Journal articles: 'Root microbiota'

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Salas-González, Isai, Guilhem Reyt, Paulina Flis, Valéria Custódio, David Gopaulchan, Niokhor Bakhoum, Tristan P. Dew, et al. "Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis." Science 371, no. 6525 (November 19, 2020): eabd0695. http://dx.doi.org/10.1126/science.abd0695.

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Plant roots and animal guts have evolved specialized cell layers to control mineral nutrient homeostasis. These layers must tolerate the resident microbiota while keeping homeostatic integrity. Whether and how the root diffusion barriers in the endodermis, which are critical for the mineral nutrient balance of plants, coordinate with the microbiota is unknown. We demonstrate that genes controlling endodermal function in the model plant Arabidopsis thaliana contribute to the plant microbiome assembly. We characterized a regulatory mechanism of endodermal differentiation driven by the microbiota with profound effects on nutrient homeostasis. Furthermore, we demonstrate that this mechanism is linked to the microbiota’s capacity to repress responses to the phytohormone abscisic acid in the root. Our findings establish the endodermis as a regulatory hub coordinating microbiota assembly and homeostatic mechanisms.

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Fitzpatrick, Connor R., and Adam C. Schneider. "Unique bacterial assembly, composition, and interactions in a parasitic plant and its host." Journal of Experimental Botany 71, no. 6 (January 6, 2020): 2198–209. http://dx.doi.org/10.1093/jxb/erz572.

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Abstract How plant-associated microbiota are shaped by, and potentially contribute to, the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities of the root holoparasite Orobanche hederae and its host Hedera spp. from natural populations. Root bacteria inhabiting Orobanche were less diverse, had fewer co-associations, and displayed increased compositional similarity to leaf bacteria relative to Hedera. Overall, Orobanche bacteria exhibited significant congruency with Hedera root bacteria across sites, but not the surrounding soil. Infection had localized and systemic effects on Hedera bacteria, which included effects on the abundance of individual taxa and root network properties. Collectively, our results indicate that the parasitic plant microbiome is derived but distinct from the host plant microbiota, exhibits increased homogenization between shoot and root tissues, and displays far fewer co-associations among individual bacterial members. Host plant infection is accompanied by modest changes of associated microbiota at both local and systemic scales compared with uninfected individuals. Our results are a first step towards extending the growing insight into the assembly and function of the plant microbiome to include the ecologically unique but often overlooked guild of heterotrophic plants.

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Takenaka, Shoji, Naoki Edanami, Yasutaka Komatsu, Ryoko Nagata, Traithawit Naksagoon, Maki Sotozono, Takako Ida, and Yuichiro Noiri. "Periodontal Pathogens Inhabit Root Caries Lesions Extending beyond the Gingival Margin: A Next-Generation Sequencing Analysis." Microorganisms 9, no. 11 (November 13, 2021): 2349. http://dx.doi.org/10.3390/microorganisms9112349.

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We performed a comprehensive microbiome analysis of root caries lesions using 22 teeth extracted from patients with severe periodontitis. The carious lesions were mechanically collected and cryo-pulverized following tooth extraction. Differences in the microbiome were compared between independent lesions at the supragingival site (SG) and lesions extending beyond the gingival margin (GCB). DNA was extracted and the microbiome was characterized on the basis of the V3-V4 hypervariable region of the 16S rRNA gene using paired-end sequencing on an Illumina MiSeq device. The microbiota in root caries lesions showed compositionally distinct microbiota depending on the location. The most abundant OTUs in the SG group were Streptococcus (26.0%), Actinomyces (10.6%), and Prevotella (7.6%). GCB presented Prevotella (11.1%) as the most abundant genus, followed by Fusobacterium (9.6%) and Actinomyces (8.7%). The SG group showed a lack of uniformity in microbiota compared with the GCB group. The bacterial profiles of GCB varied considerably among patients, including periodontal pathogens such as Porphyromonas, Selenomonas, Filifactor, Peptococcus, and Tannerella. Periodontal pathogens inhabit root caries lesions that extend beyond the gingival margin. This study provides a new perspective for elucidating the microbial etiology of root caries.

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Ramírez-Puebla, Shamayim T., Luis E. Servín-Garcidueñas, Berenice Jiménez-Marín, Luis M. Bolaños, Mónica Rosenblueth, Julio Martínez, Marco Antonio Rogel, Ernesto Ormeño-Orrillo, and Esperanza Martínez-Romero. "Gut and Root Microbiota Commonalities." Applied and Environmental Microbiology 79, no. 1 (October 26, 2012): 2–9. http://dx.doi.org/10.1128/aem.02553-12.

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ABSTRACTAnimal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

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Hines, Pamela J. "Mix of metabolites tunes root microbiota." Science 364, no. 6440 (May 9, 2019): 542.12–544. http://dx.doi.org/10.1126/science.364.6440.542-l.

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Mapelli, Francesca, Valentina Riva, Lorenzo Vergani, Redouane Choukrallah, and Sara Borin. "Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere." Microbial Ecology 80, no. 4 (June 25, 2020): 822–36. http://dx.doi.org/10.1007/s00248-020-01543-4.

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Abstract The microbiota associated to xerophyte is a “black box” that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota’s structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.

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French, Elizabeth, Tri Tran, and Anjali S. Iyer-Pascuzzi. "Tomato Genotype Modulates Selection and Responses to Root Microbiota." Phytobiomes Journal 4, no. 4 (January 2020): 314–26. http://dx.doi.org/10.1094/pbiomes-02-20-0020-r.

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Using microbial inoculants to enhance plant health is promising for crop improvement. However, for success, knowledge of how different cultivars within a crop species select and respond to the root microbiome is critical. The aims of this study were to (i) determine the contribution of tomato genotype to the tomato root bacterial microbiome and (ii) investigate whether closely related tomato genotypes differ in their selection of and response to root endophytes. We used 16S ribosomal RNA amplicon sequencing to examine the root bacterial communities of six Solanum lycopersicum (domesticated tomato) and two S. pimpinellifolium (wild tomato) accessions. We found that, across accessions, both the root endosphere and rhizosphere were affected by genotype. Genotype accounted for 10% of the variation in root microbiota. Two bacterial families, Bacillaceae and Rhizobiaceae, were significantly enriched in the root endosphere in at least six of the eight tomato genotypes. To investigate whether closely related tomato genotypes differed in selection of these endosphere-enriched taxa, we profiled the root endosphere of 20 recombinant inbred lines (RILs) derived from two of the genotypes. The abundance of Bacillaceae and Rhizobiaceae isolates varied quantitatively in the root endosphere of the RILs. Inoculation of 16 RILs with a Bacillaceae isolate identified from the root endosphere of field-grown tomato showed that RIL responses, in terms of shoot and root growth, varied from less than 5% growth enhancement to more than 40%. Our data show that tomato genotypes have distinct but overlapping root bacterial microbiomes and respond differently to specific bacterial endophytes.

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Rovai, Emanuel da Silva, Felipe de Souza Matos, Warley David Kerbauy, Flávia Goulart da Rosa Cardoso, Frederico Canato Martinho, Luciane Dias de Oliveira, Marcia Carneiro Valera, and Cláudio Antonio Talge Carvalho. "Microbial Profile and Endotoxin Levels in Primary Periodontal Lesions with Secondary Endodontic Involvement." Brazilian Dental Journal 30, no. 4 (July 2019): 356–62. http://dx.doi.org/10.1590/0103-6440201902471.

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Abstract This study was carried out to investigate the microbial profile and endotoxin levels of endodontic-periodontal lesions of periodontal origin. Periodontal and endodontic samples were taken from periodontal pockets and necrotic root canals of 10 teeth with endodontic-periodontal lesions. Evidencing of 40 different bacterial species were determined in each endodontic and periodontal sample using the checkerboard DNA-DNA hybridization method and Kinetic chromogenic LAL assay was used for quantification of endotoxins. Fisher’s exact test correlated the bacterial species with the endodontic or periodontal microbiota. The endotoxin levels (EU/mL) found in samples of the root canal and periodontal pocket were compared by the Wilcoxon test (p<0.05). Bacteria and LPS units were found in 100% of the endodontic and periodontal samples. The species E. faecium, P. acnes, G. morbillorum, C. sputigena and L. buccalis were strongly correlated with the endodontic microbiota and P. nigrescens with the periodontal microbiota. P. intermedia, P. endodontalis and V. parvula were more prevalent in both endodontic and periodontal microbiots. The endotoxin levels in the periodontal pocket (89600 EU/mL) were significantly higher than in the root canal (2310 EU/mL). It was concluded that the microbiota present in the periodontal and endodontic tissues is similar, with a higher prevalence of species of the orange complex and a higher level of endotoxin in the periodontal pockets.

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Bodenhausen, Natacha, Vincent Somerville, Alessandro Desirò, Jean-Claude Walser, Lorenzo Borghi, Marcel G. A. van der Heijden, and Klaus Schlaeppi. "Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation." Phytobiomes Journal 3, no. 2 (January 2019): 112–24. http://dx.doi.org/10.1094/pbiomes-12-18-0057-r.

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Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to various levels of P supplementation remains ill-defined. Here we investigated the responses of the root-associated bacteria and fungi to varying levels of P supply using 16S rRNA gene and internal transcribed spacer amplicon sequencing. We grew Petunia, which forms symbiosis with AMF, and the nonmycorrhizal model species Arabidopsis as a control in a soil that is limiting in plant-available P and we then supplemented the plants with complete fertilizer solutions that varied only in their phosphate concentrations. We searched for microbes, whose abundances varied by P fertilization, tested whether a core microbiota responding to the P treatments could be identified and asked whether bacterial and fungal co-occurrence patterns change in response to the varying P levels. Root microbiota composition varied substantially in response to the varying P application. A core microbiota was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. Microbes with P-dependent abundance patterns included Mortierellomycotina in Arabidopsis, while in Petunia, they included AMF and their symbiotic endobacteria. Of note, the P-dependent root colonization by AMF was reliably quantified by sequencing. The fact that the root microbiotas of the two plant species responded differently to low-P conditions suggests that plant species specificity would need to be considered for the eventual development of microbial products that improve plant P nutrition. [Formula: see text]Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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Watanabe, Aya, Hiroyuki Sasaki, Hiroki Miyakawa, Yuki Nakayama, Yijin Lyu, and Shigenobu Shibata. "Effect of Dose and Timing of Burdock (Arctium lappa) Root Intake on Intestinal Microbiota of Mice." Microorganisms 8, no. 2 (February 6, 2020): 220. http://dx.doi.org/10.3390/microorganisms8020220.

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Water-soluble dietary fiber such as inulin improves the beta diversity of the intestinal microbiota of mice fed with a high-fat diet (HFD). The circadian clock is the system that regulates the internal daily rhythm, and it affects the pattern of beta diversity in mouse intestinal microbiota. Burdock (Arctium lappa) root contains a high concentration of inulin/fructan (approximately 50%) and is a very popular vegetable in Japan. Arctium lappa also contains functional substances that may affect intestinal microbiota, such as polyphenols. We compared the effects of inulin and A. lappa powder on the diversity of the intestinal microbiota of HFD-fed mice. 16S rDNA from the intestinal microbiota obtained from feces was analyzed by 16S Metagenomic Sequencing Library Preparation. It was found to have a stronger effect on microbiota than inulin alone, suggesting that inulin has an additive and/or synergic action with other molecules in A. lappa root. We examined the effects of intake timing (breakfast or dinner) of A. lappa on intestinal microbiota. The intake of A. lappa root in the evening had a stronger effect on microbiota diversity in comparison to morning intake. Therefore, it is suggested that habitual consumption of A. lappa root in the evening may aid the maintenance of healthy intestinal microbiota.

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Sato, Takuichi, Keiko Yamaki, Naoko Ishida, Kazuhiro Hashimoto, Yasuhisa Takeuchi, Megumi Shoji, Emika Sato, Junko Matsuyama, Hidetoshi Shimauchi, and Nobuhiro Takahashi. "Cultivable Anaerobic Microbiota of Infected Root Canals." International Journal of Dentistry 2012 (2012): 1–5. http://dx.doi.org/10.1155/2012/609689.

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Objective. Periapical periodontitis is an infectious and inflammatory disease of the periapical tissues caused by oral bacteria invading the root canal. In the present study, profiling of the microbiota in infected root canals was performed using anaerobic culture and molecular biological techniques for bacterial identification.Methods. Informed consent was obtained from all subjects (age ranges, 34–71 years). Nine infected root canals with periapical lesions from 7 subjects were included. Samples from infected root canals were collected, followed by anaerobic culture on CDC blood agar plates. After 7 days, colony forming units (CFU) were counted and isolated bacteria were identified by 16S rRNA gene sequencing.Results. The mean bacterial count (CFU) in root canals was(0.5±1.1)×106(range8.0×101–3.1×106), and anaerobic bacteria were predominant (89.8%). The predominant isolates wereOlsenella(25.4%),Mogibacterium(17.7%),Pseudoramibacter(17.7%),Propionibacterium(11.9%) andParvimonas(5.9%).Conclusion. The combination of anaerobic culture and molecular biological techniques makes it possible to analyze rapidly the microbiota in infected root canals. The overwhelming majority of the isolates from infected root canals were found to be anaerobic bacteria, suggesting that the environment in root canals is anaerobic and therefore support the growth of anaerobes.

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Tkacz, A., and P. Poole. "Role of root microbiota in plant productivity." Journal of Experimental Botany 66, no. 8 (April 1, 2015): 2167–75. http://dx.doi.org/10.1093/jxb/erv157.

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Chandel, Ankush, Ross Mann, Jatinder Kaur, Sally Norton, Desmond Auer, Jacqueline Edwards, German Spangenberg, and Timothy Sawbridge. "The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes." Microorganisms 10, no. 4 (March 30, 2022): 750. http://dx.doi.org/10.3390/microorganisms10040750.

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Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.

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Hou, Shiji, Thorsten Thiergart, Nathan Vannier, Fantin Mesny, Jörg Ziegler, Brigitte Pickel, and Stéphane Hacquard. "A microbiota–root–shoot circuit favours Arabidopsis growth over defence under suboptimal light." Nature Plants 7, no. 8 (July 5, 2021): 1078–92. http://dx.doi.org/10.1038/s41477-021-00956-4.

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AbstractBidirectional root–shoot signalling is probably key in orchestrating stress responses and ensuring plant survival. Here, we show that Arabidopsis thaliana responses to microbial root commensals and light are interconnected along a microbiota–root–shoot axis. Microbiota and light manipulation experiments in a gnotobiotic plant system reveal that low photosynthetically active radiation perceived by leaves induces long-distance modulation of root bacterial communities but not fungal or oomycete communities. Reciprocally, microbial commensals alleviate plant growth deficiency under low photosynthetically active radiation. This growth rescue was associated with reduced microbiota-induced aboveground defence responses and altered resistance to foliar pathogens compared with the control light condition. Inspection of a set of A. thaliana mutants reveals that this microbiota- and light-dependent growth–defence trade-off is directly explained by belowground bacterial community composition and requires the host transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be modulated by signals from microbial root commensals.

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George, Marina, and Romana Ivančaková. "Root Canal Microflora." Acta Medica (Hradec Kralove, Czech Republic) 50, no. 1 (2007): 7–15. http://dx.doi.org/10.14712/18059694.2017.53.

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Modern day endodontics is undergoing a massive change with the introduction of new molecular based techniques for microbial identification. This review focuses on the microbiota in untreated and root-filled canals. It will also describe briefly the recent developments in microbial identification and the mechanisms by which certain species of microbes are able to invade and establish themselves in the root canal.

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Schüpbach, P., V. Osterwalder, and B. Guggenheim. "Human Root Caries: Microbiota of a Limited Number of Root Caries Lesions." Caries Research 30, no. 1 (1996): 52–64. http://dx.doi.org/10.1159/000262137.

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Sare, Abdoul Razack, Gilles Stouvenakers, Mathilde Eck, Amber Lampens, Sofie Goormachtig, M. Haïssam Jijakli, and Sebastien Massart. "Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?" Microorganisms 8, no. 3 (February 28, 2020): 342. http://dx.doi.org/10.3390/microorganisms8030342.

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Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.

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Etalo, Desalegn W., Je-Seung Jeon, and Jos M. Raaijmakers. "Modulation of plant chemistry by beneficial root microbiota." Natural Product Reports 35, no. 5 (2018): 398–409. http://dx.doi.org/10.1039/c7np00057j.

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Siqueira, José F., Flávio R. F. Alves, and Isabela N. Rôças. "Pyrosequencing Analysis of the Apical Root Canal Microbiota." Journal of Endodontics 37, no. 11 (November 2011): 1499–503. http://dx.doi.org/10.1016/j.joen.2011.08.012.

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Kristin, Aleklett, and Hart Miranda. "The root microbiota—a fingerprint in the soil?" Plant and Soil 370, no. 1-2 (March 2, 2013): 671–86. http://dx.doi.org/10.1007/s11104-013-1647-7.

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Chen, Yalin, Zongmu Yao, Yu Sun, Enze Wang, Chunjie Tian, Yang Sun, Juan Liu, Chunyu Sun, and Lei Tian. "Current Studies of the Effects of Drought Stress on Root Exudates and Rhizosphere Microbiomes of Crop Plant Species." International Journal of Molecular Sciences 23, no. 4 (February 21, 2022): 2374. http://dx.doi.org/10.3390/ijms23042374.

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With the warming global climate, drought stress is considered to be the most important abiotic factor limiting plant growth and yield in the world. Drought stress has serious impacts on crop production. Many researchers have studied the influences of drought stress on crop production and plant physiology; however, few researchers have combined root exudates with root-associated microbiomes for their mutual effects under drought conditions. In this review, we systematically illustrate the impact of drought stress on root exudates and root-associated microbiomes, and then we discuss the mutual regulation of root-associated microbiomes and the host plant in helping the plant adapt to drought. Finally, we construct a framework for the mutual connections between the plant, root exudates, and the microbiome. We hope this review can provide some significant guidelines to promote the study of drought resistance in plants in association with the rhizosphere microbiota.

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Xu, Xin, Jane Robb, and Ross N. Nazar. "A “whole pot” strategy for root growth quantification or microbiota-root interaction studies." Soil Biology and Biochemistry 111 (August 2017): 154–56. http://dx.doi.org/10.1016/j.soilbio.2017.04.013.

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Huang, Ancheng C., Ting Jiang, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai, and Anne Osbourn. "A specialized metabolic network selectively modulates Arabidopsis root microbiota." Science 364, no. 6440 (May 9, 2019): eaau6389. http://dx.doi.org/10.1126/science.aau6389.

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Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community.

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Bai, Yang, Daniel B. Müller, Girish Srinivas, Ruben Garrido-Oter, Eva Potthoff, Matthias Rott, Nina Dombrowski, et al. "Functional overlap of the Arabidopsis leaf and root microbiota." Nature 528, no. 7582 (December 2015): 364–69. http://dx.doi.org/10.1038/nature16192.

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Rocas, I. N., and J. F. Siqueira. "Root Canal Microbiota of Teeth with Chronic Apical Periodontitis." Journal of Clinical Microbiology 46, no. 11 (September 3, 2008): 3599–606. http://dx.doi.org/10.1128/jcm.00431-08.

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Korona-Glowniak, Izabela, Dominika Piatek, Emilia Fornal, Anna Lukowiak, Yuriy Gerasymchuk, Anna Kedziora, Gabriela Bugla-Płoskonska, Ewelina Grywalska, Teresa Bachanek, and Anna Malm. "Patterns of Oral Microbiota in Patients with Apical Periodontitis." Journal of Clinical Medicine 10, no. 12 (June 19, 2021): 2707. http://dx.doi.org/10.3390/jcm10122707.

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In this study, microbial diversity of the root canal microbiota related to different endodontic infections was investigated. In total, 45 patients with endo–perio lesions (8 patients), chronic periapical periodontitis (29 patients) and pulp necrosis (8 patients) were recruited. In 19 (42.2%) patients there was secondary infection of root canals. Microbial specimens were collected from root canals of non-vital teeth with or without changes in periapical area visible in X-ray. Then, oral microbiota were detected and identified using the culture method and real-time PCR amplification primers and hydrolysis-probe detection with the 16S rRNA gene as the target. Overall, 1434 species/genes from 41 different genera of 90 various microbial species were retrieved. Of the major reported phyla, Firmicutes (62.9%), Actinobacteria (14.0%), Bacteroidetes (12.1%), Proteobacteria (9.1%) and Fusobacteria (4.2%) were detected. Of the bacterial species, 54.6% were strict anaerobes. Corynebacterium matruchotii (p = 0.039) was present significantly more frequently in chronic periapical periodontitis. Moreover, the higher values of Decayed, Missing and Filled Permanent Teeth index were positively correlated with relative abundance of Actinomyces spp. (p = 0.042), Lactobacillus spp. (p = 0.006), Propionibacterium spp. (p = 0.024) and Rothia spp. (p = 0.002). The multivariate analyses revealed differences in total root canal samples, where components that affected grouping of root samples into four main categories were identified. Anaerobic Gram-negative bacteria predominated in root canals of teeth with pulp necrosis and periapical lesions. Facultative anaerobic Gram-positive bacteria predominated in canals with secondary infections. All detected members of mixed population groups that might serve as keystone species contributed to the entire community in its clinical relevance.

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Chen, Shaotong, Jun Dai, Xiangwen Song, Xueping Jiang, Qun Zhao, Chuanbo Sun, Cunwu Chen, Naifu Chen, and Bangxing Han. "Endophytic Microbiota Comparison of Dendrobium huoshanense Root and Stem in Different Growth Years." Planta Medica 86, no. 13/14 (November 25, 2019): 967–75. http://dx.doi.org/10.1055/a-1046-1022.

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AbstractThe endophytic microbiome in medicinal plants is rich and diverse, but few studies have followed the endophytic microbiome of medicinal plants in different tissues with their growth. In this study, we examined the endophytic bacterial and fungal community structures associated with both the stem and root compartments of Dendrobium huoshanense at different growth years via high-throughput sequencing of 16S rRNA genes and nrDNA fragments of internal transcribed spacer regions. Results indicated that more diverse prokaryotic and fungal operational taxonomic units were detected in roots than in stems, and the alpha diversity of endophytic prokaryotic significantly differed among the 1-, 2-, and 3-year-old roots. The dominant bacterial phyla Proteobacteria Firmicutes, Actinobacteria, Bacteroidetes, and Acidobacteria, and fungal phyla Ascomycota, Basidiomycota, and Ascomycota were detected in the stems and roots with 3 growth years. Moreover, linear discriminant effect size analysis revealed 138 differentially abundant taxonomic clades in the bacterial level, and 197 in the fungal level in six groups. Our results provide evidence for endophytic microbiota communities depending on the tissues and growth years of D. huoshanense. The results from this study should be useful to better understand medicinal plant-microbe interactions.

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Schüpbach, P., V. Osterwalder, and B. Guggenheim. "Human Root Caries: Microbiota in Plaque Covering Sound, Carious and Arrested Carious Root Surfaces." Caries Research 29, no. 5 (1995): 382–95. http://dx.doi.org/10.1159/000262097.

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Shen, Chwan-Li, Rui Wang, Moamen Elmassry, Volker Neugebauer, and Abdul Hamood. "Dietary Ginger Root Extract Supplementation Mitigated Diabetic Peripheral Neuropathy in Streptozotocin-Induced Diabetic Rats by Modulating Gut Microbiota." Current Developments in Nutrition 5, Supplement_2 (June 2021): 1179. http://dx.doi.org/10.1093/cdn/nzab054_034.

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Abstract Objectives Diabetic peripheral neuropathy (DPN) is a prevalent complication of diabetes with no effective treatment currently. The relationship between gut microbiota and neurological diseases, including DNP, has received increasing attention. Previous studies have shown gingerol-enriched gingerol (GEG) has potential pain-reduction and prebiotic abilities due to its anti-inflammatory capacity. This study examined the effect of GEG on pain sensitivity and gut microbiota in DNP rats. Methods Thirty-three male rats were randomly divided into 3 groups: control group (low-fat diet), DPN group (high-fat diet plus single dose of streptozotocin at 36 mg/kg BW), and DPN + GEG at 0.75% in diet for 6 weeks. Von Frey test was used for for pain assessment. 16S rRNA gene sequencing was done from cecal samples and microbiome data analysis was performed using QIIME 2. Results Relative to the control group, the DNP group showed increased pain hypersensitivity, measured as decreased mechanical withdrawal thresholds. GEG supplementation mitigated pain sensitivity in DNP-treated animals. Principal component analysis showed that GEG treatment shifts the microbiome profile from control and DNP samples. Although GEG did not alter the richness of the microbiome, it significantly increased the alpha-diversity in terms of evenness in comparison to DNP (P < 0.05). Using Kruskal–Wallis test followed by the post-hoc Dunn's test, we identified 9 specific taxa, and their abundance was significantly altered among the control, DNP, and DNP + GEG groups (P < 0.05). In comparison to the control group, the DNP group reduced the relative abundance of Eubacterium coprostanoligenes, Lachnospiraceae, Oscillospiraceae, and Peptococcceae, while DNP increased the abundance of Muribaculum intestinale. Relative to DNP group, the DNP + GEG treatment reversed DNP's effect and reduced the abundance of Muribaculum intestinale to a level similar to the control group. GEG treatment increased the abundance of Acinetobacter, Azospirillum, Colidextribacter, and Fournierella. Conclusions This study demonstrated that GEG supplementation not only reduced pain but also favored the composition of gut microbiome in the DNP model, suggesting targeting gut microbiota by GEG may represent a new therapeutic strategy for the management of DNP. Funding Sources Texas Tech University Health Sciences Center.

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Zhatova, H. O., L. M. Bondarieva, and Y. V. Koplyk. "Features of the rhiospheric microbiota of medicinal plants." Bulletin of Sumy National Agrarian University. The series: Agronomy and Biology, no. 4(38) (December 25, 2019): 61–65. http://dx.doi.org/10.32845/agrobio.2019.4.9.

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Medicinal plants are the source of biologically active compounds that are in constant demand for the pharmacological industry. Active production of plant secondary metabolites is possible only under optimal conditions of plant growth and development. The state of medicinal plants is controlled not only by genotype and environmental conditions but by the qualitative and quantitative composition of their microbiota as well. The study of the structure and function of the rhizospheric communities of medicinal plants is important for obtaining of high quality medicinal raw materials. Microorganisms are the constant companions of higher plants, which can be used as a medicinal raw material. The rhizosphere microbiota is highly specific, even between different varieties of the same plant species. Each plant species has a specific microbiome of the rhizosphere, depending on the existing soil community. The rhizosphere of medicinal plants is marked by a special highly specific microbiome due to the specificity of root exudates. Active cell secretion of the roots provides nutrient substrates with microorganisms that form strong associations both inside the root tissues and on the root surface as well as in the soil around the roots. The purpose of the research was to study the effect of medicinal plants of different systematic groups on the composition of the microbial communities of the rhizosphere. The experiments were conducted in 2018–2019 at the nursery medicinal plant plot of the Department of ecology and botany of Sumy National Agrarian University. Ecological-trophic groups of microorganisms associated with the roots of medicinal plants in the experiment were represented by ammonifying bacteria, nitrogen-fixing bacteria and bacterias that destroyed of plant residues (cellulose-destroying bacteria). In the analysis of the total number of microorganisms of the rhizosphere revealed differences in the quantitative and qualitative composition of microbiota, due to the specific features of a medicinal plant. Positive influence on the development of microflora in the area of the roots and individual ecological-trophic groups had Mentha longifolia (L)., and a negative effect was observed in plants of Bergenia crassifolia L. It has been established that the number of microorganisms and the diversity of ecological-trophic groups is due to the belonging of a medicinal plant to a particular taxon. The number of microorganisms and their diversity decreased in the direction of: Mentha longifolia – Lysimachia vulgaris – Aristolochia clematitis – Achillea submillefolium – Bergenia crassifolia.

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Carbone, María Julia, Sandra Alaniz, Pedro Mondino, Matías Gelabert, Ales Eichmeier, Dorota Tekielska, Rebeca Bujanda, and David Gramaje. "Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome." Journal of Fungi 7, no. 9 (August 25, 2021): 686. http://dx.doi.org/10.3390/jof7090686.

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Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO4 when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

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Mahdi, Lisa K., Shingo Miyauchi, Charles Uhlmann, Ruben Garrido-Oter, Gregor Langen, Stephan Wawra, Yulong Niu, et al. "The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley." ISME Journal 16, no. 3 (October 22, 2021): 876–89. http://dx.doi.org/10.1038/s41396-021-01138-y.

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AbstractPlant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.

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Elmassry, Moamen, Rui Wang, Abdul Hamood, Volker Neugebauer, and Chwan-Li Shen. "Two Isomers of Ginger Root Extracts Modify Composition and Function of Gut Microbiota in Rats Treated with Neuropathic Pain." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 394. http://dx.doi.org/10.1093/cdn/nzaa045_027.

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Abstract Objectives Emerging evidence has suggested that gut microbiota plays a key role during the development of chronic pain, such as neuropathic pain (NP). This study was to evaluate the effects of two ginger root extract isomers (gingerols and shogaols) on the composition and function of gut microbiota in animals with NP. Methods Sixteen male Sprague-Dawley rats were randomly assigned into 4 groups: sham group, spinal nerve ligation (SNL) group as the pain control group, SNL + gingerols-enriched ginger (GEG) extract group, and SNL + shogaols-enriched ginger (SEG) extract group. Animals in GEG and SEG groups were fed their respective diets on the day of SNL surgery for 30 days. At day 30, fecal samples were collected for microbiota composition and functional analyses. 16S rRNA gene sequencing was conducted from fecal samples and microbiome data analysis was performed with QIIME2 and PICRUSt2. Data were analyzed using non-parametric Kruskal–Wallis test to compare GEG and SEG with SNL group. Results Based on the results of alpha-diversity analyses, neither GEG nor SEG treatment affected the evenness of microbiome. Gingerols or shogaols supplementation into the diet reduced the richness of the gut microbiome, compared to the SNL group. Relative to the SNL group, GEG group had an increase in the relative abundance of the genus Faecalitalea, while SEG group had an increase in the relative abundance of the genus Aerococcus and species Bacteroides massiliensis. In comparison to SNL group, both GEG and SEG groups showed a decrease in the relative abundance of the family Muribaculaceae and the genus Rikenellaceae RC9 gut group. Functional profiling results revealed that relative to the SNL group, both GEG and SEG supplementation increased the proportion of biosynthetic pathways related to energy metabolism (i.e., pentose phosphate pathway and sugar degradation) and peptidoglycan biosynthesis. Furthermore, GEG and SEG differentially modified amino acid-related metabolic pathways, i.e., tyrosine degradation, tryptophan biosynthesis, arginine, and ornithine biosynthesis. Conclusions GEG and SEG exhibited differential effects on the microbiome composition and function, suggesting a prebiotic potential for dietary ginger root intake in the management of NP. Funding Sources Texas Tech University Health Sciences Center.

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Almario, Juliana, Ganga Jeena, Jörg Wunder, Gregor Langen, Alga Zuccaro, George Coupland, and Marcel Bucher. "Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition." Proceedings of the National Academy of Sciences 114, no. 44 (October 2, 2017): E9403—E9412. http://dx.doi.org/10.1073/pnas.1710455114.

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Most land plants live in association with arbuscular mycorrhizal (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) from soil. The ability to establish this partnership has been lost in some plant lineages like the Brassicaceae, which raises the question of what alternative nutrition strategies such plants have to grow in P-impoverished soils. To understand the contribution of plant–microbiota interactions, we studied the root-associated fungal microbiome of Arabis alpina (Brassicaceae) with the hypothesis that some of its components can promote plant P acquisition. Using amplicon sequencing of the fungal internal transcribed spacer 2, we studied the root and rhizosphere fungal communities of A. alpina growing under natural and controlled conditions including low-P soils and identified a set of 15 fungal taxa consistently detected in its roots. This cohort included a Helotiales taxon exhibiting high abundance in roots of wild A. alpina growing in an extremely P-limited soil. Consequently, we isolated and subsequently reintroduced a specimen from this taxon into its native P-poor soil in which it improved plant growth and P uptake. The fungus exhibited mycorrhiza-like traits including colonization of the root endosphere and P transfer to the plant. Genome analysis revealed a link between its endophytic lifestyle and the expansion of its repertoire of carbohydrate-active enzymes. We report the discovery of a plant–fungus interaction facilitating the growth of a nonmycorrhizal plant under native P-limited conditions, thus uncovering a previously underestimated role of root fungal microbiota in P cycling.

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Nguyen, Binh. "The effect of diet on the fluctuations of human gut microbiota." MedPharmRes 3, no. 1 (May 31, 2019): 22–24. http://dx.doi.org/10.32895/ump.mpr.3.1.22.

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It was previously thought that the establishment of the gut microbiota was completed within the first two years of life, and this community maintains fairly stable throughout the adult lifetime thereafter. However, recent evidence shows that the gut microbiota composition is constantly changing in the gut environment and is heavily influenced by diet. The individual differences responding to diets would root on the fluctuations of gut microbiota if dietary fluctuations affect the composition of gut microbiota so significantly.

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Lopes, Erica M., Maicon R. Z. Passini, Luciano T. Kishi, Tsute Chen, Bruce J. Paster, and Brenda P. F. A. Gomes. "Interrelationship between the Microbial Communities of the Root Canals and Periodontal Pockets in Combined Endodontic-Periodontal Diseases." Microorganisms 9, no. 9 (September 10, 2021): 1925. http://dx.doi.org/10.3390/microorganisms9091925.

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Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets (PPs) contribute to the development of endodontic-periodontal diseases. This study performed a systemic analysis using state-of-the-art sequence data to assess the microbial composition of infected RCs and PPs to further assess the microbiota and verify the possibility of cross-infection between these sites. The microbiomes of these combined diseases were examined with a focus on the V3-V4 hypervariable region of the 16S rRNA gene. The number of species in PP was higher than in RC, and there was a predominance of obligate anaerobes and gram-negative bacteria. In the RCs, the genera Enterococcus, Parvimonas, Stomatobaculum predominated, in contrast, the PPs revealed a predominance of Enterococcus, Parvimonas, Stomatobaculum, Peptostreptococcus and Mogibacterium. The RC and PP microbiome was not similar with regards to the sharing of OTUs for phyla and genera (8 and 67, respectively). The evaluation of molecular markers revealed a large number of markers for resistance to antibiotics of the carbapenem and beta-lactam type (broad spectrum). Another relevant finding of this study was the markers related to systemic diseases related to cardiac muscle and rheumatology, among others. In conclusion, the RC microbiota was less complex and diverse than PP. Interactions between microbial communities were present. The shared genus can signal communication between the endodontic and periodontal microbiomes.

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Chialva, Matteo, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco, and Paola Bonfante. "Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota." Microorganisms 8, no. 1 (December 24, 2019): 38. http://dx.doi.org/10.3390/microorganisms8010038.

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Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research.

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FENDRIHAN, SERGIU, and CRISTIAN-EMILIAN POP. "Biotechnological potential of plant associated microorganisms." Romanian Biotechnological Letters 26, no. 3 (April 11, 2021): 2700–2706. http://dx.doi.org/10.25083/rbl/26.3/2700-2706.

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This paper shortly reviews the potential of plants associated microorganisms collectively termed “phytomicrobiome” (epiphytes, endophytes, root microbiome and phyllosphere microbiota), fungi and bacteria, that produce valuable molecules which can be use in pharma industry, in medicine and in different other industries as well as in environment protection and bioremediation. In the last ten years many papers on this subject were issued following scientific investigations, attracting the attention of the scientific community as an answer to some of our problems.

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Biget, Marine, Cendrine Mony, Marc Aubry, Olivier Jambon, Achim Quaiser, Véronique Chable, Sabrina Pernet, and Philippe Vandenkoornhuyse. "The drivers of vine-plant root microbiota endosphere composition include both abiotic and plant-specific factors." OENO One 55, no. 3 (September 16, 2021): 299–315. http://dx.doi.org/10.20870/oeno-one.2021.55.3.4616.

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Microorganisms associated with plants are determinant for their fitness, but also in the case of vine grapes, for the quality and quantity of the wine. Plant microbiota is, however highly variable in space despite deterministic recruitment from the soil reservoir. Therefore, understanding the drivers that shape this microbiota is a key issue. Most studies that have analysed microorganisms associated with vines have been conducted at large scales (e.g., over 100 km) and have analysed the bulk soil and the rhizosphere. In this study, we focused on the root-microbiota endosphere, the most intimate fraction of microorganisms associated with plants. We sampled vine roots in 37 fields distributed throughout a vineyard to investigate drivers shaping the grapevine microbiota at the α- (i.e., within-field) and γ- (i.e., between-field) diversity scales. We demonstrated that vine endospheric microbiota differed according to both the edaphic and plant-specific parameters including cultivar type and age. This work supports the idea of an existing microbial terroir occurring within a domain and offers a new perspective for winemakers to include the microbial terroir in their management practices.

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Hou, Shiji, Katarzyna W. Wolinska, and Stéphane Hacquard. "Microbiota-root-shoot-environment axis and stress tolerance in plants." Current Opinion in Plant Biology 62 (August 2021): 102028. http://dx.doi.org/10.1016/j.pbi.2021.102028.

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Castrillo, Gabriel, Paulo José Pereira Lima Teixeira, Sur Herrera Paredes, Theresa F. Law, Laura de Lorenzo, Meghan E. Feltcher, Omri M. Finkel, et al. "Root microbiota drive direct integration of phosphate stress and immunity." Nature 543, no. 7646 (March 2017): 513–18. http://dx.doi.org/10.1038/nature21417.

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Thiergart, Thorsten, Paloma Durán, Thomas Ellis, Nathan Vannier, Ruben Garrido-Oter, Eric Kemen, Fabrice Roux, et al. "Root microbiota assembly and adaptive differentiation among European Arabidopsis populations." Nature Ecology & Evolution 4, no. 1 (December 23, 2019): 122–31. http://dx.doi.org/10.1038/s41559-019-1063-3.

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Dries, Leonie, Maximilian Hendgen, Sylvia Schnell, Otmar Löhnertz, and Anne Vortkamp. "Rhizosphere engineering: leading towards a sustainable viticulture?" OENO One 55, no. 2 (June 11, 2021): 353–63. http://dx.doi.org/10.20870/oeno-one.2021.55.2.4534.

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Microorganisms are a substantial component of the rhizosphere, and the activity and composition of rhizosphere microbial populations markedly affect interactions between plants and the soil environment. In addition, the microbiota of the rhizosphere can positively influence plant development, growth and vitality. In vineyards, management practices influence both grapevine root growth directly and the rhizosphere microbiota, but the exact mode of action is largely unknown. Recently, however, two new research approaches are increasingly coming into focus to enhance grapevine growth and health: plant engineering and rhizosphere engineering. In plant engineering, knowledge about plant-microbiome interactions is used for plant breeding strategies. In rhizosphere engineering, microbial communities are modified by adding specific fertilisers, nutrients or by bio-inoculation with certain bacteria and/or fungi. Taken together, these new methods suggest a potential for reaching a more sustainable development of pesticide-reduced viticulture in the future.

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Zhang, Xiaoping, Zhiyuan Huang, Zheke Zhong, Qiaoling Li, Fangyuan Bian, Guibin Gao, Chuanbao Yang, and Xing Wen. "Evaluating the Rhizosphere and Endophytic Microbiomes of a Bamboo Plant in Response to the Long-Term Application of Heavy Organic Amendment." Plants 11, no. 16 (August 16, 2022): 2129. http://dx.doi.org/10.3390/plants11162129.

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Root-associated bacteria play a major role in plant health and productivity. However, how organic amendment influences root-associated bacteria is uncertain in Lei bamboo (Phyllostachys praecox) plantations. Here, we compared the rhizosphere and endophytic microbiomes in two Lei bamboo plantations with (IMS) and without (TMS) the application of organic amendment for 16 years. The results showed IMS significantly increased (p < 0.05) the relative abundance of Proteobacteria and significantly decreased (p < 0.05) the relative abundance of Acidobacteria, Bacteroidetes, and Verrucomicrobiota. The root endophytic Proteobacteria and Acidobacteria were significantly higher in abundance (p < 0.05) in the IMS than in the TMS, while Actinobacteria and Firmicutes were significantly lower in abundance. Five taxa were assigned to Proteobacteria and Acidobacteria, which were identified as keystones in the rhizosphere soil microbiome, while two species taxonomically affiliated with Proteobacteria were identified as keystones in the root endophytic microbiota, indicating this phylum can be an indicator for a root-associated microbiome in response to IMS. The soil pH, soil total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and TOC:TP ratio were significantly correlated (p < 0.05) with the bacterial community composition of both rhizosphere soils and root endophytes. TMS increased the microbial network complexity of root endophytes but decreased the microbial network complexity of rhizosphere soil. Our results suggest IMS shapes the rhizosphere and endophytic bacterial community compositions and their interactions differently, which should be paid attention to when designing management practices for the sustainable development of forest ecosystems.

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Vojdani, Aristo, Elroy Vojdani, Avi Z. Rosenberg, and Yehuda Shoenfeld. "The Role of Exposomes in the Pathophysiology of Autoimmune Diseases II: Pathogens." Pathophysiology 29, no. 2 (June 3, 2022): 243–80. http://dx.doi.org/10.3390/pathophysiology29020020.

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In our continuing examination of the role of exposomes in autoimmune disease, we use this review to focus on pathogens. Infections are major contributors to the pathophysiology of autoimmune diseases through various mechanisms, foremost being molecular mimicry, when the structural similarity between the pathogen and a human tissue antigen leads to autoimmune reactivity and even autoimmune disease. The three best examples of this are oral pathogens, SARS-CoV-2, and the herpesviruses. Oral pathogens reach the gut, disturb the microbiota, increase gut permeability, cause local inflammation, and generate autoantigens, leading to systemic inflammation, multiple autoimmune reactivities, and systemic autoimmunity. The COVID-19 pandemic put the spotlight on SARS-CoV-2, which has been called “the autoimmune virus.” We explore in detail the evidence supporting this. We also describe how viruses, in particular herpesviruses, have a role in the induction of many different autoimmune diseases, detailing the various mechanisms involved. Lastly, we discuss the microbiome and the beneficial microbiota that populate it. We look at the role of the gut microbiome in autoimmune disorders, because of its role in regulating the immune system. Dysbiosis of the microbiota in the gut microbiome can lead to multiple autoimmune disorders. We conclude that understanding the precise roles and relationships shared by all these factors that comprise the exposome and identifying early events and root causes of these disorders can help us to develop more targeted therapeutic protocols for the management of this worldwide epidemic of autoimmunity.

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Walters, William A., Zhao Jin, Nicholas Youngblut, Jason G. Wallace, Jessica Sutter, Wei Zhang, Antonio González-Peña, et al. "Large-scale replicated field study of maize rhizosphere identifies heritable microbes." Proceedings of the National Academy of Sciences 115, no. 28 (June 25, 2018): 7368–73. http://dx.doi.org/10.1073/pnas.1800918115.

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Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.

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Medina-Paz, Francisco, Luis Herrera-Estrella, and Martin Heil. "All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication." Plants 11, no. 13 (June 21, 2022): 1631. http://dx.doi.org/10.3390/plants11131631.

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Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing ‘at home’.

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AG, Khan. "Role of Rhizosphere Microbiota of Plants Growing in Heavy Metal Contaminated Environments as Ecofriendly Decontamination Bio-Tools and their Role in the Context of Human Health – A Short Review." Open Access Journal of Microbiology & Biotechnology 7, no. 2 (April 6, 2022): 1–7. http://dx.doi.org/10.23880/oajmb-16000220.

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Air, soil and water resources of our world are contaminated by heavy metals (HMs) via agricultural, urban, industrial, mining and smelting human activities which are threatening human health causing various human health issues such as sleeping disorders, kidney damage, tubular damage in various human organs, stomach cancer, heart diseases, brain damage and various neurological disorders, lung damage, anxiety/depression, etc. Various physio-chemical and biological decontamination mechanisms and strategies are being proposed for decontamination purposes, involving habitat-adapted plants growing on such contaminated sites and their rhizosphere associated microbiota, i.e. Phyto degradations or breakdown of HMs by Nanoparticles (NPs) synthesised by plant-root tissues and their associated symbiotic microbiota including Plant Growth Promoting Microbes (PGPM) and universal and ubiquitous Arbuscular Mycorrhizal Fungi (Nano-Mycorrhizo-PhytoRemediation-NMPR). This phenomenon has recently attracted much research attention and it could be adapted for a variety of environments with no added cost or any special requirements to remediate land and water ecosystems, including indoor closed areas like high rise buildings, Gardens, and Parks, aquaria, etc. Plants growing in the HM-contaminated soil or water ecosystems and their root-associated microbiota offer an environmentally green-clean technology for air, soil and water purification and bio-decontamination measures. This short review discusses the use of plants and their root associated microbiota as a novel line of inquiry, i.e. use of ecofriendly bio-tools for bio-decontamination of heavy metal contaminated ecosystems and their role in the context of human health.

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Henning, Jeremiah A., David J. Weston, Dale A. Pelletier, Collin M. Timm, Sara S. Jawdy, and Aimée T. Classen. "Root bacterial endophytes alter plant phenotype, but not physiology." PeerJ 4 (November 1, 2016): e2606. http://dx.doi.org/10.7717/peerj.2606.

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Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from thePopulusroot microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype ofPopulus trichocarpaand measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.

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Rp, Jayaswal, Vijayasimha M, and Prabhakar Pk. "GUT MICROBIOTA AND DIABETES MELLITUS - AN INTERLINKAGE." Asian Journal of Pharmaceutical and Clinical Research 11, no. 1 (January 1, 2018): 13. http://dx.doi.org/10.22159/ajpcr.2017.v11i1.22305.

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In recent years, the curiosity to investigate the relationship between gut microbiota and diabetes development has increased. Evidence from previous studies suggests that gut microbiota manipulation may assure to prevent diabetes development in future, primarily in susceptible individuals. Here, we reviewed special gut microbiota types proposing development of Type 1 (T1D) and Type 2 diabetes (T2D) in humans and laboratory animals. The available data we found are still inconclusive and required more attention in discriminating specific groups of gut microbiomes strongly indicating T1D and T2D development or prevention. Further, we suggested for the first time to study the gut microbiota in different ways to find the root cause of diabetes development.

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Journal articles on the topic 'Root microbiota'

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