Rhizosphere Microbes Research Articles

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization.

The rhizosphere, which serves as the primary interface between plant roots and the soil, constitutes an ecological niche for a huge diversity of microbial communities. Currently, there is little knowledge on the nature and the function of the different metabolites released by rhizospheric microbes to facilitate colonization of this highly competitive environment. Here, we demonstrate how the production of galbonolides, a group of polyene macrolides that inhibit plant and fungal inositol phosphorylceramide synthase (IPCS), empowers the rhizospheric Streptomyces strain AgN23, to thrive in the rhizosphere by triggering the plant's defence mechanisms. Metabolomic analysis of AgN23-inoculated Arabidopsis roots revealed a strong induction in the production of an indole alkaloid, camalexin, which is a major phytoalexin in Arabidopsis. By using a plant mutant compromised in camalexin synthesis, we show that camalexin production is necessary for the successful colonization of the rhizosphere by AgN23. Conversely, hindering galbonolides biosynthesis in AgN23 knock-out mutant resulted in loss of inhibition of IPCS, a deficiency in plant defence activation, notably the production of camalexin, and a strongly reduced development of the mutant bacteria in the rhizosphere. Together, our results identified galbonolides as important metabolites mediating rhizosphere colonization by Streptomyces.

Dynamic changes in rhizosphere bacterial communities of Rhododendron simsii at different growth stages

Rhododendron simsii plays important roles in maintaining ecological system stability in the north temperate zone. However, its natural growth is greatly affected by soil microorganisms, particularly rhizosphere microbes. In this study, a comparative analysis was conducted of the bacterial community structure in the rhizosphere of R. simsii at the old, adult, juvenile, and seedlings stages. The results showed that Proteobacteria (38.53%?47.63%), Actinobacteria (23.45%?34.03%), and Acidobacteria (10.33%?17.79%) were the dominant phyla in the R. simsii rhizosphere. In particular, 3, 5, 42, and 33 OTUs were unique to the soil samples of ?old trees?, ?adult trees?, ?juvenile trees?, and ?seedlings?, respectively. Across four sets of R. simsii rhizosphere microbes sampled from seedlings to old trees, the OTUs first increased, then decreased, and finally increased. Overall, alpha diversity (Chao, ACE, and Sobs) revealed similar trends with the highest value i?n recorded for the rhizosphere sample of ?adult trees? and the lowest for the ?seedlings? sample. The bacterial genera in the rhizosphere samples from ?old trees? and ?adult trees? exhibited close clustering. Notably, the R. simsii population of ?juvenile trees?, demonstrating the highest genetic diversity, were rich in Bradyrhizobium and Streptomycetes. This research serves to benefit the domestication of wild R. simsii and other Rhododendron resources.

Rhizosphere Fungi Abundance on Acid Dry and Tidal Soils in Borneo Prima Citrus Fields, East Kalimantan

Acid dry and Tidal land in East Kalimantan is one of the suboptimal land ecosystems, that needs to increase the quality of its fertility to support the production of citrus of the Borneo Prima variety. One of them with rhizosphere microbes can increase fertility, decomposition process and and as biological control agents to plant diseases. The aim of the study was to determine the abundance of rhizosphere fungi on citrus trees on dry acid and tidal soils and their relationship with soil physico-chemical factors. Rhizosphere fungi was isolated from the soil around citrus plant roots, East Kalimantan were analysed for their abundance and their correlation with soil physio-chemical factors. The results showed that found 29 rhizosphere fungi. The highest importance value index was found TR25 rhizosphere fungi isolates in the acid dry land block A and TR 17 in block B. The highest importance value index is at TR1 in block A tidal land, and TR23 in block B. Principal Component Analysis results showed that there is a strong relationship between the abundance of rhizosphere fungi and soil physicochemical. The highest number of rhizosphere fungal colonies was on tidal land B. The number of colonies was directly proportional to humidity.

Effects of Rhizosphere Microbial Composition on the Growth of Cajanus cajan in Coal Gangue Reclaimed Soil

This study aimed to investigate the microbial diversity and functions of Cajanus cajan root systems planted in plateau waste dumps collected in Liupanshui City, Guizhou Province, China. The gangue dump (1,390 m above sea level) in the Guizhou Plateau was covered with soil and planted with YN and JX C. cajan. After 1 year, the C. cajan root system was collected, and high-throughput sequencing was used to examine its bacterial and fungal biodiversity. The unclassified_f_Enterobacteriaceae and Cedecea were the most abundant genera. Venn and heatmap analyses revealed differences in the dominant species Lactococcus and Fusarium in the rhizosphere of C. cajan varieties. In JX and YN, Pseudoarthrobacter is a unique genus of bacteria; in JX, Robillarda is a unique genus of fungi; and in YN, Scytalidium is a unique genus of fungi. Endophytic fungi mainly play the roles of saprotroph, plant pathogen, and endophyte. Among the bacterial properties, L-arabinose isomerase and adenosine triphosphatase were the most abundant in all samples, while chitinase, catalase, and laccase played important roles in photosynthesis and the degradation of lignin, chitin, and chitosan. Our findings may guide the selection of reclamation plants and strategies for the mitigation and restriction of heavy metals in soil.

Uji Potensi Mikrob Rizosfer sebagai Pengendali Hayati Penyebab Penyakit Tanaman

Biological control is an alternative to reducing the use of pesticides because it can suppress the growth of plant pathogens and has no negative impact on the environment. This study aimed to test the effectiveness of rhizosphere microbes as biological controllers that cause plant diseases. This study contains three rhizosphere microbes (Trichoderma sp., Gliocladium sp., Bacillus sp.) and three pathogenic test fungi (Rhizoctonia sp., Sclerotium sp., Botryodiplodia sp.) were used. This study was divided into three experiments, namely (1) an in vitro antagonist test, (2) a secondary metabolite test, and (3) a growth test on sengon seeds (in vivo). The parameters measured were percentage inhibition, germination rate, growth rate, disease incidence, and disease intensity. The fungus Trichoderma sp. and Gliocladium sp. can inhibit the growth of pathogenic fungi Sclerotium sp., Rhizoctonia sp., and Botryodiplodia sp. ranging from 61.82% to 80.00%. Secondary metabolites of the fungus Gliocladium sp. are more able to inhibit the mycelia growth of pathogenic fungi Rhizoctonia sp., Sclerotium sp., and Botryodiplodia sp. compared to the fungus Trichoderma sp. with inhibition values were 71.13%, 33.83%, 23.58%, respectively. Gliocladium sp., Trichoderma sp., and Bacillus sp. can suppress disease incidence (14.29%, 12.38%, and 15.24%) and intensity of damping-off attacks caused by Rhizoctonia sp. (8.91%, 8.57%, and 9.43%). This shows that biological agents have the potential to control plant diseases
 Keywords: Bacillus aereus, damping-off, secondary metabolites, Trichoderma

Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease.

Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.

Simulation Study on the Effect of Iron Nanoparticles on Rhizospheric and Rhizoplane Microbes of Paddy (Oryza sativa) Plant

ABSTRACT Rhizospheric microbes play a crucial role in plant growth promotion. Due to advancements in technology, many nano fertilizers are now applied in the agricultural field. However, its effect on the microbial community is less explored. The present study examines the impact of iron (Fe) nanoparticles (INPs) on paddy rhizospheric (RS) and rhizoplanar (RP) microbes. The effect of different concentrations of INPs iron nanoparticles on the growth of rhizospheric and rhizoplanar microbes was observed by the plate count method. The results showed that bacterial and fungal counts were higher in control than all treatments on 15, 30, and 45 days after sowing seeding (DAS). Nitrogen-fixing bacteria were higher in control on 15 and 30 DAS; however, on 45 DAS, higher nitrogen-fixing bacteria were reported in T4. Phosphate solubilizing microbes were higher in all the treatments compared to the control. Siderophore-producing microbes were higher in control on 15 DAS compared to other treatments. However, after 30 and 45 DAS siderophore-producing microbes were higher in T4 than in control and other treatments. Thus, the results suggest that treatment − 4 (T4) (Seed + Soil +2 g/kg soil) was the best treatment and can be used for plant growth promotion of rice.

Dynamic Changes in Rhizosphere Microbial Communities of Watermelon During Continuous Monocropping with Gravel Mulch

Dynamic Changes in Rhizosphere Microbial Communities of Watermelon During Continuous Monocropping with Gravel Mulch

Cultivation modes impacting root microbiomes and metabolites in medicinal orchid Dendrobium denneanum

IntroductionThe plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.MethodsIn this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.ResultsThe main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).ConclusionThis study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.

The Significance Of Nanomaterials In Enhancing Soil Microbial Communitya Short Review

A severe threat to agricultural output and sustainability are global problems including soil erosion, contaminants, and agricultural productivity loss brought on by urbanization and agricultural expansion. Many technological advancements are being used to improve the quality of contaminated soils or purify contaminants in the soil, but they haven't been able to restore or improve the condition of the soil to the desired levels because they are expensive, impractical, or, to a lesser extent, require a lot of labour. Recent developments in nanotechnology promise to raise crop yields and soil quality indices while maintaining environmental sustainability. It has been discovered that the existence of nanomaterials (NMs) within soils may influence or enhance the efficiency of rhizosphere microbes or farming crucial microbes, allowing the access of nutrients to crops and improving the functioning of root systems as well as crop growth in general, creating up an opportunity for the enhancement of soil health. It could be useful to assess nanotechnology in order to learn more about the actual utilization of NMs for enhancing soil health.

Importance of biodiversity in rhizosphere microbes for crop response and methodsto assess the biodiversity

Microbes play a vital role in influencing the quality and health of soil and plants. Several studies had led to understanding of diversity and structure in the plant rhizosphere: linking with Soil Microbial diversity to Modern Agriculture, amrita gupta et.al (2022); Influence of long-term fertilization on soil microbial biomass, dehydrogenase activity, and bacterial and fungal community structure in a brown soil of northeast, China Peiyu Luo et.al (2013). The microbial population has many applications and advantages which are determined only through Long term fertilizer studies. Some of the methods used for assessing the biodiversity of these rhizosphere microbes are: 16s rRNA sequencing, DDGE, TDGE, SEM, etc. Some advantages of rhizosphere microbes are improved crop yield, fighting climate change with minimal soil and environmental degradation, the protection of human health for current and future generations, macro and micro-nutrient cycling for optimum agricultural growth, higher crop yield, and also prevents land degradation. In this article we will study about importance of biodiversity of rhizosphere microbes and various methods to identify the microbial population.

Root colonization by beneficial rhizobacteria.

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

E-Waste: a Concise Update on Global Movement, Impacts, Management, and Site Remediation

The rapid rise of electronic waste (e-waste) worldwide has become a public health concern. Wealthy countries are disposing of their e-waste to other countries taking advantage of their less stringent environmental laws and regulations. China used to receive large amounts of e-waste through Hong Kong (a free port) but banned the entry of e-waste in 2013. Salvaging or recycling different parts of the e-waste using primitive and uncontrolled techniques generated a wide range of toxic chemicals (mainly heavy metals and persistent organic pollutants). Most studies concerning the environmental and health impacts of the emitted toxic chemicals were conducted in China. The principal aim of this short article is to review the various environmental problems and health impacts of e-waste recycling, policies, management, and remediation of contaminated sites. Out of the primitive methods used for recycling, the two most destructive ones causing harm to the environment and human health are (1) Open-burning of e-waste for disposing of the salvaged e-waste and (2) Acid-stripping of electronic boards for collecting precious metals (gold, silver, platinum). There is sufficient evidence showing the associations between the toxic chemicals in different media (i.e., water, soil/sediment, air) and local food items (i.e., fish, meat, vegetables), linking with body burdens (hair, milk, placenta) of workers and residents. The epidemiological data further demonstrated the abrupt rise of several significant diseases (i.e., respiratory disease, cardiovascular disease, malignant tumors) in Taizhou (China), one of the two e-waste recycling sites. Effective policies and vigorous enforcement in managing e-waste are essential. International cooperation is necessary to prohibit the transboundary movement of e-waste. Sites contaminated by e-waste recycling contain incredibly high concentrations of toxic pollutants, which should be removed using excavation, degradation (via microbes, nanoparticles, biochar), soil washing, etc. Planting appropriate plants with associated rhizospheric microbes would achieve longer-term stability.

Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress.

Soil salinization is a global environmental issue and a significant abiotic stress that threatens crop production. Root-associated rhizosphere microbiota play a pivotal role in enhancing plant tolerance to abiotic stresses. However, limited information is available concerning the specific variations in rhizosphere microbiota driven by different plant genotypes (varieties) in response to varying levels of salinity stress. In this study, we compared the growth performance of three alfalfa varieties with varying salt tolerance levels in soils with different degrees of salinization. High-throughput 16S rRNA and ITS sequencing were employed to analyze the rhizosphere microbial communities. Undoubtedly, the increasing salinity significantly inhibited alfalfa growth and reduced rhizosphere microbial diversity. However, intriguingly, salt-tolerant varieties exhibited relatively lower susceptibility to salinity, maintaining more stable rhizosphere bacterial community structure, whereas the reverse was observed for salt-sensitive varieties. Bacillus emerged as the dominant species in alfalfa's adaptation to salinity stress, constituting 21.20% of the shared bacterial genera among the three varieties. The higher abundance of Bacillus, Ensifer, and Pseudomonas in the rhizosphere of salt-tolerant alfalfa varieties is crucial in determining their elevated salt tolerance. As salinity levels increased, salt-sensitive varieties gradually accumulated a substantial population of pathogenic fungi, such as Fusarium and Rhizoctonia. Furthermore, rhizosphere bacteria of salt-tolerant varieties exhibited increased activity in various metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and biosynthesis of amino acids. It is suggested that salt-tolerant alfalfa varieties can provide more carbon sources to the rhizosphere, enriching more effective plant growth-promoting bacteria (PGPB) such as Pseudomonas to mitigate salinity stress. In conclusion, our results highlight the variety-mediated enrichment of rhizosphere microbiota in response to salinity stress, confirming that the high-abundance enrichment of specific dominant rhizosphere microbes and their vital roles play a significant role in conferring high salt adaptability to these varieties.

Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes.

Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP). Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing. Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms. Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.

Long-Term Heavy Metal Pollution Induces Complex Differences in Farmland Topsoil and Rhizosphere Microbial Communities

The microbial effect of long-term heavy metal pollution on farmland remains unclear. Here, we investigated microbial (bacterial and fungal) communities in topsoil and rhizosphere samples with heavy metal (Cd, Cu, Pb, and Zn) pollution from four different types of tillage plots around an abandoned zinc smelter set up 85 years ago and analyzed the complex relationship between microorganisms, plants, and heavy metals (HMs) in soil to guide strategies for further soil remediation measures. The abundance and diversity index results showed that the bacterial and fungal diversities of the four plots were significantly different. Meanwhile, correlation analysis of the microbial communities and HMs showed that bacteria Pseudomonas and fungi Chaetothyriales and Fusarium had a good tolerance for HM pollution, but bacteria Vicinamibacteraceae, JG30_KF_CM45, RB41, Gaiella, MB-A2-108, 67-14, and Microvirga, and fungi Glomerellales, Hypocreales, Chaetomium, and Mortierella all showed indications of being sensitive to HM toxicity. Our structural equation model (SEM) attributed the inhibition of Zn and the promotion of Cd to bacterial diversity, attributed a weak inhibition of Cd to fungal diversity, and revealed the effects of the tillage type on these diversities.

Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana.

The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.

Alfalfa Plant Age (3 to 8 Years) Affects Soil Physicochemical Properties and Rhizosphere Microbial Communities in Saline–Alkaline Soil

Increasing soil salinization can severely restrict local agricultural production. Planting alfalfa is considered an effective measure to ameliorate saline–alkali soil. However, it remains unclear how alfalfa planting years affect the sustained impact on soil and rhizosphere microecology. This study analyzed the effects of alfalfa planted 3, 6, and 8 years ago on soil physicochemical properties and key soil enzyme activities and investigated the rhizosphere microbial community structure and diversity. The results indicate that cultivating alfalfa plants for six years can improve soil physicochemical properties and enhance soil fertility to a certain extent. This is attributed to a higher abundance of plant growth-promoting bacteria, such as Bradyrhizobium and Allorhizobium, as well as degradation bacteria, such as Flavobacterium, Stenotrophomonas, Brevundimonas, and Massilia, in the rhizosphere of alfalfa plants. These microorganisms promote alfalfa growth, improve soil quality, and inhibit the accumulation of autotoxins. This not only maintains high alfalfa yields but also optimizes soil physicochemical properties and enzyme activity, facilitating more effective nutrient cycling and metabolic processes in the soil. However, extending plant growth to 8 years is not beneficial.

A Review on Rhizosphere Microbiota of Tea Plant (Camellia sinensis L): Recent Insights and Future Perspectives.

Rhizosphere microbial colonization of the tea plant provides many beneficial functions for the host, But the factors that influence the composition of these rhizosphere microbes and their functions are still unknown. In order to explore the interaction between tea plants and rhizosphere microorganisms, we summarized the current studies. First, the review integrated the known rhizosphere microbial communities of tea tree, including bacteria, fungi, and arbuscular mycorrhizal fungi. Then, various factors affecting tea rhizosphere microorganisms were studied, including: endogenous factors, environmental factors, and agronomic practices. Finally, the functions of rhizosphere microorganisms were analyzed, including (a) promoting the growth and quality of tea trees, (b) alleviating biotic and abiotic stresses, and (c) improving soil fertility. Finally, we highlight the gaps in knowledge of tea rhizosphere microorganisms and the future direction of development. In summary, understanding rhizosphere microbial interactions with tea plants is key to promoting the growth, development, and sustainable productivity of tea plants.

Lentil Landrace Seed Origin and Genotype Affects Rhizosphere Microbiome

Lentil (Lens culinaris Medik.) is an essential legume crop providing healthy and nutritious food for people in low- to middle-income countries, worldwide. Lentil roots support symbiotic interactions with soil rhizobia species fostering nitrogen fixation; however, assemblage and diversity of the complete microbial rhizosphere community and the effect of seed genotype and origin remain largely unexplored. In this study we examined, via metagenomic analysis, the effects of seed origin on the rhizosphere’s communities in samples of the famous Greek lentil landrace, Eglouvis, derived from different local farmers and farming systems (including a Gene Bank sample), in comparison to a commercial variety. The landrace exhibited higher rhizosphere microbiome diversity compared to the commercial variety for all indexes. A core microbiome comprised of 158 taxa was present in all samples, while a greater number of unique bacterial taxa was recorded in the landrace samples compared to the commercial cultivar. Notably, landrace samples originated from organic farming had more than double the number of unique taxa compared to conventional counterparts. The study revealed a higher diversity of N2 fixers and archaea, Crenarchaeota and Thaumarchaeota, in landrace samples and particularly in those derived from organic farming, underpinning the distinct recruiting efficiency of beneficial soil microbes by the landrace.