these isolates were evaluated for their potential to produce indole-3-acetic acid (IAA), siderophores, and cellulolytic enzymes while having phosphate-solubilizing and tannin tolerance capacity. Most isolated bacterial endophytes belonged to the Bacillus genus and exhibited multiple plant-growth-promoting abilities. All bacterial endophytes could produce varied concentrations of the indole-related compounds, and the strain Curtobacterium citreum P-5.19 had the highest production of IAA at 367.59 µg/mL, followed by Pseudarthrobacter enclensis P-3.12 at 266.97 µg/mL. Seventy-eight percent (78%) of the total isolates solubilized inorganic phosphate, while 77%, 65%, and 52% were positive for extracellular proteases, cellulases, and pectinases, respectively. Remarkably, 80% of the isolates were capable of growth on nutrient agar supplemented with 1% (w/v) tannic acid. C. citreum P-5.19 and P. enclensis P-3.12 were selected for evaluation of plant growth promotion, and it was found that both bacterial endophytes enhanced seed germination rate and improved seedling growth parameters such as fresh and/or dry weight, root length, and shoot lengths of sunflower and tomato seeds. The selected bacterial endophytes isolated from tea leaves in this study could be used in bioformulation for plant growth promotion and advancing sustainable agricultural practices contributing to the decreased use of chemical inputs. This is the first report of an endophytic bacterium, Pseudarthrobacter enclensis, being isolated from C. sinensis.

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.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca.

Gastrodia elata f.glauca (G. elata) is a commonly used Chinese Medicinal Materials with great medicinal value. The medicinal plant and its endophytic bacteria are a symbiotic whole, and the endophytic bacteria are rich in species, and their metabolites are a treasure trove of natural compounds. However, there is a relative lack of analysis on the diversity, flora composition and network interactions of the endophytic bacteria of G. elata. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to reveal the core microbiota by examining the diversity and community structures of tuber endophytic bacteria in G. elata grown under different regions and exploring the effect of region on its endophytic bacteria. Here, 1,265 endophytic ASVs were found to coexist with G. elata tuber in Guizhou and Hubei. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria and Acdobacteriota. At the family level, the dominant family were Comamonadaceae, Nocardicaece, Xanthobacteraceae, and Burkholderiaceae. At the genus level, Delftia and Rhodococcus were represented the core microbiota in G. elata tuber, which served as the dominant genera that coexisted in all samples tested. Moreover, we found that the beta diversity of endophytic bacteria in G. elata tuber was higher level in the Guizhou region than Hubei region. Overall, this study results to provide a reference for screening active strains and interaction between plants and endophytic bacteria.

Nitrogen fixation of Cyndon dactylon: A possible strategy coping with long-term flooding in the Three Gorges Reservoir

The Three Gorges Reservoir (TGR) is one of the largest hydropower projects around the world which greatly alters the ecological function of the original ecosystem. The riparian zone of TGR is subject to a frequent fluctuation of water level, leading to severe nitrogen loss by leaching. Cyndon dactylon, a perennial stress tolerant plant, is one of the dominant plant species in the riparian zone of TGR. The underlying mechanism that C. dactylon can survive the nitrogen limitation has been under debate. In this study, we sampled the plant tissues of C. dactylon and the surrounding soils across different water levels and seasons in the riparian zone of TGR to explore the possible strategy for them to mining nitrogen. Our study found that the C. dactylon in the TGR riparian zone had endophytic nitrogen-fixing bacteria, particularly enriched in the plant foliage. The abundance of endophytic nitrogen-fixing bacteria was significantly negatively correlated with soil ammonia, nitrate, and organic matter, and significantly positively correlated with total phosphorous and moisture content. The endophytic nitrogen-fixing bacteria in C. dactylon were highly diverse, with Proteobacteria as the main dominant genera. The mutual cooperation mode among bacterial species made the endophytic nitrogen-fixing bacteria community of C. dactylon more resilient to environmental pressure, thus more readily adapting to conditions of repeated long-term flooding in the riparian zone of the TGR.

Comparative analysis of the endophytic bacteria inhabiting the phyllosphere of aquatic fern Azolla species by high-throughput sequencing

BackgroundAzolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood.ResultsIn this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata > A. pinnata > A. filiculoides > A. mexicana > A. caroliniana. The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata, and they were significantly distinct from the community of A. filiculoides. The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla. Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides. The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns.ConclusionsIn summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species.

A field study on the composition, structure, and function of endophytic bacterial community of Robinia pseudoacacia at a composite heavy metals tailing

Robinia pseudoacacia (R. pseudoacacia) is a well reported plant species for heavy metal phytoremediation, and it was capable to improve Cd uptake efficiency after inoculated with plant growth promoting endophytes. However, the knowledge on R. pseudoacacia associated endophytes in field condition and the relationship between these microbial communities and heavy metal uptake capacities are still scarce. In this study, the characteristics of heavy metal bioaccumulation and translocation in R. pseudoacacia, and the structure and function of its endophytic bacterial communities were revealed. The results showed that heavy metal pollution made microbes more sensitive to the environment as the diversity (Shannon) of endophyte community decreased but the abundance (Chao) increased. Redundancy analysis (RDA) also showed that heavy metals were the key factor affecting the composition of endophyte. In the co-occurrence network, 27 keystone taxa mainly from Actinobacteria, Proteobacteria and Firmicutes occupied the dominant niches, among which 16 OTUs mainly from lactobacillus, bacteroides, staphylococcus, methylorubrum and bifidobacterium were positively related to bioaccumulation and translocation of Cd, Cu, Pb and Zn. Besides, heavy metal stress enhanced the functional adaptability of endophytic bacteria community. Related predicted genes were enriched in immune response, physiological metabolism pathway and stress-resistant enzyme synthesis. This study showed that heavy metal stress enhanced the structural and functional adaptability of endophyte community and keystone taxa played significant role in improving the efficiency of phytoremediation.

Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds.

ABSTRACTSeeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a “black box” of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination.IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.

Diversity of Endophytic Bacteria in Parasitic and Non-Parasitic Centranthera grandiflora Benth. Based on High-Throughput Sequencing

The community of endophytic bacteria varies with the genotypes, nutritional status and growth environment of host plants, and in turn it also affects the growth, metabolism and biochemical synthesis of plants. Using the root, stem and leaf of parasitic and non-parasitic Centranthera grandiflora Benth. (PR, PS, PL and NR, NS, NL) as materials, the differences of endophytic bacteria community and diversity were analyzed by high-throughput sequencing. Alpha diversity analysis shows that the richness and diversity of endophytic bacteria in NR were lower than those in PR; while those in NS were higher than those in PS. At the phylum level, Proteobacteria was the dominant phyla, followed by Bacteroidetes and Actinobacteria; the relative abundance of Proteobacteria in each tissue of non-parasitic sample (NR 93.87%, NS 84.27%, NL 90.00%) was higher than that in parasitic sample (PR 77.06%, PS 78.28%, PL 84.96%). The relative abundance in roots increased the most, up to 16.84%. At the genus level, each sample had its own dominant group, Acinetobacter (37.90%) was the dominant in NR, and the relative abundance was 9.56 times than that in PR. The nutritional status and the endophytic bacteria community of host plants have an impact on the structure and diversity of endophytic bacteria in Centranthera grandiflora Benth.; the nutrients needed for Centranthera grandiflora Benth. growth may not only come from the host plant, but also from endophytic bacteria. The results aim to provide a theoretical basis for related study in the relationship between root hemiparasitic plants and their hosts.

Largely invariant communities of bacterial endophytes in the nonphotosynthetic mycoheterotrophic plant Pterospora andromedea.

Mycoheterotrophic plants rely on fungi to obtain their carbon requirements. Recent experiments demonstrated the presence of endophytic bacteria associated with mycoheterotrophs. Although mycoheterotrophs show high specificity for their fungal partners, it is not known whether they also show high specificity for associated bacteria or whether the bacteria have a definite function in the symbiosis. Two 16S rRNA sequencing experiments were designed to explore endophytic microbial community composition and function in root ball fractions of the mycoheterotroph Pterospora andromedea (Ericaceae), and rhizosphere soil and control soil 5 m away from each plant. One experiment compared microbial assemblages in fractions of six plants to those in rhizosphere and control soil samples. Another experiment documented bacterial endophyte diversity in root balls of 97 plants from across North America. Soil samples were similar in bacterial community structure but were significantly more diverse and less consistently structured than were bacterial communities within root balls. The proportion of endophytic bacterial species varied slightly but not their community composition despite differences in P. andromedea lineage, geography, conifer species, and fungi. Predictive metagenomic profiling of the endophytes in P. andromedea-only root ball fractions showed many of the bacterial endophytes likely function in N-metabolism and N-fixation. Our results document a consistent and largely invariant community of endophytic bacteria in P. andromedea across biotic and abiotic environmental conditions at a continental scale. It is unknown what role these bacteria may play in the quad-partite symbiotic network centered on P. andromedea; however, the predictive metagenomic profiling suggests a possible function in N-metabolism or N-fixation. Discovery of a ubiquitous community of endophytic bacteria with a putative function centered on N-metabolism or N-fixation could have a previously unrecognized impact on understanding of mycoheterotroph ecophysiology.

Selection of Endophytic Strains for Enhanced Bacteria-Assisted Phytoremediation of Organic Pollutants Posing a Public Health Hazard.

Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and derivatives of common organic compounds are currently not included in these regulations. Classical methods of removal of organic pollutants involve economically challenging processes. In this regard, remediation with biological agents can be an alternative. For in situ decontamination, the plant-based approach called phytoremediation can be used. However, the main disadvantages of this method are the limited accumulation capacity of plants, sensitivity to the action of high concentrations of hazardous pollutants, and no possibility of using pollutants for growth. To overcome these drawbacks and additionally increase the efficiency of the process, an integrated technology of bacteria-assisted phytoremediation is being used recently. For the system to work, it is necessary to properly select partners, especially endophytes for specific plants, based on the knowledge of their metabolic abilities and plant colonization capacity. The best approach that allows broad recognition of all relationships occurring in a complex community of endophytic bacteria and its variability under the influence of various factors can be obtained using culture-independent techniques. However, for practical application, culture-based techniques have priority.

Metagenomic analyses, isolation and characterization of endophytic bacteria associated with Eucalyptus urophylla BRS07-01 in vitro plants.

Eucalyptus is the main species for the forestry industry in Brazil. Biotechnology and, more recently, gene editing offer significant opportunities for rapid improvements in Eucalyptus breeding programs. However, the recalcitrance of Eucalyptus species to in vitro culture is also a major limitation for commercial deployment of biotechnology techniques in Eucalyptus improvement. We evaluated various clones of Eucalyptus urophylla for their in vitro regeneration potential identified a clone, BRS07-01, with considerably higher regeneration rate (85%) in organogenesis, and significantly higher than most works described in literature. Endophytic bacteria are widely reported to improve in vitro plant growth and development. Hence, we believe that inclusion of endophytic plant growth promoting bacteria enhanced was responsible for the improved plantlets growth and development of this clone under in vitro culture. Metagenomic analysis was performed to isolate and characterize the prominent endophytic bacteria on BRS07-01 leaf tissue in vitro micro-cultures, and evaluate their impact on plant growth promotion. The analysis revealed the presence of the phyla Firmicutes (35%), Proteobacteria (30%) and much smaller quantities of Actinobacteria, Bacteroidetes, Gemmatimonadetes, Crenarchaeota, Euryarchaeota and Acidobacteria. Of the thirty endophytic bacterial strains isolated, eleven produced indole-3-acetic acid. Two of the isolates were identified as Enterobacter sp. and Paenibacillus polymyxa, which are nitrogen-fixing and capable of phosphate and produce ammonium. These isolates also showed similar positive effects on the germination of common beans (Phaseolus spp.). The isolates will now be tested as a growth promoter in Eucalyptus in vitro cultures. Graphical abstract for the methodology using cultivation independent and dependent methodologies to investigate the endophytic bacteria community from in vitro Eucalyptus urophylla BRS07-01.

Communities of endophytic bacteria from Cereus peruvianus Mill. (Cactaceae) plants obtained from seeds and from in vitro-regenerated somaclone

Bioprospecting of endophytic microorganisms has been considered a promising resource for obtaining new biomolecules with biotechnological applications. Since few studies are available on the diversity of endophytic bacteria associated with species of the Cactaceae family, current analysis isolates and characterizes the communities of endophytic bacteria associated with the species of C. peruvianus grown in vivo obtained from seed and with somaclone of the same species regenerated in vitro to prospect for their plant-growth promoting activity. Isolation of endophytic bacteria from plants obtained from seeds and from regenerated somaclone in vitro identified nine species of endophytic bacteria (Moraxela osloensis, Corynebacterium mycetoides, Micrococcus luteus, Kocuria palustris, Staphylococcus epidermidis, Staphylococcus cohnii, Pseudomonas stuzeri, Bacillus licheniformis and Microbacterium sp.) not previously described in cacti, and signalized the somaclones as the most promising source of endophytic bacteria for obtaining new biomolecules with biotechnological applications. Somaclones are indicated as the most promising source of endophytic bacteria due to their high concentration of endophytes per gram identified in fresh somaclone tissue, the identification of the highest proportion endophytic bacteria, a source of IAA, and with the highest capacity of biological nitrogen fixation, and EPS production exclusively by the endophytic bacteria isolated from the in vitro regenerated somaclone.

Endophytic bacteria associated with the enhanced cadmium resistance in NHX1- overexpressing tobacco plants

Human industrial activities have left large area of land polluted with cadmium (Cd), which poses tremendous threat to ecosystem. Na+/H+ antiporter 1 (NHX1) was a transporter located on vacuoles, which mediated the compartmentation of Na+ into vacuole and transportation of H+ into the cytoplasm. And the overexpressing of its code gene (NHX1 gene) was previously identified to enhance Cd resistance in tobacco (Nicotiana tabacum) plants possibly by maintaining the change of ion content. However, the mechanisms of Cd resistance in NHX1-overexpressing plants have not been well elucidated yet. In this study, the endophytic bacteria communities, the activities of soil enzymes and the antioxidant enzymes were characterized to explore possible mechanisms of the enhanced Cd resistance in NHX1-overeexpressing tobacco plants. Some differences in the endophytic bacterial community structure in roots of transgenic and WT tobaccos under Cd stress were observed, in which, Sphingomonas, Steroidobacter and Actinoplanes were proposed as vital endophytic bacteria for enhancing Cd resistance of transgenic tobacco plants. In addition, the soil enzymes were increased in the rhizospheric soil around the transgenic tobacco plants compared to WT plants under Cd stress. Under Cd exposure, the SOD and CAT activities were 1.65 times and 1.88 times of that in WT plants, respectively. The content of MDA and H2O2 were also observed to be 35 % and 28 % lower in transgenic tobacco roots compared to WT plants under Cd stress. Moreover, the Cd content of transgenic plants decreased by 38 % under Cd stress compared to WT plants. These findings suggested that the endophytic bacteria communities associated with the NHX1-overexpressing plants might lead to the increased Cd resistance by enhancing the rhizosphere soil enzyme activities, strengthening the antioxidative defense system, and better maintaining of the ion changes. Taken together, this study suggested that the enhanced Cd resistance was observed in transgenic tobacco plants associated with the increase of soil enzyme activities and changes of endophytic bacteria community, and the possible mechanisms involved in this process were also discussed.

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.

Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.

Molecular Identification of Endophytic Bacteria in Leucojum aestivum In Vitro Culture, NMR-Based Metabolomics Study and LC-MS Analysis Leading to Potential Amaryllidaceae Alkaloid Production.

In this study, endophytic bacteria belonging to the Bacillus genus were isolated from in vitro bulblets of Leucojum aestivum and their ability to produce Amaryllidaceae alkaloids was studied. Proton Nuclear Magnetic Resonance (1H NMR)-based metabolomics combined with multivariate data analysis was chosen to compare the metabolism of this plant (in vivo bulbs, in vitro bulblets) with those of the endophytic bacteria community. Primary metabolites were quantified by quantitative 1H NMR (qNMR) method. The results showed that tyrosine, one precursor of the Amaryllidaceae alkaloid biosynthesis pathway, was higher in endophytic extract compared to plant extract. In total, 22 compounds were identified including five molecules common to plant and endophyte extracts (tyrosine, isoleucine, valine, fatty acids and tyramine). In addition, endophytic extracts were analyzed using Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS) for the identification of compounds in very low concentrations. Five Amaryllidaceae alkaloids were detected in the extracts of endophytic bacteria. Lycorine, previously detected by 1H NMR, was confirmed with LC-MS analysis. Tazettine, pseudolycorine, acetylpseudolycorine, 1,2-dihydro-chlidanthine were also identified by LC-MS using the positive ionization mode or by GC-MS. In addition, 11 primary metabolites were identified in the endophytic extracts such as tyramine, which was obtained by decarboxylation of tyrosine. Thus, Bacillus sp. isolated from L. aestivum bulblets synthesized some primary and specialized metabolites in common with the L. aestivum plant. These endophytic bacteria are an interesting new approach for producing the Amaryllidaceae alkaloid such as lycorine.

Phylogenetic diversity of the endophytic bacterial component of the microbiome of apple clonal rootstocks during in vitro reproduction and cultivation under various agroecological conditions

The phylogenetic diversity of the endophytic bacterial component of the clonal apple rootstock microbiome 57-490 and 54-118 was studied for microplants and 5-year-old plants grown from the same tissue culture and growing on sod-podzolic soils of different granulometric composition with different chemical, physicochemical and physical properties. Proteobacteria (91.6%) in rootstock 57-490, Proteobacteria (52.5%) and Firmicutes (47.4%) in rootstock 54-118 are the predominant phylum of endophytic bacteria in apple rootstock plant tissues in vitro culture. The relative amount of phylum Firmicutes endophytic bacteria, in comparison with in vitro culture, decreases in the roots to 0.7-2.0%, and even more significantly in the leaves (to 0-0.2%). At cultivation on heavy loamy soil, endophytic bacteria belonging to the phylum Actinobacteriota (11.7%) are found in the studied rootstock roots, the relative content of which, when grown on medium loamy soil, in the roots decreases to 2.7-4.1%, in the leaves – to 0,1-0.2%. The data show that in the endosphere of the culture in vitro, the diversity and uniformity of the community of endophytic bacteria is significantly lower (Shannon index 0.42-1.00) than in the roots of rootstocks grown in the outdoor growing (1.34-2.08). For leaves, the Shannon index is characterized by the lowest values (0.06-0.13).

AKTIVITAS METABOLIT SEKUNDER PEMACU PERTUMBUHAN DARI BAKTERI ENDOFIT ASAL KUNYIT PUTIH (Curcuma zedoaria ROSC)

<em><span>Endophytic bacteria colonize the plant tissue and contribute to the host plant's growth, development, and adaptation. This study aimed to examine the endophytic bacteria diversity associated with white turmeric (</span></em><span>Curcuma zedoaria</span><em><span>) and determine its activity as a plant growth promoter. White turmeric plants were obtained from the Indonesian Spices and Medicinal Crop Research Institute (Balittro). The isolation of endophytic bacteria from leaves, a primary and secondary rhizome of white turmeric using Nutrient Agar (NA) medium. Identification of the isolates was conducted based on 16S rDNA. The isolates were tested for their ability as a plant growth promoter and enzyme producer. Based on the morphological characteristic, 21 isolates were obtained from the primary rhizome (47.62%), secondary rhizome (19.05%), and leaves (33.33%), respectively. The sequencing result of 16S rDNA showed that the endophytic bacteria community consisted of four phyla, </span></em><span>β-proteobacteria</span><span>, γ-proteobacteria, Flavobacteria,<em> </em>Firmicutes,<em> which represented eight genera. Five isolates had several activities as a plant growth promoter, while six isolates had several enzymatic activities. Thirteen isolates had both activities, as a plant growth promoter and enzyme producer, while eight isolates only had single action. Endophytic bacteria potential as plant growth promoters can be used for supporting the cultivation of white turmeric plants.</em></span>