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1
Karpenko, V. P., S. P. Poltoretskyi, V. V. Liubych, D. M. Adamenko, I. S. Kravets, R. M. Prytuliak, V. S. Kravchenko, N. I. Patyka, and V. P. Patyka. "Microbiota in the Rhizosphere of Cereal Crops." Mikrobiolohichnyi Zhurnal 83, no. 1 (February 17, 2021): 21–31. http://dx.doi.org/10.15407/microbiolj83.01.021.
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Today, spelt wheat grain is used to produce high quality food. Intermediate wheatgrass is a promising crop for prairie restoration. One of the elements of biologization is the influence of growing crops on the microbiota of soil rhizosphere. The microbiota of spelt wheat and intermediate wheatgrass soil rhizosphere remains insufficiently studied. Aim. To study the number of individual groups of microbiota in dynamics in the rhizosphere of cereal crops (spelt wheat, intermediate wheatgrass) depending on the weather conditions and the phase of plants development. Methods. Classical microbiological, statistical methods were used in the work. In particular, the study of the number of microorganisms of different ecological and trophic groups (ammonifying, nitrifying, cellulolytic and nitrogen-fixing) was carried out according to generally accepted methods in soil microbiology. The reliability of the influence of factors was determined by the probability value «р» level which was calculated using STATISTICA 8 program. Results. The amount of ammonifying and cellulolytic microorganisms in the soil rhizosphere of spelt wheat is significantly higher compared to soft wheat. The rhizosphere microbiota amount of the intermediate wheatgrass on the 2–3 year of cultivation was more resistant to adverse environmental factors compared to soft wheat. The soil rhizosphere microbiota did not change a lot depending on the phase of plant development during the vegetation period of cereal crops (spelt wheat, intermediate wheatgrass). Conclusions. The formation of rhizosphere microbiota of spelt wheat and intermediate wheatgrass was first analyzed under the conditions of the Right-Bank forest-steppe of Ukraine. The conducted studies indicate the feasibility of growing and use of spelt wheat in breeding programs to create cultivars of soft wheat with higher activity of rhizosphere microbiota. The number of ammonifying, nitrifying and cellulolytic microorganisms of soil rhizosphere of intermediate wheatgrass was significantly higher compared to soft wheat during all growth stages. The conducted studies confirm the practical application of intermediate wheatgrass to preserve and increase soil fertility. Intermediate wheatgrass can be grown for up to three years in one field, as microbiological activity reaches its maximum development.
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Cheng, Zhiqiang, Shaonan Lei, Ye Li, Wei Huang, Rongqin Ma, Juan Xiong, Ting Zhang, et al. "Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota." Microorganisms 8, no. 2 (January 25, 2020): 170. http://dx.doi.org/10.3390/microorganisms8020170.
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Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.
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Zhang, Xiaoke, Huili Wang, Zhifei Li, Jun Xie, and Jiajia Ni. "Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas." PeerJ 8 (September 29, 2020): e10078. http://dx.doi.org/10.7717/peerj.10078.
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Background Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied. Methods The spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing. Results Our results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas.
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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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Han, Gil, Mohamed Mannaa, Hyoseong Jeon, Hyejung Jung, Jin-Cheol Kim, Ae Ran Park, and Young-Su Seo. "Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana)." Plants 11, no. 7 (April 5, 2022): 990. http://dx.doi.org/10.3390/plants11070990.
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The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.
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Zhang, Zhen, Lu Chang, Xiuxiu Liu, Jing Wang, Xianhong Ge, Jiasen Cheng, Jiatao Xie, et al. "Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota." Microorganisms 11, no. 3 (March 11, 2023): 724. http://dx.doi.org/10.3390/microorganisms11030724.
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Rhizosphere microbiota is important for plant growth and health. Domestication is a process to select suitable plants to satisfy the needs of humans, which may have great impacts on the interaction between the host and its rhizosphere microbiota. Rapeseed (Brassica napus) is an important oilseed crop derived from the hybridization between Brassica rapa and Brassica oleracea ~7500 years ago. However, variations in rhizosphere microbiota along with rapeseed domestication remain poorly understood. Here, we characterized the composition and structure of the rhizosphere microbiota among diverse rapeseed accessions, including ten B. napus, two B. rapa, and three B. oleracea accessions through bacterial 16S rRNA gene sequencing. B. napus exhibited a higher Shannon index and different bacterial relative abundance compared with its wild relatives in rhizosphere microbiota. Moreover, artificial synthetic B. napus lines G3D001 and No.2127 showed significantly different rhizosphere microbiota diversity and composition from other B. napus accessions and their ancestors. The core rhizosphere microbiota of B. napus and its wild relatives was also described. FAPROTAX annotation predicted that the synthetic B. napus lines had more abundant pathways related to nitrogen metabolism, and the co-occurrence network results demonstrated that Rhodoplanes acted as hub nodes to promote nitrogen metabolism in the synthetic B. napus lines. This study provides new insights into the impacts of rapeseed domestication on the diversity and community structure of rhizosphere microbiota, which may highlight the contribution of rhizosphere microbiota to plant health.
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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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Sánchez-Salazar, Angela M., Jacquelinne J. Acuña, Michael J. Sadowsky, and Milko A. Jorquera. "Bacterial Community Composition and Presence of Plasmids in the Endosphere- and Rhizosphere-Associated Microbiota of Sea Fig (Carpobrotus aequilaterus)." Diversity 15, no. 11 (November 20, 2023): 1156. http://dx.doi.org/10.3390/d15111156.
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The plant microbiome is one of the most important environments for ecological interactions between bacteria that impact the plant and the ecosystem. However, studies on the diversity of mobile genetic elements (such as plasmids) associated with the plant microbiome are very scarce. Here, we determined the bacterial community composition and the occurrence of plasmids in the microbiota associated with sea fig, Carpobrotus aequilaterus (N.E. Br.), a succulent species widely used as an ornamental plant in Chile. The abundance and composition of the endophytic and rhizospheric bacterial communities were determined by quantitative PCR (qPCR) and DNA metabarcoding analysis. Plasmid diversity in the plant microbiome was determined by plasmid DNA extraction and screened by endpoint PCR of backbone genes for four different incompatibility groups (Inc). The results showed about 106 copies of the 16S rRNA gene in the endosphere and rhizosphere, showing significant differences according to the diversity index. Proteobacteria (Pseudomonadota; 43.4%), Actinobacteria (Actinomycetota; 25.7%), and Bacteroidetes (Bacteroidota; 17.4%) were the most dominant taxa in both plant compartments, and chemoheterotrophy (30%) was the main predicted function assigned to the microbiota. Plasmid diversity analysis showed the presence of transferable plasmids in the endosphere and rhizosphere of C. aequilaterus, particularly among environmental plasmids belonging to the IncP and IncN incompatibility groups.
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May-Mutul, Carla G., Miguel A. López-Garrido, Aileen O’Connor-Sánchez, Yuri J. Peña-Ramírez, Natalia Y. Labrín-Sotomayor, Héctor Estrada-Medina, and Miriam M. Ferrer. "Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens." Plants 11, no. 22 (November 15, 2022): 3098. http://dx.doi.org/10.3390/plants11223098.
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During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota’s alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Xu, Junhuan, Tyson Knight, Donchel Boone, Muhammad Saleem, Sheree J. Finley, Nicole Gauthier, Joseph A. Ayariga, et al. "Influence of Fungicide Application on Rhizosphere Microbiota Structure and Microbial Secreted Enzymes in Diverse Cannabinoid-Rich Hemp Cultivars." International Journal of Molecular Sciences 25, no. 11 (May 28, 2024): 5892. http://dx.doi.org/10.3390/ijms25115892.
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Microbes and enzymes play essential roles in soil and plant rhizosphere ecosystem functioning. However, fungicides and plant root secretions may impact the diversity and abundance of microbiota structure and enzymatic activities in the plant rhizosphere. In this study, we analyzed soil samples from the rhizosphere of four cannabinoid-rich hemp (Cannabis sativa) cultivars (Otto II, BaOx, Cherry Citrus, and Wife) subjected to three different treatments (natural infection, fungal inoculation, and fungicide treatment). DNA was extracted from the soil samples, 16S rDNA was sequenced, and data were analyzed for diversity and abundance among different fungicide treatments and hemp cultivars. Fungicide treatment significantly impacted the diversity and abundance of the hemp rhizosphere microbiota structure, and it substantially increased the abundance of the phyla Archaea and Rokubacteria. However, the abundances of the phyla Pseudomonadota and Gemmatimonadetes were substantially decreased in treatments with fungicides compared to those without fungicides in the four hemp cultivars. In addition, the diversity and abundance of the rhizosphere microbiota structure were influenced by hemp cultivars. The influence of Cherry Citrus on the diversity and abundance of the hemp rhizosphere microbiota structure was less compared to the other three hemp cultivars (Otto II, BaOx, and Wife). Moreover, fungicide treatment affected enzymatic activities in the hemp rhizosphere. The application of fungicides significantly decreased enzyme abundance in the rhizosphere of all four hemp cultivars. Enzymes such as dehydrogenase, dioxygenase, hydrolase, transferase, oxidase, carboxylase, and peptidase significantly decreased in all the four hemp rhizosphere treated with fungicides compared to those not treated. These enzymes may be involved in the function of metabolizing organic matter and degrading xenobiotics. The ecological significance of these findings lies in the recognition that fungicides impact enzymes, microbiota structure, and the overall ecosystem within the hemp rhizosphere.
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Sugiyama, Akifumi. "Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture." Bioscience, Biotechnology, and Biochemistry 85, no. 9 (June 10, 2021): 1919–31. http://dx.doi.org/10.1093/bbb/zbab106.
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ABSTRACT Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.
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Qu, Peng, Butian Wang, Meijun Qi, Rong Lin, Hongmei Chen, Chun Xie, Zhenwei Zhang, Junchao Qiu, Huabo Du, and Yu Ge. "Medicinal Plant Root Exudate Metabolites Shape the Rhizosphere Microbiota." International Journal of Molecular Sciences 25, no. 14 (July 16, 2024): 7786. http://dx.doi.org/10.3390/ijms25147786.
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The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities.
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He, Li, Yanzhen Ren, Weimin Zeng, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, and Jiaokun Li. "Deciphering the Endophytic and Rhizospheric Microbial Communities of a Metallophyte Commelina communis in Different Cu-Polluted Soils." Microorganisms 9, no. 8 (August 9, 2021): 1689. http://dx.doi.org/10.3390/microorganisms9081689.
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Metallophytes microbiota play a key role in plant growth and resistance to heavy metal stress. Comparing to the well-studied single or some specific plant growth-promoting (PGP) bacterial strains, our current understanding of the structural and functional variations of microbiome of metallophytes is still limited. Here, we systematically investigated the endophytic and rhizosphere bacterial community profiles of a metallophyte Commelina communis growing in different Cu-polluted soils by high-throughput sequencing technology. The results showed that the rhizosphere communities of C. communis exhibited a much higher level of diversity and richness than the endosphere communities. Meanwhile, shifts in the bacterial community composition were observed between the rhizosphere and endosphere of C. communis, indicating plant compartment was a strong driver for the divergence between rhizosphere and endosphere community. Among the environmental factors, soil Cu content, followed by OM, TP and TN, played major roles in shaping the bacterial community structure of C. communis. At the highly Cu-contaminated site, Pseudomonas and Sphingomonas were the predominant genera in the endophytic and rhizospheric bacterial communities, respectively, which might enhance copper tolerance as PGP bacteria. In summary, our findings will be useful to better understand metallophyte–microbe interactions and select suitable bacterial taxa when facilitating phytoremediation.
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Kovacs, Emoke Dalma, Luminita Silaghi-Dumitrescu, Cecilia Roman, and Di Tian. "Structural and Metabolic Profiling of Lycopersicon esculentum Rhizosphere Microbiota Artificially Exposed at Commonly Used Non-Steroidal Anti-Inflammatory Drugs." Microorganisms 10, no. 2 (January 24, 2022): 254. http://dx.doi.org/10.3390/microorganisms10020254.
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In this study, the effect of common non-steroidal anti-inflammatory drugs on Lycopersicon esculentum rhizosphere microbiota was monitored. The experiments were performed with artificially contaminated soil with ibuprofen (0.5 mg·kg−1), ketoprofen (0.2 mg·kg−1) and diclofenac (0.7 mg·kg−1). The results evidenced that the rhizosphere microbiota abundance decreased especially under exposure to diclofenac (187–201 nmol·g−1 dry weight soil) and ibuprofen (166–183 nmol·g−1 dry weight soil) if compared with control (185–240 nmol·g−1 dry weight soil), while the fungal/bacteria ratio changed significantly with exposure to diclofenac (<27%) and ketoprofen (<18%). Compared with control samples, the average amount of the ratio of Gram-negative/Gram-positive bacteria was higher in rhizosphere soil contaminated with ibuprofen (>25%) and lower in the case of diclofenac (<46%) contamination. Carbon source consumption increased with the time of assay in case of the control samples (23%) and those contaminated with diclofenac (8%). This suggests that rhizosphere microbiota under contamination with diclofenac consume a higher amount of carbon, but they do not consume a larger variety of its sources. In the case of contamination with ibuprofen and ketoprofen, the consumption of carbon source presents a decreasing tendency after day 30 of the assay. Rhizosphere microbiota emitting volatile organic compounds were also monitored. Volatile compounds belonging to alcohol, aromatic compounds, ketone, terpene, organic acids, aldehyde, sulphur compounds, esters, alkane, nitrogen compounds, alkene and furans were detected in rhizosphere soil samples. Among these, terpene, ketone, alcohol, aromatic compounds, organic acids and alkane were the most abundant compound classes (>75%), but their percentage changed with exposure to diclofenac, ketoprofen and ibuprofen. Such changes in abundance, structure and the metabolic activity of Lycopersicon esculentum rhizosphere microbiota under exposure to common non-steroidal anti-inflammatory drugs suggest that there is a probability to also change the ecosystem services provided by rhizosphere microbiota.
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Belkacem, El Amrani. "Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem." Vavilov Journal of Genetics and Breeding 26, no. 5 (September 3, 2022): 442–48. http://dx.doi.org/10.18699/vjgb-22-54.
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Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the influence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specifically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microflora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the field of protecting and maintaining the proper functioning of the soil ecosystem.
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Russi, Luigi, Gianpiero Marconi, Nicoletta Ferradini, Beatrice Farda, Marika Pellegrini, and Loretta Pace. "Investigating Population Genetic Diversity and Rhizosphere Microbiota of Central Apennines’ Artemisia eriantha." Sustainability 14, no. 18 (September 11, 2022): 11405. http://dx.doi.org/10.3390/su141811405.
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The present study aimed to characterize the genetic structure of Artemisia eriantha Ten. and the diversity of the rhizosphere microbiota. Plant leaves and rhizosphere soils were sampled from three areas of Central Italy, namely Monte Corvo, Monte Portella (both from the Gran Sasso massif), and Monte Focalone (Majella massif). The plant samples were subjected to genetic structure analysis by amplified fragment length polymorphism (AFLP) markers. The microbiota from the rhizosphere soils was investigated by 16S rRNA gene metabarcoding. The within and among population variability was typical of outbreeding species. The AFLP polymorphisms revealed a marked closeness among plant populations collected in Monte Focalone and Monte Corvo, despite the geographical proximity of the latter with Monte Portella, a result confirmed by cluster, STRUCTURE, and discriminant analyses. 16S rRNA gene metabarcoding showed higher values of diversity for Monte Corvo (H, 5.7; Chao1, 445) and Monte Focalone (H′, 5.57; Chao1, 446) than Monte Portella (H′, 5.3; Chao1, 275). At the phylum level, the communities were mainly represented by Proteobacteria, Actinobacteria, and Acidobacteria (>10%). At the genus level, the Monte Focalone and Monte Corvo microbiotas were closer than Monte Portella, thus confirming the results from the plant communities. The findings provided evidence for the first time of an association between the Artemisia eriantha plant and microbiota communities. The relevance of the results in terms of biodiversity and the conservation strategies of plant and microbiota communities in the Central Apennines are discussed.
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Kusstatscher, Peter, Wisnu Adi Wicaksono, Dhivya P. Thenappan, Eveline Adam, Henry Müller, and Gabriele Berg. "Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health." Microorganisms 8, no. 10 (September 30, 2020): 1506. http://dx.doi.org/10.3390/microorganisms8101506.
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The targeted application of plant growth-promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood, but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as a seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. The plant performances and rhizosphere compositions of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however, overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite the fact that treatments had a significant impact on the rhizosphere microbiota (9–12%), the field site was identified as the main driver (27–37%). The soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show the first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way, first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are made.
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Pinho, Diogo, Cristina Barroso, Hugo Froufe, Nathan Brown, Elena Vanguelova, Conceição Egas, and Sandra Denman. "Linking Tree Health, Rhizosphere Physicochemical Properties, and Microbiome in Acute Oak Decline." Forests 11, no. 11 (October 30, 2020): 1153. http://dx.doi.org/10.3390/f11111153.
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Forest decline diseases are complex processes driven by biotic and abiotic factors. Although information about host–microbiome–environment interactions in agricultural systems is emerging rapidly, similar studies on tree health are still in their infancy. We used acute oak decline (AOD) as a model system to understand whether the rhizosphere physicochemical properties and microbiome are linked to tree health by studying these two factors in healthy and diseased trees located in three sites in different AOD stages—low, mid and severe. We found significant changes in the rhizosphere properties and microbiome composition across the different AOD sites and between the tree health conditions. Rhizosphere pH correlated with microbiome composition, with the microbial assemblages changing in more acidic soils. At the severe AOD site, the oak trees exhibited the lowest rhizosphere pH and distinct microbiome, regardless of their health condition, whereas, at the low and mid-stage AOD sites, only diseased trees showed lower pH and the microbial composition differed significantly from healthy trees. On these two sites, less extreme soil conditions and a high presence of host-beneficial microbiota were observed in the healthy oak trees. For the first time, this study gathers evidence of associations among tree health conditions, rhizosphere properties and microbiome as well as links aboveground tree decline symptoms to the belowground environment. This provides a baseline of rhizosphere community profiling of UK oak trees and paves the way for these associations to be investigated in other tree species suffering decline disease events.
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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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Damo, Jean Louise Cocson, Takashi Shimizu, Hinako Sugiura, Saki Yamamoto, Shin-ichiro Agake, Julieta Anarna, Haruo Tanaka, et al. "The Application of Sulfur Influences Microbiome of Soybean Rhizosphere and Nutrient-Mobilizing Bacteria in Andosol." Microorganisms 11, no. 5 (May 3, 2023): 1193. http://dx.doi.org/10.3390/microorganisms11051193.
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This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were compared. High-throughput sequencing of 16S rRNA was used to analyze the effect of S on microbial community structure of the soybean rhizosphere. Several plant growth-promoting bacteria (PGPB) isolated from the rhizosphere were identified that can be harnessed for crop productivity. The amount of malic acid secreted from the soybean roots was significantly induced by S application. According to the microbiota analysis, the relative abundance of Polaromonas, identified to have positive association with malic acid, and arylsulfatase-producing Pseudomonas, were increased in S-applied soil. Burkholderia sp. JSA5, obtained from S-applied soil, showed multiple nutrient-mobilizing traits among the isolates. In this study, S application affected the soybean rhizosphere bacterial community structure, suggesting the contribution of changing plant conditions such as in the increase in organic acid secretion. Not only the shift of the microbiota but also isolated strains from S-fertilized soil showed PGPB activity, as well as isolated bacteria that have the potential to be harnessed for crop productivity.
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Bao, Lijun, Bo Sun, Yingxue Wei, Nan Xu, Shiwei Zhang, Likun Gu, and Zhihui Bai. "Grape Cultivar Features Differentiate the Grape Rhizosphere Microbiota." Plants 11, no. 9 (April 20, 2022): 1111. http://dx.doi.org/10.3390/plants11091111.
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Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants’ metabolisms and activation of plants’ responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.
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Fonseca, Jose P., Venkatachalam Lakshmanan, Clarissa Boschiero, and Kirankumar S. Mysore. "The Pattern Recognition Receptor FLS2 Can Shape the Arabidopsis Rhizosphere Microbiome β-Diversity but Not EFR1 and CERK1." Plants 11, no. 10 (May 17, 2022): 1323. http://dx.doi.org/10.3390/plants11101323.
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Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) is the first line of plant defense. We hypothesized that the absence of pattern recognition receptors (PRRs) in plants could influence the rhizosphere microbiome. Here, we report sequencing of the 16S ribosomal RNA gene and the fungal ribosomal RNA internal transcribed spacer region of rhizosphere DNA from three Arabidopsis PRR mutants involved in plant innate immunity (efr1, fls2, and cerk1). We conducted experiments in a growth chamber using native soil from the Red River Farm (Terral, OK, USA) to detect microbial community shifts in the rhizosphere that may occur in the absence of PRR receptors compared to wild-type (WT; Col-0) plants. No difference in the α-diversity of the rhizosphere microbial population was observed between the PRR mutants tested and the WT. Plant host genotype had a significant impact in bacterial β-diversity only between the fls2 mutant and the WT. Surprisingly, no significant changes in fungal β-diversity were observed between the PRR mutants and WT, although we observed an increase in relative abundance for the cup fungi (Pezizaceae) in the cerk1 mutant. This finding suggests that the FLS2 receptor can modulate the rhizosphere-associated microbiome β-diversity and expands the list of current known genotypes that can modulate the rhizosphere microbiota.
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Bourak, Kaoutar, Abdoul Razack Sare, Abdelmounaaim Allaoui, M. Haissam Jijakli, and Sébastien Massart. "Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota." International Journal of Molecular Sciences 24, no. 12 (June 8, 2023): 9879. http://dx.doi.org/10.3390/ijms24129879.
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Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant–microbiome interactions for P uptake.
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Karpenko, Viktor, Vasyl Krasnoshtan, Ivan Mostoviak, and Ruslan Prytuliak. "Microorganisms number in sorghum (Sorghum bicolor (L.) Moench) rhizosphere after herbicide, plant growth regulator, and a biopreparation use." Agronomy Science 76, no. 2 (July 21, 2021): 17–26. http://dx.doi.org/10.24326/as.2021.2.2.
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In the modern agricultural production, the use of herbicides and other biologically active substances is an important part of the cultivation technologies of most cereals, including the grain sorghum. It is known that most preparations, including the chemical ones, can directly or indirectly influence the development of microorganisms in the rhizosphere of plants, but the nature of their effect on the microbiota of grain sorghum rhizosphere has not been studied enough, which reasoned the relevance of this research. Microbiological activity of the grain sorghum rhizosphere (hybrid Milo W) was studied during 2019–2020 under the treatment by the herbicide Citadel 25 OD (0.6; 0.8 and 1.0 l/ha), plant growth regulator Endophit L1 (30 ml/ha) and biological preparation Bioarsenal (800 g/ 100 kg). The analysis of the obtained experimental data showed that use of the studied preparations both separately and in different compositions had a stimulating effect on the number of grain sorghum rhizosphere microbiota, which was observed in its increase, especially in variants with the combined use of the herbicide Citadel 25 OD, plant growth regulator Endophit L1 and the biopreparation Bioarsenal (compared to the control the number of rhizosphere microbiota increased by 29.4–80.6% in average by groups).
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Ruan, Rujue, Zhifang Jiang, Yuhuan Wu, Maojun Xu, and Jun Ni. "High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba." PeerJ 7 (November 15, 2019): e8051. http://dx.doi.org/10.7717/peerj.8051.
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Background The narrow region of soil, in contact with and directly influenced by plant roots, is called the rhizosphere. Microbes living in the rhizosphere are considered to be important factors for the normal growth and development of plants. In this research, the structural and functional diversities of microbiota between the Ginkgo biloba root rhizosphere and the corresponding bulk soil were investigated. Methods Three independent replicate sites were selected, and triplicate soil samples were collected from the rhizosphere and the bulk soil at each sampling site. The communities of bacteria and fungi were investigated using high-throughput sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) of the rRNA gene, respectively. Results A number of bacterial genera showed significantly different abundance in the rhizosphere compared to the bulk soil, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira. Functional enrichment analysis of bacterial microbiota revealed consistently increased abundance of ATP-binding cassette (ABC) transporters and decreased abundance of two-component systems in the rhizosphere community, compared to the bulk soil community. In contrast, the situation was more complex and inconsistent for fungi, indicating the independency of the rhizosphere fungal community on the local microenvironment.
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Mao, Han-Cheng, Yifei Sun, Chengyuan Tao, Xuhui Deng, Xu Xu, Zhenquan Shen, Laijie Zhang, et al. "Rhizosphere Microbiota Promotes the Growth of Soybeans in a Saline–Alkali Environment under Plastic Film Mulching." Plants 12, no. 9 (May 5, 2023): 1889. http://dx.doi.org/10.3390/plants12091889.
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The rhizosphere microbiota plays a critical and crucial role in plant health and growth, assisting plants in resisting adverse stresses, including soil salinity. Plastic film mulching is an important method to adjust soil properties and improve crop yield, especially in saline–alkali soil. However, it remains unclear whether and to what extent the association between these improvements and rhizosphere microbiota exists. Here, from a field survey and a greenhouse mesocosm experiment, we found that mulching plastic films on saline–alkali soil can promote the growth of soybeans in the field. Results of the greenhouse experiment showed that soybeans grew better in unsterilized saline–alkali soil than in sterilized saline–alkali soil under plastic film mulching. By detecting the variations in soil properties and analyzing the high-throughput sequencing data, we found that with the effect of film mulching, soil moisture content was effectively maintained, soil salinity was obviously reduced, and rhizosphere bacterial and fungal communities were significantly changed. Ulteriorly, correlation analysis methods were applied. The optimization of soil properties ameliorated the survival conditions of soil microbes and promoted the increase in relative abundance of potential beneficial microorganisms, contributing to the growth of soybeans. Furthermore, the classification of potential key rhizosphere microbial OTUs were identified. In summary, our study suggests the important influence of soil properties as drivers on the alteration of rhizosphere microbial communities and indicates the important role of rhizosphere microbiota in promoting plant performance in saline–alkali soil under plastic film mulching.
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Kaushal, Manoj, Rony Swennen, and George Mahuku. "Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions." Microorganisms 8, no. 3 (March 20, 2020): 443. http://dx.doi.org/10.3390/microorganisms8030443.
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We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa.
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Sanon, A., Z. N. Andrianjaka, Y. Prin, R. Bally, J. Thioulouse, G. Comte, and R. Duponnois. "Rhizosphere microbiota interfers with plant-plant interactions." Plant and Soil 321, no. 1-2 (May 9, 2009): 259–78. http://dx.doi.org/10.1007/s11104-009-0010-5.
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Sanon, A., Z. N. Andrianjaka, Y. Prin, R. Bally, J. Thioulouse, G. Comte, and R. Duponnois. "Rhizosphere microbiota interfers with plant-plant interactions." Plant and Soil 325, no. 1-2 (August 8, 2009): 351–52. http://dx.doi.org/10.1007/s11104-009-0100-4.
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Santos, J. B., E. A. Ferreira, C. M. T. Fialho, E. A. Santos, L. Galon, G. Concenço, I. Asiazú, and A. A. Silva. "Biodegradation of glyphosate in rhizospheric soil cultivated with Glycine max, Canavalia ensiformis e Stizolobium aterrimum." Planta Daninha 27, no. 4 (2009): 781–87. http://dx.doi.org/10.1590/s0100-83582009000400016.
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Biodegradation of glyphosate was evaluated in rhizospheric soil cultivated with Glycine max (soybean, var. BRS245-RR), Canavalia ensiformis and Stizolobium aterrimum. After these species were cultivated for 60 days, soil samples were collected, placed in flasks and treated with 14C-glyphosate. After 30 days of incubation, the total release rate of C-CO2 was determined along with microbial biomass (MBC), metabolic quotient (qCO2), and degradation percentage of the radio-labeled glyphosate released as 14C-CO2. A higher mass of rhizosphere-associated microorganisms was verified in the soil samples from pots cultivated with soybean, regardless of glyphosate addition. However, in the presence of the herbicide, this characteristic was the most negatively affected. Microorganisms from the C. ensiformis rhizosphere released a lower amount of 14C-CO2, while for those originated from S. aterrimum, the amount released reached 1.3% more than the total carbon derived from the respiratory activity. The rhizospheric soil from S. aterrimum also presented higher glyphosate degradation efficiency per microbial biomass unit. However, considering qCO2, the microbiota of the rhizospheric soil cultivated with soybean was more efficient in herbicide degradation.
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Tistechok, S. I., V. Ya Syrvatka, V. O. Fedorenko, and O. M. Gromyko. "Actinomycetes of Juniperus excelsa Bield. rhizosphere – antagonists of phytopathogenic microbiota." Faktori eksperimental'noi evolucii organizmiv 23 (September 9, 2018): 340–45. http://dx.doi.org/10.7124/feeo.v23.1038.
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Aim. Phytopathogenic microorganisms are one of the main causes of agricultural productivity losses. Thereby, the goal of this study was to evaluate actinomycetes strains, isolated from Juniperus excelsa Bield. rhizosphere, antagonistic activity against plant pathogenic bacteria and fungi. Methods. In this study we used microbiological methods for isolation actinomycetes from rhizosphere. Antagonistic activity was evaluated by using the dual culture method. Results. 372 actinomycete stains were isolated from J. excelsa Bield. rhizosphere. More than 60 % actinomyces isolates showed antibacterial activity against to lest one of the tested phytopathogenic bacteria genus Pseudomonas, Pectobacterium, Agrobacterium, Erwinia, Xanthomonas and 20.5 % of the tested phytopathogenic fungi genus Aspergillus, Alternaria, Fusarium, Botrytis. Only 2 strains had antagonistic activity to the all of the tested microorganisms and 62 strains, which had antagonistic activity to the one test-microorganism. Conclusions. Actinomicetes of J. excelsa Bield. rhizosphere are source for bioactive compounds against phytopatogenic microorganisms and showed good biotechnology potential. These results are the first step to the screening new biopesticides for controlling phytopatogenic diseases in plan.
Keywords: actynomicetes, phytopathogens, biocontrol.
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Shi, YingWu, HongMei Yang, Ming Chu, XinXiang Niu, XiangDong Huo, Yan Gao, Jun Zeng, et al. "Diversity and space–time dynamics of the bacterial communities in cotton (Gossypium hirsutum) rhizosphere soil." Canadian Journal of Microbiology 66, no. 3 (March 2020): 228–42. http://dx.doi.org/10.1139/cjm-2019-0196.
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Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.
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Ma, Xiaojing, Sambhaji Balaso Thakar, Huimin Zhang, Zequan Yu, Li Meng, and Junyang Yue. "Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types." Current Bioinformatics 15, no. 5 (October 14, 2020): 503–14. http://dx.doi.org/10.2174/1574893615666200129104523.
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Background: The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types. Objective: In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil. Methods: A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level. Result: Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens. Conclusion: Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.
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Carrascosa, Angel, Jose Antonio Pascual, Alvaro López-García, Maria Romo-Vaquero, Margarita Ros, Spyridon A. Petropoulos, and Maria del Mar Alguacil. "Different Functional and Taxonomic Composition of the Microbiome in the Rhizosphere of Two Purslane Genotypes." Agronomy 13, no. 7 (July 4, 2023): 1795. http://dx.doi.org/10.3390/agronomy13071795.
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Soil microbial communities have an important role in plant establishment and health. Particularly, the role of the soil microbiome in agriculture is of current interest. The study of microbial communities associated with purslane could open questions about the rational exploitation of the microbiota for sustainable agricultural purposes. In this study, the composition of the fungal and bacterial communities and the bacterial metabolic functions, associated with the rhizospheres of two purslane genotypes (one commercially available and one collected from the wild in Spain) were evaluated. The results showed a clear effect of purslane genotype on fungal and bacterial community composition and functional profiles. The bacterial community of the commercial purslane rhizosphere was characterized by more numerous metabolic pathways, mainly pathways related to Terpenoids and Polyketides, Carbohydrate, Lipid, and Amino Acid metabolism. By contrast, the rhizosphere bacterial community of the Spanish (wild) genotype was characterized by the enrichment of functions related to cellular processes such as cell motility and transport. We hypothesize that these differences could be due to differential effects of root exudate composition on the microbial functional community composition. This finding points out the need to consider differences in the functional characteristics of plant genotypes when selecting the beneficial microorganisms to be used as biofertilizers aiming to maximize plant growth and resistance to environmental stressors.
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Ahmed, Bulbul, Lawrence B. Smart, and Mohamed Hijri. "Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil." Frontiers in Microbiology 12 (November 15, 2021). http://dx.doi.org/10.3389/fmicb.2021.741597.
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Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, “TJ’s CBD,” in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant – ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.
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Becker, Maximilian Fernando, Manfred Hellmann, and Claudia Knief. "Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees." Environmental Microbiome 17, no. 1 (June 17, 2022). http://dx.doi.org/10.1186/s40793-022-00427-z.
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Abstract Background The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees. Results The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R2-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R2-values of 0.454 and 0.371, respectively). Conclusions The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.
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Cadot, Selma, Hang Guan, Moritz Bigalke, Jean-Claude Walser, Georg Jander, Matthias Erb, Marcel G. A. van der Heijden, and Klaus Schlaeppi. "Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field." Microbiome 9, no. 1 (May 7, 2021). http://dx.doi.org/10.1186/s40168-021-01049-2.
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Abstract Background Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties. Results Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments. Conclusions These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.
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Li, Baolong, Gaofu Qi, Yiting Li, and Xiuyun Zhao. "Microbial network and composition changes according to tobacco varieties and interferes differently in black shank disease defense." Journal of Applied Microbiology 134, no. 1 (December 13, 2022). http://dx.doi.org/10.1093/jambio/lxac001.
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Abstract Aims The soil-borne oomycete pathogen Phytophthora parasitica can cause black shank disease in tobacco plants. The use of resistant varieties can be used to control black shank disease. The potential relationships of the composition of the rhizosphere microbiome to resistance to black shank disease are poorly understood. This work aims to compare the rhizosphere microbial community and network of the tobacco resistant variety HB202 with the susceptible variety XY3. Methods and Results Rhizospheric soils were collected from tobacco plants of HB202 and XY3 in the fields with same soil types and agricultural operations. The compositions of the rhizosphere microbial communities were revealed by Illumina sequencing of bacterial 16S rRNA genes and fungal spacer (ITS) sequences and analysed with molecular ecological network pipeline. The alpha diversity of fungal communities of the two varieties was significantly different. The structure and composition of bacterial and fungal communities in the resistant variety in the rhizosphere was different from the susceptible variety. Relative abundances of beneficial genera in the HB202 microbiota were higher than in the XY3. Conversely, the XY3 microbiota exhibited a higher abundance of deleterious genera compared to the HB202 microbiota. The resistant variety influences the topological properties and microbial interactions in the rhizosphere against the disease. The network of the HB202 was more complex and had higher connectivity compared to the XY3 network. Conclusions The rhizosphere microbial communities and networks of two tobacco varieties are very different. These changes in the microbial communities and their interactions may play an important role in tobacco resistance to black shank disease.
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Li, Jiajia, Miaochun Fan, Le Yang, Zhen Yang, and Zhouping Shangguan. "Temporal shifts in root exudates driven by vegetation restoration alter rhizosphere microbiota in Robinia pseudoacacia plantations." Tree Physiology, March 13, 2023. http://dx.doi.org/10.1093/treephys/tpad030.
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Abstract Plant–soil–microbiota interactions mediated by root exudates regulate plant growth and drive rhizosphere microbial feedbacks. It remains unknown how root exudates affect rhizosphere microbiota and soil functions in the course of forest plantation restoration. The metabolic profiles of tree root exudates are expected to shift with stand age, leading to variation in rhizosphere microbiota structure, and in turn, potentially altering soil functions. To unravel the effects of root exudates, a multi-omics study was conducted using untargeted metabonomic profiling, high-throughput microbiome sequencing, and functional gene array. The interactions among root exudates, rhizosphere microbiota, and nutrient cycling-related functional genes were explored under 15–45-year-old Robinia pseudoacacia plantations in the Loess Plateau region of China. Root exudate metabolic profiles, rather than chemodiversity, markedly changed with an increase in stand age. A total of 138 age-related metabolites were extracted from a key module of root exudates. The relative contents of six biomarker metabolites, such as glucose 1-phosphate, gluconic acid, and N-acetylneuraminic acid increased distinctly over time. The biomarker taxa (16 classes) of rhizosphere microbiota varied in a time-sensitive manner, which played potential roles in nutrient cycling and plant health. Nitrospira, Alphaproteobacteria, and Acidobacteria were enriched in the rhizosphere of older stands. Key root exudates influenced functional gene abundances in the rhizosphere via directed effects or indirectly through biomarker microbial taxa (e.g., Nitrososphaeria). Overall, root exudates and rhizosphere microbiota are essential for soil function maintenance under R. pseudoacacia plantation restoration.
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Becker, Maximilian Fernando, A. Michael Klueken, and Claudia Knief. "Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings." Environmental Microbiome 18, no. 1 (May 27, 2023). http://dx.doi.org/10.1186/s40793-023-00502-z.
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Abstract Background The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota. Results The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant. Conclusions Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.
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Zhang, Yan, Wei Wang, Zhangjun Shen, Jingjing Wang, Yajun Chen, Dong Wang, Gang Liu, and Maozhen Han. "Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties." BMC Microbiology 21, no. 1 (January 22, 2021). http://dx.doi.org/10.1186/s12866-021-02092-7.
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Abstract Background Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Results In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.
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Zhao, Mengli, Jun Yuan, Zongzhuan Shen, Menghui Dong, Hongjun Liu, Tao Wen, Rong Li, and Qirong Shen. "Predominance of soil vs root effect in rhizosphere microbiota reassembly." FEMS Microbiology Ecology 95, no. 10 (September 2, 2019). http://dx.doi.org/10.1093/femsec/fiz139.
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ABSTRACT Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.
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Yamazaki, Shinichi, Hossein Mardani-korrani, Rumi Kaida, Kumiko Ochiai, Masaru Kobayashi, Atsushi J. Nagano, Yoshiharu Fujii, Akifumi Sugiyama, and Yuichi Aoki. "Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere." Scientific Reports 11, no. 1 (April 23, 2021). http://dx.doi.org/10.1038/s41598-021-87384-8.
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AbstractThe plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere are different from the outer soil region (bulk soil). They establish characteristic conditions including microbiota, metabolites, and minerals, and they can directly affect plant growth and development. However, comprehensive insights into those characteristic environments, especially the rhizosphere, and molecular mechanisms of their formation are not well understood. In the present study, we investigated the spatiotemporal dynamics of the root-associated environment in actual field conditions by multi-omics analyses (mineral, microbiome, and transcriptome) of soybean plants. Mineral and microbiome analyses demonstrated a characteristic rhizosphere environment in which most of the minerals were highly accumulated and bacterial communities were distinct from those in the bulk soil. Mantel’s test and co-abundance network analysis revealed that characteristic community structures and dominant bacterial taxa in the rhizosphere significantly interact with mineral contents in the rhizosphere, but not in the bulk soil. Our field multi-omics analysis suggests a rhizosphere-specific close association between the microbiota and mineral environment.
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Lewin, Simon, Davide Francioli, Andreas Ulrich, and Steffen Kolb. "Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota." Environmental Microbiome 16, no. 1 (October 12, 2021). http://dx.doi.org/10.1186/s40793-021-00387-w.
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Abstract Background The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.
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Nasslahsen, Bouchra, Yves Prin, Hicham Ferhout, Abdelaziz Smouni, and Robin Duponnois. "Mycorrhizae helper bacteria for managing the mycorrhizal soil infectivity." Frontiers in Soil Science 2 (November 15, 2022). http://dx.doi.org/10.3389/fsoil.2022.979246.
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Arbuscular mycorrhizal fungi are major components of soil microbiota and mainly interact with other microorganisms in the rhizosphere. Mycorrhiza establishment impacts the plant physiology and some nutritional and physical properties of the rhizospheric soil. These effects alter the development of the root or mycorrhizas resulting from the activity of soil microorganisms. The rhizosphere of mycorrhizal plants (mycorrhizosphere), is inhabited by large microbial activities responsible for several key ecosystem processes. This review is focused on the microbial interactions between mycorrhizal fungi and components of rhizosphere microbiota and highlight the agronomic potentialities of the Mycorrhiza Helper Bacteria on mycorrhiza formation. The main conclusion is that this MHB effect in the rhizosphere of mycorrhizal plants, enhance plant fitness and soil quality and are of great interest to ensure sustainable agricultural development and ecosystem functioning.
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Kumar, Murugan, Waquar Akhter Ansari, Mohammad Tarique Zeyad, Arjun Singh, Hillol Chakdar, Adarsh Kumar, Mohammad Samir Farooqi, Anu Sharma, Sudhir Srivastava, and Alok Kumar Srivastava. "Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties." Frontiers in Plant Science 14 (May 15, 2023). http://dx.doi.org/10.3389/fpls.2023.1186162.
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Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.
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Miao, Yujing, Xinke Zhang, Guoshuai Zhang, Zhan Feng, Jin Pei, Chang Liu, and Linfang Huang. "From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity." Environmental Microbiome 18, no. 1 (February 22, 2023). http://dx.doi.org/10.1186/s40793-023-00471-3.
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Abstract Background Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism. Results The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R2 = 0.29971; fungi, R2 = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite. Conclusions Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.
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Escudero-Martinez, Carmen, Max Coulter, Rodrigo Alegria Terrazas, Alexandre Foito, Rumana Kapadia, Laura Pietrangelo, Mauro Maver, et al. "Identifying plant genes shaping microbiota composition in the barley rhizosphere." Nature Communications 13, no. 1 (June 16, 2022). http://dx.doi.org/10.1038/s41467-022-31022-y.
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AbstractA prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.
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Lee, Seung Yeup, Roniya Thapa Magar, Kihyuck Choi, Hyo Jeong Kim, Insoo Park, and Seon-Woo Lee. "Phage-dependent alteration of rhizosphere microbiota in tomato plants." Phytobiomes Journal, February 28, 2024. http://dx.doi.org/10.1094/pbiomes-07-23-0061-r.
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Bacteriophages (phages) that infect bacterial pathogens are an alternative means of controlling bacterial diseases in humans, animals, and plants. However, the effects of targeted phage therapy on indigenous microbial community has not been fully understood. In this study, we hypothesized that phages infecting plant pathogenic bacteria play a role in modulating the microbial community in the plant rhizosphere. To explore this, we used the soil-borne plant bacterial pathogen Ralstonia pseudosolanacearum as the host bacterium and its phages as a model system in the tomato rhizosphere. The effect of phages on microbiota was compared using a narrow host range phage RpY1, and a combination of two phages (RpY2 and RpT1, termed the phage combo) with a broad host range, under the natural rhizosphere microbiota of tomato plants. Both RpY1 and phage combo altered the tomato rhizosphere microbiota. The phage combo displayed phage effects mostly in the presence of R. pseudosolanacearum. However, RpY1 affected the rhizosphere microbiota even in the absence of the host bacterium. The effect of phage RpY1 on the microbiota was further investigated in the tomato rhizosphere using a synthetic community (SynCom) mimicking the natural tomato rhizosphere microbiota. Phage RpY1 affected the microbial community structure of SynCom in the tomato rhizosphere in the absence of the host bacterium. The analyses of natural microbiota and SynCom in the tomato rhizosphere indicated an indirect effect of phage RpY1 on the microbiota. This study suggests that phage application modulates indigenous microbiota through unknown interactions with non-host bacterial members in the plant rhizosphere.
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Newman, Amy, Emma Picot, Sian Davies, Sally Hilton, Isabelle A. Carré, and Gary D. Bending. "Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota." BMC Biology 20, no. 1 (October 20, 2022). http://dx.doi.org/10.1186/s12915-022-01430-z.
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Abstract Background Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY). Results Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota. Conclusions These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity.