Статті в журналах: "Rhizobiote"

1

Ariza-Mejía, Daniella, Guadalupe Oyoque-Salcedo, Valentina Angóa-Pérez, Hortencia G. Mena-Violante, Dioselina Álvarez-Bernal, and Jesús R. Torres-García. "Diversity and Potential Function of the Bacterial Rhizobiome Associated to Physalis Ixocarpa Broth. in a Milpa System, in Michoacan, Mexico." Agronomy 12, no. 8 (July 28, 2022): 1780. http://dx.doi.org/10.3390/agronomy12081780.

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Michoacan state has a long history in plant domestication’s. Physalis ixocarpa is a native plant that growth associated to maize crops from this region. Due to the domestication process includes the adaptation to environmental factors, we ask if (1) Does P. ixocarpa has the capacity of association with bacterial communities of the zone where it was domesticated? and (2) Does the rhizobiome of this plant can increase the potential functions in the soil? An experiment was established in a traditional milpa system. Samples of rhizobiome from corn, P. ixocarpa, P. philadelphica, and soil were sequenced using Next Generation Sequencing in the region 16S. The potential function, metabolic pathway reconstruction and participation of each bacteria genus was inferred using iVikodak platform. A total of 34 Phyla and 795 genera were identified. Purine metabolism’s was the principal function, where all rhizobiomes showed similar metabolic pathways. However, the difference among plant species is the participation of the distinct genera in the Purine metabolism. We conclude that the rhizobiome of P. ixocarpa maintains the capacity of bacterial association in the region and shows complementarity for the soil functions. Therefore, their utilization can be helpful in zones where the agricultural practices have degraded microbiological soil conditions.

2

Vieira, Selma, Johannes Sikorski, Sophie Dietz, Katharina Herz, Marion Schrumpf, Helge Bruelheide, Dierk Scheel, Michael W. Friedrich, and Jörg Overmann. "Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands." ISME Journal 14, no. 2 (October 28, 2019): 463–75. http://dx.doi.org/10.1038/s41396-019-0543-4.

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Abstract The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

3

Quattrone, Amanda, Yuguo Yang, Pooja Yadav, Karrie A. Weber, and Sabrina E. Russo. "Nutrient and Microbiome-Mediated Plant–Soil Feedback in Domesticated and Wild Andropogoneae: Implications for Agroecosystems." Microorganisms 11, no. 12 (December 13, 2023): 2978. http://dx.doi.org/10.3390/microorganisms11122978.

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Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73-wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative PSF based on growth, phenotypic traits, and foliar nutrient concentrations for maize B73-wt, which grew slower in maize-conditioned soil than prairie grass-conditioned soil. In contrast, teosinte and A. gerardii showed few consistent feedback responses. Both rhizobiome and nutrient-mediated mechanisms were implicated in PSF. Based on 16S rRNA gene amplicon sequencing, the rhizosphere bacterial community composition differed significantly after conditioning by prairie grass and maize plants, and the final soil nutrients were significantly influenced by conditioning, more so than by the feedback plants. These results suggest PSF-mediated soil domestication in agricultural settings can develop quickly and reduce crop productivity mediated by PSF involving changes to both the soil rhizobiomes and nutrient availability.

4

Orozco-Mosqueda, Ma del Carmen, Ajay Kumar, Olubukola Oluranti Babalola, and Gustavo Santoyo. "Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement." Plants 12, no. 18 (September 11, 2023): 3226. http://dx.doi.org/10.3390/plants12183226.

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The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.

5

Pollak, Shaul, and Otto X. Cordero. "Rhizobiome shields plants from infection." Nature Microbiology 5, no. 8 (July 24, 2020): 978–79. http://dx.doi.org/10.1038/s41564-020-0766-1.

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6

Kuramae, Eiko E., Stan Derksen, Thiago R. Schlemper, Maurício R. Dimitrov, Ohana Y. A. Costa, and Adriana P. D. da Silveira. "Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics." Microorganisms 8, no. 5 (May 13, 2020): 725. http://dx.doi.org/10.3390/microorganisms8050725.

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Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.

7

Harsono, A., D. Sucahyono, E. Pratiwi, A. Sarjia, H. Pratiwi, D. Andreas, and T. Simarmata. "The effectiveness of technology packages of 15 biofertilizer formulas to increase soybean productivity on acidic soils." IOP Conference Series: Earth and Environmental Science 911, no. 1 (November 1, 2021): 012041. http://dx.doi.org/10.1088/1755-1315/911/1/012041.

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Abstract The potentcy of acidic soils for soybean development in Indonesia is quite large. However low of soil fertility and microorganisms population become contrains for achieving high productifity of soybean. The aim of this research is to determine the effectiveness of technology packages for 15 biofertilizers formula to increase soybean productivity in acidic soils. The research was conducted during the end of rainy season in South Kalimantan. The soil use in the study had pH 5.2 and soil Al-saturation 34.2%. The reasearch was arranged in a randomized block design, three replications consisted of 20 treatmens, namely: 1) 0 NPK, 2) 50% NPK, 3) 50% NPK +2 t/ha organic fertilizer 4) 70% NPK, 5) 100% NPK (100 kg urea + 100 kg SP36 + 100 kg KCl/ha), 6) Iletrisoy+ Biovam+Starmix, 7) Iletrosoy Plus, 8) Beyonic, 9 Biotrico, 10) Probio New, 11) RhizoBIOST, 12) Bio-SRF, 13) Biopim, 14) BioMIGE, 15) Biocoat, 16) FajarSOYA, 17) Rhizobion, 18) Agrizone, 19) Rhizoplus, and 20) BISRF. For each biological fertilizer, 50-75% of recommended NPK fertilizers were given at 15 days after planting. The results indicated that combination of Biovam + Iletrisoy + Startmix biofertilizers, Iletrisoy plus, Biotricho, Probio New, Bio Mige, and Fajar SOYA were effective for increasing soybean productivity on acidic soils. These biological fertilizers + 50% recommended NPK + 1.5 t/ha organic fertilizer increases pods number, and soybean productivity more than 10% compared to the recommended NPK fertilizer dosage whic was 1.81 t/ha. Several of these biological fertilizers have good prospects to be developed as bio-fertilizers for soybeans in acidic soils.

8

Prabha, Ratna, Dhananjaya P. Singh, Shailendra Gupta, Vijai Kumar Gupta, Hesham A. El-Enshasy, and Mukesh K. Verma. "Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities." Microorganisms 7, no. 12 (November 23, 2019): 608. http://dx.doi.org/10.3390/microorganisms7120608.

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Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.

9

Cotton, T. E. Anne, Pierre Pétriacq, Duncan D. Cameron, Moaed Al Meselmani, Roland Schwarzenbacher, Stephen A. Rolfe, and Jurriaan Ton. "Metabolic regulation of the maize rhizobiome by benzoxazinoids." ISME Journal 13, no. 7 (February 22, 2019): 1647–58. http://dx.doi.org/10.1038/s41396-019-0375-2.

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10

Somera, Tracey, Mark Mazzola, and Chris Cook. "Directing the Apple Rhizobiome toward Resiliency Post-Fumigation." Agriculture 13, no. 11 (November 6, 2023): 2104. http://dx.doi.org/10.3390/agriculture13112104.

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Currently, there are no standard management practices to counteract the adverse effects of fumigation on the soil microbiome. In this study, a variety of pre-plant soil amendments were examined for their ability to recruit and maintain apple rhizosphere microbiomes that are suppressive to pathogen re-infestation of fumigated orchard soils. The capacity of these amendments to improve other characteristics of soil productivity was also evaluated. Results suggest that composted chicken manure and liquid chitin are likely to be detrimental to plant and soil health when used as a post-fumigation soil amendment. In comparison, insect frass (IF) resulted in a significant increase in tree trunk diameter relative to the fumigated control. Following pathogen re-infestation of fumigated soil, however, IF induced a significant increase in Pythium ultimum in the rhizosphere. Therefore, IF can benefit the growth of young apple trees in fumigated soil but may stimulate pathogen activity upon re-infestation. To date, the possibility of using soil amendments to suppress pathogen re-infestation of fumigated soils has not been tested. Results from this study ground support the use of soil amendments as an intervention strategy for “steering” the soil and rhizosphere microbiome in more beneficial and/or prophylactic directions following fumigation.

11

Olanrewaju, Oluwaseyi Samuel, Ayansina Segun Ayangbenro, Bernard R. Glick, and Olubukola Oluranti Babalola. "Plant health: feedback effect of root exudates-rhizobiome interactions." Applied Microbiology and Biotechnology 103, no. 3 (December 20, 2018): 1155–66. http://dx.doi.org/10.1007/s00253-018-9556-6.

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12

Kindtler, Nikolaj L., Sanea Sheikh, Jesper Richardy, Emilie Krogh, Lorrie Maccario, Mette Vestergård, Rute R. da Fonseca, Flemming Ekelund, and Kristian H. Laursen. "Fertilizer regime and cultivar affect barley growth and rhizobiome composition." Applied Soil Ecology 198 (June 2024): 105384. http://dx.doi.org/10.1016/j.apsoil.2024.105384.

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13

Schmidt, Jennifer E., Jorge L. Mazza Rodrigues, Vanessa L. Brisson, Angela Kent, and Amélie C. M. Gaudin. "Impacts of directed evolution and soil management legacy on the maize rhizobiome." Soil Biology and Biochemistry 145 (June 2020): 107794. http://dx.doi.org/10.1016/j.soilbio.2020.107794.

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14

Liao, Hui-Ling, Gregory Bonito, J. Alejandro Rojas, Khalid Hameed, Steven Wu, Christopher W. Schadt, Jessy Labbé, et al. "Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition." Molecular Plant-Microbe Interactions® 32, no. 7 (July 2019): 853–64. http://dx.doi.org/10.1094/mpmi-05-18-0133-r.

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Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth.

15

Ortiz, Yakshi, Carla Restrepo, Brayan Vilanova-Cuevas, Eugenio Santiago-Valentin, Susannah G. Tringe, and Filipa Godoy-Vitorino. "Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla." PLOS ONE 15, no. 4 (April 7, 2020): e0231083. http://dx.doi.org/10.1371/journal.pone.0231083.

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16

Refai, Mohammed Y., Aala A. Abulfaraj, Israa J. Hakeem, Nehad A. Shaer, Mashael D. Alqahtani, Maryam M. Alomran, Nahaa M. Alotaibi, et al. "Rhizobiome Signature and Its Alteration Due to Watering in the Wild Plant Moringa oleifera." Sustainability 15, no. 3 (February 2, 2023): 2745. http://dx.doi.org/10.3390/su15032745.

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Metagenomic approach was used to detect microbial gene abundance and relative abundance in the rhizosphere of Moringa oleifera and surrounding bulk soil and to detect the response of soil microbes to watering. Expectedly, the number and abundance of non-redundant genes were extremely higher in bacteria followed by archaea, eukaryota and viruses. Results demonstrated unexpected high abundance of some microbes (ex., endophyte genus Nocardioides) in the rhizosphere that are supposed to exist mainly in other rhizocompartments. We suggest this differential distribution of microbes is due to the specific pattern of host-microbe interaction. Other endosymbiont microbes, ex., fungi Mucoromycota and Ascomycota, were highly abundant in the bulk soil possibly because they are phytopathogens where plant exudates might inhibit their growth or force these fungi to approach reverse chemotaxis. Our data indicated high abundance of other symbiont microbes in the rhizosphere of M. oleifera at phylum (ex., Actinobacteria) and genus (ex., Streptomyces) levels. Watering experiment indicated that phylum Actinobacteria and the descending genus Streptomyces are among the highest. Rhizobiome of M. oleifera seems to harbor a wealth of new species of the genus Streptomyces that are required to be deciphered for function in order to be eventually utilized in pharmaceutical and agricultural applications.

17

Reazin, Christopher, Richard Baird, Stacy Clark, and Ari Jumpponen. "Chestnuts bred for blight resistance depart nursery with distinct fungal rhizobiomes." Mycorrhiza 29, no. 4 (May 25, 2019): 313–24. http://dx.doi.org/10.1007/s00572-019-00897-z.

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18

Acuña, Jacquelinne J., Luis G. Marileo, Macarena A. Araya, Joaquin I. Rilling, Giovanni A. Larama, María Luz Mora, Slava Epstein, and Milko A. Jorquera. "In Situ Cultivation Approach to Increase the Culturable Bacterial Diversity in the Rhizobiome of Plants." Journal of Soil Science and Plant Nutrition 20, no. 3 (March 24, 2020): 1411–26. http://dx.doi.org/10.1007/s42729-020-00222-0.

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19

García-Gonzalo, P., A. E. Pradas del Real, M. Pirredda, M. J. Gismera, M. C. Lobo, and A. Pérez-Sanz. "Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome." Ecotoxicology and Environmental Safety 144 (October 2017): 283–90. http://dx.doi.org/10.1016/j.ecoenv.2017.06.043.

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20

Zhang, Baogang, Shuo Jiao, Gaodi Zhu, Huai Chen, Yanjiang Cai, and Scott X. Chang. "Neighboring plant community attributes drive rhizobiome assemblages of a focal plant in a Kobresia meadow." Geoderma 432 (April 2023): 116409. http://dx.doi.org/10.1016/j.geoderma.2023.116409.

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21

Jamil, Fatima, Hamid Mukhtar, Mireille Fouillaud, and Laurent Dufossé. "Rhizosphere Signaling: Insights into Plant–Rhizomicrobiome Interactions for Sustainable Agronomy." Microorganisms 10, no. 5 (April 25, 2022): 899. http://dx.doi.org/10.3390/microorganisms10050899.

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Rhizospheric plant–microbe interactions have dynamic importance in sustainable agriculture systems that have a reduced reliance on agrochemicals. Rhizosphere signaling focuses on the interactions between plants and the surrounding symbiotic microorganisms that facilitate the development of rhizobiome diversity, which is beneficial for plant productivity. Plant–microbe communication comprises intricate systems that modulate local and systemic defense mechanisms to mitigate environmental stresses. This review deciphers insights into how the exudation of plant secondary metabolites can shape the functions and diversity of the root microbiome. It also elaborates on how rhizosphere interactions influence plant growth, regulate plant immunity against phytopathogens, and prime the plant for protection against biotic and abiotic stresses, along with some recent well-reported examples. A holistic understanding of these interactions can help in the development of tailored microbial inoculants for enhanced plant growth and targeted disease suppression.

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Jamil, Fatima, Hamid Mukhtar, Mireille Fouillaud, and Laurent Dufossé. "Rhizosphere Signaling: Insights into Plant–Rhizomicrobiome Interactions for Sustainable Agronomy." Microorganisms 10, no. 5 (April 25, 2022): 899. http://dx.doi.org/10.3390/microorganisms10050899.

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Rhizospheric plant–microbe interactions have dynamic importance in sustainable agriculture systems that have a reduced reliance on agrochemicals. Rhizosphere signaling focuses on the interactions between plants and the surrounding symbiotic microorganisms that facilitate the development of rhizobiome diversity, which is beneficial for plant productivity. Plant–microbe communication comprises intricate systems that modulate local and systemic defense mechanisms to mitigate environmental stresses. This review deciphers insights into how the exudation of plant secondary metabolites can shape the functions and diversity of the root microbiome. It also elaborates on how rhizosphere interactions influence plant growth, regulate plant immunity against phytopathogens, and prime the plant for protection against biotic and abiotic stresses, along with some recent well-reported examples. A holistic understanding of these interactions can help in the development of tailored microbial inoculants for enhanced plant growth and targeted disease suppression.

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Rojas-Sánchez, Blanca, Hugo Castelán-Sánchez, Esmeralda Y. Garfias-Zamora, and Gustavo Santoyo. "Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System." Plants 13, no. 7 (March 26, 2024): 954. http://dx.doi.org/10.3390/plants13070954.

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Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.

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Anggrainy, Eka Dewi, Arifah Hidayati, Roby Ibnu Syarifain, Muhammad Faizal Rezha Zulkarnain, and Tualar Simarmata. "Superior Nitrogen Fixing Bacteria Screening from Various Rhizobiome in Palm Oil Plantion, North Sangatta, East Kalimantan." IOP Conference Series: Earth and Environmental Science 748, no. 1 (April 1, 2021): 012007. http://dx.doi.org/10.1088/1755-1315/748/1/012007.

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Abstract Nitrogen fixing bacteria (NFB) plays an important role in increasing N availability for plants. Research to examine the ability of nitrogen fixing bacteria isolates to produce nitrogenase, phytohormone and the ability of nitrogen fixing bacteria isolates in the biological test process using the corn plant indicator as an indicator has been carried out from September 2018 to February 2019 in laboratories and greenhouses. The ability of nitrogen fixing bacteria was tested by the ARA method, while the phytohormone testing of nitrogen fixing bacteria was tested using the HPLC method. Bioassays using Murphy media and corn plants as indicators were performed using a randomized block design consisting of six treatments (one control and five selected NFB isolates from the selection results) and given five replications. Measurement of root length, plant height, and dry weight of plants were carried out every 2 days for 14 days. The results showed that the nitrogen fixing bacteria isolates used from North Sangattarhizobiome, East Kalimantan had different nitrogenase and differentphytohormone test results, and obtained five selected isolates based on the selection results. The results of the bioassay did not show any significant differences based on the Duncan test at the level of 5%. However, it can be seen visually the significant difference in which plants in the biological test using nitrogen fixing bacterial isolates have relatively higher plant growth and dry weight of plants than plants that are not given treatment or control.

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Lupwayi, Newton Z., Myriam Fernandez, Renee M. Petri, Andrea H. Brown, and Derrick A. Kanashiro. "Alteration of the organic wheat rhizobiome and enzyme activities by reduced tillage and diversified crop rotation." European Journal of Agronomy 144 (March 2023): 126726. http://dx.doi.org/10.1016/j.eja.2022.126726.

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Tang, Lu, Yimeng Shi, Yilu Zhang, Dihe Yang, and Changhong Guo. "Effects of Plant-Growth-Promoting Rhizobacteria on Soil Bacterial Community, Soil Physicochemical Properties, and Soil Enzyme Activities in the Rhizosphere of Alfalfa under Field Conditions." Diversity 15, no. 4 (April 7, 2023): 537. http://dx.doi.org/10.3390/d15040537.

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Background: Inoculation with plant-growth-promoting rhizobacteria (PGPR) effectively increases plant growth in agriculture. However, the role of the rhizobiome in plant growth remains unclear. Methods: Biolog Ecoplate and 16S rRNA gene high-throughput sequencing techniques were used to analyze the changes in microbial community diversity, composition, and function after PGPR inoculation. Soil physicochemical and enzyme activities were also measured. Results: PGPR inoculation significantly promoted the growth of alfalfa. Using a Biolog Ecoplate, inoculation improved the metabolic activity and carbon source utilization of soil microorganisms. PGPR inoculation significantly increased the diversity and richness of the soil bacterial community in the rhizosphere of alfalfa and increased the relative abundance of key bacterial taxa such as Arthrobacter, Sphingomonas, and Bacillus, which are conducive to plant growth. Conclusions: Inoculation with PGPR enriched bacterial taxa and improved the utilization of carbon sources beneficial for plant growth. PGPR inoculation induced changes in microbial community diversity, and relevant functions in the rhizosphere contributed to alfalfa growth under field conditions.

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De Zutter, Noémie, Maarten Ameye, Jane Debode, Caroline De Tender, Sarah Ommeslag, Jan Verwaeren, Pieter Vermeir, Kris Audenaert, and Leen De Gelder. "Shifts in the rhizobiome during consecutive in planta enrichment for phosphate‐solubilizing bacteria differentially affect maize P status." Microbial Biotechnology 14, no. 4 (May 22, 2021): 1594–612. http://dx.doi.org/10.1111/1751-7915.13824.

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Abán, Carla L., Giovanni Larama, Antonella Ducci, Jorgelina Huidobro, Michel Abanto, Silvina Vargas-Gil, and Carolina Pérez-Brandan. "Soil Properties and Bacterial Communities Associated with the Rhizosphere of the Common Bean after Using Brachiaria brizantha as a Service Crop: A 10-Year Field Experiment." Sustainability 15, no. 1 (December 28, 2022): 488. http://dx.doi.org/10.3390/su15010488.

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Intensive agricultural farming practices, such as monoculture, require long bare fallow periods and the overuse of agrochemicals, which compromise soil health over time. Increasing plant diversity in agroecosystems with service crops represents a promising alternative to achieving sustainability goals. However, how specific cover crop species influence the abundance and structure of soil bacterial communities remains to be solved. In this study, we assessed the effects of B. brizantha in two different agricultural cycles for 10 years in a common bean monoculture system in the northwestern region of Argentina (NWA) by measuring chemical, physical, and microbiological parameters in the rhizosphere, as well as by screening the rhizobiome using 16S rRNA sequencing. The ten-year inclusion of B. brizantha had a positive impact on properties in the rhizosphere compared to the common bean monoculture. The bacterial beta-diversity was different among treatments, but not the alpha-diversity. The most abundant phyla were Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi and Myxococcota. The predicted functions related to chemoheterotrophy and aerobic chemoheterotrophy were increased under B. brizantha treatments compared to the bean monoculture. The inclusion of the pasture B. brizantha contributed to restoring soil health and minimizing soil degradation.

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Provorov, N. A., E. E. Andronov, O. P. Onishchuk, O. N. Kurchak, and E. P. Chizhevskaya. "Genetic structure of the introduced and local populations of Rhizobioum leguminosarum in plant-soil systems." Microbiology 81, no. 2 (April 2012): 224–32. http://dx.doi.org/10.1134/s0026261712020129.

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Cochran, Alyssa T., Jemma Bauer, Jessica L. Metcalf, Petra Lovecka, Martina Sura de Jong, Sven Warris, Paul J. W. Mooijman, Ingrid van der Meer, Rob Knight, and Elizabeth A. H. Pilon-Smits. "Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition." Phytobiomes Journal 2, no. 2 (January 2018): 82–91. http://dx.doi.org/10.1094/pbiomes-12-17-0051-r.

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Little is known about the microbiomes associated with plants with unusual properties, including plants that hyperaccumulate toxic elements such as selenium (Se). Se hyperaccumulators contain up to 1.5% of their dry weight in Se, concentrations shown to affect ecological interactions with herbivores, fungal pathogens and neighboring plants. Hyperaccumulators also enrich their surrounding soil with Se, which may alter the rhizobiome. To investigate whether plant Se affects rhizobacterial diversity and composition, we used a combination of culture-independent and culture-based approaches. Sequencing of 16S rRNA gene amplicons using the Illumina platform revealed that the rhizosphere microbiomes of Se hyperaccumulators were significantly different from nonaccumulators from the same site, with a higher average relative abundance of Pedobacter and Deviosa. Additionally, hyperaccumulators harbored a higher rhizobacterial species richness when compared with nonaccumulators from the same family on the same site. Independent from Se present at the site or in the host plant, the bacterial isolates were extremely resistant to selenate and selenite (up to 200 mM) and could reduce selenite to elemental Se. In conclusion, Se hyperaccumulation does not appear to negatively affect rhizobacterial diversity, and may select for certain taxa in the rhizosphere microbiome. Additionally, Se resistance in hyperaccumulator-associated bacteria and archaea may be widespread and not under selection by the host plant.

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Somera, Tracey S., Shiri Freilich, and Mark Mazzola. "Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals and rootstocks in the same soil/plant system." Applied Soil Ecology 157 (January 2021): 103766. http://dx.doi.org/10.1016/j.apsoil.2020.103766.

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Fazal, Aliya, Zhong-Ling Wen, Yun-Ting Lu, Xiao-Mei Hua, Min-Kai Yang, Tong-Ming Yin, Hong-Wei Han, et al. "Assembly and shifts of the bacterial rhizobiome of field grown transgenic maize line carrying mcry1Ab and mcry2Ab genes at different developmental stages." Plant Growth Regulation 91, no. 1 (February 27, 2020): 113–26. http://dx.doi.org/10.1007/s10725-020-00591-7.

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Widijanto, Hery, and Suntoro Suntoro. "Pembuatan Demplot Budidaya Tanaman Jagung Dalam Menambah Masa Tanam Di Lahan Kering Dengan Memanfaatkan Pupuk Organik." PRIMA: Journal of Community Empowering and Services 3, no. 1 (June 30, 2019): 28. http://dx.doi.org/10.20961/prima.v3i1.36111.

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Program IbM ini bekerjasama dengan dua mitra, yaitu: (1) UKM Peternakan Puyuh “Agribird ”, dan (2) Kelompok Tani “Mekar Tani”. Mitra (1) dan Mitra (2) berlokasi di dukuh Gunung Wijil, Desa Ngringo, Kec. Jaten, Kab. Karanganyar, Jawa Tengah dengan jarak tempuh sekitar ± 3,5 km. Permasalahan utama yang dihadapi oleh mitra usaha „Agribird‟ adalah produksi limbah ternak puyuh yang sangat tinggi, yaitu sekitar 300 kg limbah per hari. Produksi limbahnya sangat tinggi per hari, maka kemampuan produksi limbah jauh melibihi dari kemampuan untuk memanfaatkannya. Bila limbah ini dibuang langsung ke badan sungai terdekat, maka akan mencemari air sungai, sedangkan bila limbah akan diubah menjadi pupuk organik, maka diperlukan teknologi pembuatan pupuk organik. Permasalahan Mitra 2 (Mekar Tani) : lahan yang tiap tahunnya ditanami padi selama 2 kali musim tanam. Musim tanam yang ke-3 diberokan (tidak ditanami), termasuk sawah-sawah petani yang ada di sekitarnya.Solusi yang ditawarkan untuk mengatasi permasalahan utama yang dihadapi mitra (1) adalah teknologi pembuatan pupuk organik yang dapat digunakan sebagai pupuk organik yang sangat bermutu yang dapat digunakan sebagai pupuk organik bagi usaha budidaya tanaman jagung pada mitra (2) yang dapat menambah masa tanam.Kegiatan ini merupakan penerapan Biofilmed Fertilizer yang telah diujikan pada penelitian Pengembangan Biofilmed Biofertilizer Beragens Hayati dari Konsorsia Rhizobiota Bawang Merah (RG Strategis Nasional 2015-2016) serta Teknologi Pengelolaan Limbah untuk Pakan dan Pupuk pada Sistem Pertanian Terpadu Berbasis Perikanan, Peternakan Puyuh dan Sayur Organik (RISTEK - Insinas 2014-2015).

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Zhang, Qian, Macarena M. Araya, Marcia Astorga-Eló, Gabriela Velasquez, Joaquin I. Rilling, Marco Campos, Michael J. Sadowsky, Milko A. Jorquera, and Jacquelinne J. Acuña. "Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano." Diversity 14, no. 1 (December 28, 2021): 14. http://dx.doi.org/10.3390/d14010014.

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Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth.

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Meyer, Thibault, Armelle Vigouroux, Magali Aumont-Nicaise, Gilles Comte, Ludovic Vial, Céline Lavire, and Solange Moréra. "The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum." Journal of Biological Chemistry 293, no. 21 (March 30, 2018): 7930–41. http://dx.doi.org/10.1074/jbc.ra118.001856.

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The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose–containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum, leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.

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Muratova, Anna, Svetlana Gorelova, Sergey Golubev, Dilyara Kamaldinova, and Murat Gins. "Rhizosphere Microbiomes of Amaranthus spp. Grown in Soils with Anthropogenic Polyelemental Anomalies." Agronomy 13, no. 3 (March 6, 2023): 759. http://dx.doi.org/10.3390/agronomy13030759.

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Study of rhizospheric microbial communities of plants growing under different environmental conditions is important for understanding the habitat-dependent formation of rhizosphere microbiomes. The rhizosphere bacterial communities of four amaranth cultivars were investigated in a laboratory pot experiment. Amaranthus tricolor cv. Valentina, A. cruentus cv. Dyuimovochka, and A. caudatus cvs. Bulava and Zelenaya Sosulka were grown for six months in three soils with different anthropogenic polyelemental anomalies and in a background control soil. After the plant cultivation, the rhizosphere soils were sampled and subjected to metagenomic analysis for the 16S rRNA gene. The results showed that the taxonomic structure of the amaranth rhizosphere microbiomes was represented by the dominant bacterial phyla Actinobacteriota and Proteobacteria. A feature of the taxonomic profile of the rhizobiomes of A. tricolor cv. Valentina and A. cruentus cv. Dyuimovochka was a large abundance of sequences related to Cyanobacteria. The formation of the amaranth rhizosphere microbiomes was largely unaffected by soils, but cultivar differences in the formation of the amaranth rhizosphere microbial structure were revealed. Bacterial taxa were identified that are possibly selected by amaranths and that may be important for plant adaptation to various habitat conditions. The targeted enrichment of the amaranth rhizosphere with members of these taxa could be useful for improving the efficacy of amaranth use for agricultural and remediation purposes.

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Hou, Dandi, Zhi Lin, Runze Wang, Jun Ge, Shuai Wei, Ruohan Xie, Haixin Wang, et al. "Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere." Applied and Environmental Microbiology 84, no. 12 (April 13, 2018): e02797-17. http://dx.doi.org/10.1128/aem.02797-17.

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ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

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ENGLAND, L. S., H. LEE, and J. T. TREVORS. "Recombinant and wild-type Pseudomonas aureofaciens strains in soil: survival, respiratory activity and effects on nodulation of whitebean Phaseolus vulgaris L. by Rhizobiutn species." Molecular Ecology 2, no. 5 (October 1993): 303–13. http://dx.doi.org/10.1111/j.1365-294x.1993.tb00023.x.

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Gorelova, Svetlana V., Anna Yu Muratova, Inga Zinicovscaia, Olga I. Okina, and Aliaksandr Kolbas. "Prospects for the Use of Echinochloa frumentacea for Phytoremediation of Soils with Multielement Anomalies." Soil Systems 6, no. 1 (March 16, 2022): 27. http://dx.doi.org/10.3390/soilsystems6010027.

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In a model experiment, some adaptive characteristics, the bioaccumulation of toxic elements from technogenically-contaminated soils with polyelement anomalies, and rhizosphere microflora of Japanese millet, Echinochloa frumentacea, were studied using biochemical, microbiological, physicochemical (AAS, ICP-MS, INAA), and metagenomic (16S rRNA) methods of analysis. Good adaptive characteristics (the content of photosynthetic pigments, low molecular weight antioxidants) of E. frumentacea grown on the soils of metallurgical enterprises were revealed. The toxic effect of soils with strong polyelement anomalies (multiple excesses of MPC for Cr, Ni, Zn, As, petroleum products) on biometric parameters and adaptive characteristics of Japanese millet were shown. The rhizosphere populations of E. frumentacea grown in the background soil were characterized by the lowest taxonomic diversity compared to the rhizobiomes of plants grown in contaminated urban soils. The minimal number of all groups of microorganisms studied was noted in the soils, which contain the highest concentrations of both inorganic (heavy metals) and organic (oil products) pollutants. The taxonomic structure of the rhizospheric microbiomes of E. frumentacea was characterized. It has been established that E. frumentacea accumulated Mn, Co, As, and Cd from soils with polyelement pollution within the average values. V was accumulated mainly in the root system (transfer factor from roots to shoots 0.01–0.05) and its absorption mechanism is rhizofiltration. The removal of Zn by shoots of E. frumentacea increased on soils where the content of the element exceeded the MPC and was 100–454 mg/kg of dry weight (168–508 g/ha). Analysis of the obtained data makes it possible to recommend E. frumentacea for phytoremediation of soil from Cu and Zn at a low level of soil polyelement contamination using grass mixtures.

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Leitão, Frederico, Glória Pinto, Joana Amaral, Pedro Monteiro, and Isabel Henriques. "New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker." Tree Physiology, September 11, 2021. http://dx.doi.org/10.1093/treephys/tpab119.

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Abstract The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant-growth-promoting (PGP) traits and/or antifungal activity. Plants of this species also displayed higher levels of phenolic compounds. Fusarium circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants’ resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.

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Singh, Arjun, Murugan Kumar, Hillol Chakdar, Kuppusamy Pandiyan, Shiv Charan Kumar, Mohammad Tarique Zeyad, Bansh Narayan Singh, et al. "Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion." Frontiers in Microbiology 13 (November 14, 2022). http://dx.doi.org/10.3389/fmicb.2022.1033158.

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Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant’s fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.

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Castellano-Hinojosa, Antonio, Ute Albrecht, and Sarah L. Strauss. "Interactions between rootstocks and compost influence the active rhizosphere bacterial communities in citrus." Microbiome 11, no. 1 (April 20, 2023). http://dx.doi.org/10.1186/s40168-023-01524-y.

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Abstract Background While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizosphere bacterial communities and the availability of root nutrients for plant uptake. Rootstocks are developed to provide resistance to disease or tolerance of abiotic stresses, and compost application is a common practice to also control biotic and abiotic stresses in crops. In this field study, we examined: (i) the effect of four citrus rootstocks and/or compost application on the abundance, diversity, composition, and predicted functionality of active rhizosphere bacterial communities, and (ii) the relationships between active rhizosphere bacterial communities and root nutrient concentrations, with identification of bacterial taxa significantly correlated with changes in root nutrients in the rhizosphere. Results The rootstock genotype determined differences in the diversity of active rhizosphere bacterial communities and also impacted how compost altered the abundance, diversity, composition, and predicted functions of these active communities. Variations in the active bacterial rhizobiome were strongly linked to root nutrient cycling, and these interactions were root-nutrient- and rootstock-specific. Direct positive relationships between enriched taxa in treated soils and specific root nutrients were detected, and potentially important taxa for root nutrient uptake were identified. Significant differences in specific predicted functions were related to soil nutrient cycling (carbon, nitrogen, and tryptophan metabolisms) in the active bacterial rhizobiome among rootstocks, particularly in soils treated with compost. Conclusions This study illustrates that interactions between citrus rootstocks and compost can influence active rhizosphere bacterial communities, which impact root nutrient concentrations. In particular, the response of the rhizobiome bacterial abundance, diversity, and community composition to compost was determined by the rootstock. Specific bacterial taxa therefore appear to be driving changes in root nutrient concentrations in the active rhizobiome of different citrus rootstocks. Several potential functions of active bacterial rhizobiomes recruited by different citrus rootstocks did not appear to be redundant but rather rootstock-specific. Together, these findings have important agronomic implications as they indicate the potential for agricultural production systems to maximize benefits from rhizobiomes through the choice of selected rootstocks and the application of compost.

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Abulfaraj, Aala A., Ashwag Y. Shami, Nahaa M. Alotaibi, Maryam M. Alomran, Abeer S. Aloufi, Abeer Al-Andal, Nawwaf R. AlHamdan, et al. "Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum." AMB Express 14, no. 1 (February 21, 2024). http://dx.doi.org/10.1186/s13568-024-01678-4.

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AbstractThe operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.

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Sarkar, Soumyadev, Abigail Kamke, Kaitlyn Ward, Eli Hartung, Qinghong Ran, Brandi Feehan, Matthew Galliart, Ari Jumpponen, Loretta Johnson, and Sonny T. M. Lee. "Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience." BMC Genomics 23, no. 1 (November 30, 2022). http://dx.doi.org/10.1186/s12864-022-09019-0.

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Abstract Background Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. Results In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest – MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. Conclusions Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.

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Goemann, Hannah M., Danielle E. M. Ulrich, Brent M. Peyton, La Verne Gallegos-Graves, and Rebecca C. Mueller. "Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome." Frontiers in Microbiomes 2 (January 11, 2024). http://dx.doi.org/10.3389/frmbi.2023.1310790.

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Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.

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Meier, Michael A., Gen Xu, Martha G. Lopez-Guerrero, Guangyong Li, Christine Smith, Brandi Sigmon, Joshua R. Herr, et al. "Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize." eLife 11 (July 27, 2022). http://dx.doi.org/10.7554/elife.75790.

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The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and identified n = 622 plant loci that are linked to the abundance of n = 104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments towards harnessing the full potential of root-associated microbial symbionts in maize production.

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Schmidt, Jennifer E., Ashley DuVal, Alina Puig, Alexandra Tempeleu, and Taylor Crow. "Interactive and Dynamic Effects of Rootstock and Rhizobiome on Scion Nutrition in Cacao Seedlings." Frontiers in Agronomy 3 (November 18, 2021). http://dx.doi.org/10.3389/fagro.2021.754646.

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Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, disease-resistant rootstocks. In cacao (Theobroma cacao L.), however, rootstock selection has traditionally relied on locally available open pollinated populations with limited data on performance. Furthermore, rootstock associations with the rhizobiome, or rhizosphere microbiome, have been neglected. Better understanding of rootstock and scion effects on cacao-specific traits, particularly those involved in root-microbe interactions and nutrient acquisition, could contribute to more efficient rootstock selection and breeding. A rootstock-scion interaction study was conducted using three scion genotypes and eight rootstock populations under greenhouse conditions to better understand the relationships among rootstock and scion identities, soil fertility, and rhizobiome composition and the impacts of these factors on plant uptake of macro- and micronutrients. We show that rootstock genotype has a stronger influence than scion on nutrient uptake, bacterial and fungal diversity, and rhizobiome composition, and that the relative contributions of rootstock and scion genotype to foliar nutrient status are dynamic over time. Correlation analysis and stepwise regression revealed complex relationships of soil physicochemical parameters and the rhizobiome to plant nutrition and emphasized strong impacts of microbial diversity and composition on specific nutrients. Linear discriminant analysis effect size estimation identified rootstock-responsive taxa potentially related to plant nutrition. This study highlights the importance of considering root-associated microbial communities as a factor in cacao rootstock breeding and the need for further investigation into mechanisms underlying nutrient acquisition and microbial interactions in grafted plants.

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Yadav, Pooja, Amanda Quattrone, Yuguo Yang, Jacob Owens, Rebecca Kiat, Thirumurugen Kuppusamy, Sabrina E. Russo, and Karrie A. Weber. "Zea mays genotype influences microbial and viral rhizobiome community structure." ISME Communications 3, no. 1 (December 6, 2023). http://dx.doi.org/10.1038/s43705-023-00335-4.

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AbstractPlant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.

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Babalola, Olubukola Oluranti, Saheed Adekunle Akinola, and Ayansina Segun Ayangbenro. "Shotgun Metagenomic Survey of Maize Soil Rhizobiome." Microbiology Resource Announcements 9, no. 39 (September 24, 2020). http://dx.doi.org/10.1128/mra.00860-20.

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ABSTRACT The plant soil rhizobiome induces critical functions in the plant proximal environment. Linkages between soil microbiota and primary functional attributes are underexplored. Here, we present the metagenomes of maize soil rhizosphere organisms with functional diversity associated with farms at two different municipalities in North West and Gauteng provinces of South Africa. We describe a plenteous and diverse microbial community.

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Kaufmann, Moritz, Leilei Li, Christof Van Poucke, Nicola Rhyner, Caroline De Tender, Mieke Uyttendaele, Marc Heyndrickx, Cyril Zipfel, Joël F. Pothier, and Cottyn Bart. "Soil type and associated microbiomes influences chitin’s growth-promotion effect in lettuce." Phytobiomes Journal, February 28, 2024. http://dx.doi.org/10.1094/pbiomes-12-23-0132-r.

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Chitin amendment of peat substrate has been proven effective in promoting lettuce growth and increasing phenolic compounds in lettuce seedlings. However, the effect of chitin soil amendment on lettuce growth in mineral soil remains unexplored. The effect of chitin amendment of mineral soil on lettuce growth and metabolite changes was investigated for the first time in the present study in comparison to chitin amended peat substrate. Our findings showed that chitin addition in peat substrate increased lettuce head weight by approximately 50% at harvest, whereas this increase was 30% when added to mineral soil. Targeted metabolomics analysis indicated that chitin addition affected the phenolic compounds in lettuce seedlings, but this effect varied between soil types. Moreover, untargeted metabolomics analysis suggested that using peat substrate or mineral soil had a greater influence on produced lettuce metabolites than chitin addition. Rhizobiome analysis showed that specifically Mortierellaceae family members, known for chitin degradation and plant growth promotion, significantly increased in peat substrate upon chitin treatment. In mineral soil, three bacterial genera and five fungi, including known plant growth promoting genera, were significantly more abundant upon chitin treatment but not Mortierellaceae. We assume that the observed effects primarily stem from soil physiochemical characteristics and from chitin induced alterations in rhizobiome composition, particularly the presence of Mortierellaceae members, leading to promoted lettuce growth. Despite the variability, chitin remains an environmentally friendly alternative to synthetic fertilizers in lettuce production, but its beneficial effects are dependent on rhizobiome composition, which should be considered before chitin application.

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