Potato Rhizosphere Research Articles

Effects of Paecilomyces lilacinus and Bacillus pumilus on stem nematode and rhizosphere bacterial communities of sweet potato

Stem nematode (Ditylenchus destructor Thorne) is considered one of the most economically devastating species affecting sweet potato production. Biocontrol offers a sustainable strategy for nematode control. This study conducted a pot experiment to evaluate the biocontrol efficacy of Paecilomyces lilacinus CS-Z and Bacillus pumilus Y-26 against the stem nematode, as well as to examine their influence on the bacterial communities in the sweet potato rhizosphere. The findings indicated that B.pumilus Y-26 and P.lilacinus CS-Z exhibited respective suppression rates of 82.9% and 85.1% against the stem nematode, while also stimulating sweet potato plant growth. Both high-throughput sequencing and Biolog analysis revealed distinct impacts of the treatments on the bacterial communities. At the phylum level, B.pumilus Y-26 enhanced the abundance of Actinobacteria but reduced the abundance of Cyanobacteria, with P.lilacinus CS-Z exhibiting similar effects. Additionally, the treatment with B.pumilus Y-26 resulted in increased abundances of Crossiella, Gaiella, Bacillus, and Streptomyces at the genus level, while the treatment with P.lilacinus CS-Z showed increased abundances of Crossiella and Streptomyces. In contrast, the abundance of Pseudarthrobacter was reduced in the treatment with B.pumilus Y-26. Conversely, the application of the nematicide fosthiazate exhibited minor influence on the bacterial community. The findings indicated that the application of P.lilacinus CS-Z and B.pumilus Y-26 led to an increase in the relative abundances of beneficial microorganisms, including Gaiella, Bacillus, and Streptomyces, in the rhizosphere soil. In conclusion, P.lilacinus CS-Z and B.pumilus Y-26 demonstrated their potential as environmentally friendly biocontrol agents for managing stem nematode disease of sweet potato.

Ralstonia solanacearum Infection Drives the Assembly and Functional Adaptation of Potato Rhizosphere Microbial Communities.

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease that affects potato production, leading to severe yield losses. Currently, little is known about the changes in the assembly and functional adaptation of potato rhizosphere microbial communities during different stages of R. solanacearum infection. In this study, using amplicon and metagenomic sequencing approaches, we analyzed the changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere across four stages of R. solanacearum infection. The results showed that R. solanacearum infection led to significant changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere, with various microbial properties (including α,β-diversity, species composition, and community ecological functions) all being driven by R. solanacearum infection. The relative abundance of some beneficial microorganisms in the potato rhizosphere, including Firmicutes, Bacillus, Pseudomonas, and Mortierella, decreased as the duration of infection increased. Moreover, the related microbial communities played a significant role in basic metabolism and signal transduction; however, the functions involved in soil C, N, and P transformation weakened. This study provides new insights into the dynamic changes in the composition and functions of potato rhizosphere microbial communities at different stages of R. solanacearum infection to adapt to the growth promotion or disease suppression strategies of host plants, which may provide guidance for formulating future strategies to regulate microbial communities for the integrated control of soil-borne plant diseases.

Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions

Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.

Paramerlinius shamimi n. sp. (Nematoda: Merliniidae) from India with a tabular key for the genus Paramerlinius

Summary The population of the genus Paramerlinius was discovered from potato rhizosphere in a government potato seed farm, located in Tiksen, Munsiari, Pithoragarh, Uttarakhand, India. It is here described as Paramerlinius shamimi n. sp. based on morphological, morphometric and molecular data. The new species is characterised by having a body length of 841.8-1208.8 μm, continuous head bearing 7-8 annuli, a prominent stylet (28.4-32.3 μm) with well-developed posteriorly sloping basal knobs, six lateral incisures at the mid-body, a well-developed median bulb, a secretory-excretory (S-E) pore (123.5-160.7 μm) almost at the level of basal bulb, hemizonid covering 2-3 annuli that are located 3-4 annuli above the S-E pore, phasmids located in the front half of the tail, tail subcylindrical, having a hemispherical smooth terminus (62.7-94.1 μm) with 38-48 tail annuli, males common, spicule arcuate (27.4-31.4 μm), gubernaculum curved ventrally (8.8-9.8 μm) and peloderan bursa. Molecular characterisation of the population was performed by sequencing nuclear ribosomal DNA (rRNA) genes, viz. ITS-1, 18S (partial) and D2-D3 region of 28S rRNA. Maximum likelihood and Bayesian phylogenetic analyses of P. shamimi n.sp. using the D2-D3 region show it forms a distinct clade with other unidentified Paramerlinius spp. and P. neohexagrammus and, using 18S rRNA, groups it in the same clade as P. hexagrammus. A tabular key for 13 species including P. shami1mi n.sp. under the genus Paramerlinius is given.

Differences in Soil Fertility and Bacterial Community Structure Between Carbon Inputs such as Biochar and Organic Fertilizer and Their Relationship

The potato planting area of Guizhou Province ranks second in China. However, due to factors such as climatic conditions and unbalanced fertilization, soil organic matter in potato fields is consumed rapidly and has a large deficit, which affects soil biological function and soil fertility. Biochar and organic fertilizer are effective ways to supplement foreign aid organic matter to improve soil quality. However, the differences in soil fertility and microbial community structure and their relationships under the conditions of organic fertilizer or biochar combined with chemical fertilizer are not clear. In this study, three treatments of conventional fertilization （NPK）, increased application of biochar （NPKB）, and increased application of organic fertilizer （NPKO） were set up to investigate the characteristics of potato rhizosphere soil, bacterial community composition, and diversity； to analyze the effects of these factors on the soil integrated fertility index； and to explore the direct and indirect effects of IFI on soil fertility and bacterial community structure differences between treatments and their driving factors. The results showed that soil pH, available phosphorus （AP）, available potassium （AK）, total nitrogen （TN）, organic carbon （SOC）, and C/N ratio were significantly higher in the NPKB and NPKO treatments than in the NPK treatment （P<0.05）. Soil IFI was greatest for NPKO, followed by NPKB and least for the NPK treatment. A total of 8 214 ASVs were obtained from all the soil samples, belonging to 26 phyla, 75 classes, 165 orders, 176 families, and 251 genera （excluding unidentified fungi）. Proteobacteria, Actinobacteria, and Chloroflexi were the dominant phyla, accounting for 54.85% of all ASVs. Compared to that in the NPK and NPKB treatments, the NPKO treatment had the highest bacterial diversity and number of significantly different taxa, and soil AN, AP, AK, SOC, TN, and IFI were significant correlates of bacterial diversity index （P<0.05）. Additionally, pH, TN, and SOC were significant influencers of bacterial taxa differences （P<0.05）, with importance ranked as TN （70.59%） &gt; SOC （49.42%） &gt; pH （27.08%）. Structural equations suggested that pH-related soil properties and bacterial community diversity were the direct pathways influencing IFI, and soil pH-related soil characteristics could also indirectly affect IFI by affecting bacterial Shannon diversity. These results indicate that soil fertility and bacterial community structure were significantly different and correlated between the biochar and organic fertilizer addition treatments and that pH and bacterial community diversity were the key factors influencing IFI, with the NPKO treatment in particular having the best effect on improving IFI. Considering the effect of soil fertilization and the functional group of bacteria, NPKO is the recommended combination for the best synergistic effect of soil fertilization, that is, N 150 kg·hm-2+P2O5 135 kg·hm-2+K2O 135 kg·hm-2+organic fertilizer 6.6 t·hm-2.

Studying the pathogenic Streptomyces strains responsible for causing potato common scab in Iran and assessing the efficacy of native S. fimicarius-ghR and S. rochei-FsG in reducing scab lesion development in both potato and radish hosts in vivo

ABSTRACT Potato common scab an important widespread disease caused by Streptomyces species, usually can diminish the market value of tubers. None of the disease management methods is considered efficient. Non-pathogenic Streptomyces species owing to their source of bioactive compounds can alleviate scab severity and strengthen plant vigour. During our survey, three pathogenic strains with atypical composition of Pathogenicity Island (PAI) marker genes prevented radish seed germination by ≥98% and exhibited coalescing superficial, raised or mild pitted lesions in pot trials. Based on 16S rRNA and rpoB sequencing, Streptomyces sp. (FG1 and AAb) and S. rochei-HGs were identified. Our research findings have led us to identify S. rochei-HGs as a novel scab-causing species of potato. In addition, two beneficial Streptomyces strains obtained from potato rhizosphere and soil, including S. fimicarius-ghR and S. rochei-FsG, inhibited streptomyces sp.-FG1 growth with the inhibition halo ≥30 mm on agar plates, alleviated the lesion severity index and showed the control efficacy of 88.88 ± 6.41% and 83.33 ± 16.94% on potato, respectively under greenhouse conditions. Both of them can produce siderophore, IAA and solubilise phosphate. By measuring the plant growth attributes, the application of ghR and FsG strains in pathogen-infected soil showed enhancement in potato root and shoot length as well as radish compared with the controls. Evaluation of the inhibitory compounds of studied antagonists by chemistry methods is ongoing. The disease suppressiveness of strains and their plant growth induction should also be validated at the field level.

Potential Biofertilizers for Alkaline Soil: Bacteria Isolated from the Rhizosphere of Potatoes

Potential Biofertilizers for Alkaline Soil: Bacteria Isolated from the Rhizosphere of Potatoes

Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.).

We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.

Increase in potato yield by the combined application of biochar and organic fertilizer: key role of rhizosphere microbial diversity.

The large-scale planting of potatoes leads to soil degradation, thus limiting the potato yield. An effective method of improving soil quality involves the combined application of biochar and organic fertilizer. However, the proportion of biochar and organic fertilizer at which potato yield can be improved, as well as the improvement mechanism, remain unclear. A combined application experiment involving biochar (B) and organic fertilizer (O) with four concentration gradients was conducted using the equal carbon ratio method. On this basis, rhizosphere soil fertility, bacterial community composition, and bacterial diversity in potato crops, as well as the potato yield difference under different combined application ratios, were investigated. Then, the direct and indirect effects of these factors on potato yield were analyzed. The results suggest that soil fertility was improved by the combined application of biochar and organic fertilizer, with the best effect being achieved at a ratio of B:O=1:2. The dominant bacterial communities in the potato rhizosphere included Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes. When compared to the control, the relative abundance and diversity index of soil bacteria were significantly improved by the treatment at B:O=1:2, which exerted a stronger effect on improving the relative abundance of beneficial bacteria. Soil available phosphorus (AP), soil pH (SpH), and soil organic carbon (SOC) explained 47.52% of the variation in bacterial composition. Among them, the main factor was the content of soil available nutrients, while SpH generated the weakest effect. The bacterial diversity index showed a significant positive correlation with soil AP, SOC, available potassium (AK), total nitrogen (TN), and C/N ratio, and a significant negative correlation with SpH. Bacterial diversity directly affected the potato yield, while soil fertility indirectly affected potato yield by influencing the soil bacterial diversity. The combined application of biochar and organic fertilizer elevates potato yield mainly by improving the diversity of bacterial communities in potato rhizosphere soil, especially the combined application of biochar and organic fertilizer at a 1:2 ratio (biochar 0.66 t ha-1+organic fertilizer 4.46 t ha-1), which made the largest contribution to increasing potato yield.

Pythium oligandrum induces growth promotion in starch potato without significantly altering the rhizosphere microbiome

Plant health promoting organisms, including microbial biological control agents, are of increasing importance for the development of more sustainable agriculture. To understand the function of these microbes as biological control agents under field conditions and their overall impact on soil and plant health, we need to learn more about the impact of plant beneficial microbes on the rhizosphere microbiome of crops such as potato. The plant beneficial oomycete Pythium oligandrum has previously been reported both as a biocontrol agent and as a plant growth promoter, or biostimulant, in several crop species. To investigate the potential of P. oligandrum as a biostimulant in potato, we performed a series of controlled-environment bioassays in three cultivars. We showed that biostimulation of potato by P. oligandrum is plant genotype-specific. We confirmed the biostimulation by P. oligandrum in the starch potato cultivar Kuras under field conditions. We further investigated the effects of P. oligandrum on the potato rhizosphere microbiome, sampling individual potato plants at three time points over the growing season (representing the vegetative growth phase, flowering, and the onset of senescence). Metabarcoding using ITS and 16S amplicon sequencing revealed no significant overall effect of P. oligandrum application on the bacterial and fungal rhizosphere communities. However, some genera were significantly differentially abundant after P. oligandrum application, including some classified as plant-beneficial microbes. We conclude that P. oligandrum has a cultivar-dependent growth-promoting effect in potato and only minor effects on the rhizosphere microbiome.

Growth promotion and biological control of fungal diseases in tomato by a versatile rhizobacterium, Pseudomonas chlororaphis subsp. aureofaciens SPS-41

Pseudomonas chlororaphis subsp. aureofaciens SPS-41, a beneficial bacterium isolated from rhizosphere of sweet potato, has been explored as a biological control agent for the management of soil-borne diseases. In this study, its plant growth-promoting and antifungal properties against two major tomato fungal pathogens (Fusarium oxysporum and Botrytis cinerea) were evaluated using in vitro and in vivo experiments. Strain SPS-41 produced indole-3-acetic acid (IAA), siderophore, biofilm, protease, amylase, chitinase, and could solubilize phosphate. It also inhibited fungal mycelial growth, with an inhibition rate of more than 80% in dual culture assays. Volatile organic compounds (VOCs) produced by SPS-41 also exhibited strong antifungal activity. In addition, SPS-41 promoted the growth of tomato seedlings in greenhouse conditions, and the severity of wilt disease and grey mold decreased significantly with rhizospheric inoculation of cell suspension and VOC fumigation comparing to untreated controls. The composition of VOCs emitted by SPS-41 was analyzed, and 57 volatiles were identified by SPME/GC-MS. Of these, 2-tridecanone, 2-undecanone, 2-nonanone, 2-acetylthiazole, 9-decenyl acetate, 2-hexadecanol, α-farnesene, and nonanal were the major volatiles. Nonanal, 2-nonanone and 2-acetylthiazole were confirmed to inhibit the growth of all three pathogens. The complete genome of strain SPS-41 was sequenced and annotated. We identified a series of gene clusters responsible for the synthesis of active secondary metabolites with antimicrobial and biocontrol functions. Moreover, several genes related to plant growth promotion, such as nitrogen fixation and indole-3-acetic acid and siderophore biosynthesis were also identified. This research indicates that strain SPS-41 is a plant growth promoting bacterium with the potential for development as a new biocontrol agent for tomato fungal pathogens.

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea

We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production.

Pseudomonas PA14H7: Identification and Quantification of the 7-Hydroxytropolone Iron Complex as an Active Metabolite against Dickeya, the Causal Agent of Blackleg on the Potato Plant.

Soft rot Pectobacteriaceae (SRP), such as Pectobacterium and Dickeya, are phytopathogenic agents responsible for blackleg disease on several crops, such as potatoes, affecting the yield and depressing the seed production quality. However, neither conventional nor biocontrol products are available on the market to control this disease. In this study Pseudomonas PA14H7, a bacteria isolated from potato rhizosphere, was selected as a potential antagonist agent against Dickeya solani. In order to understand the mechanism involved in this antagonism, we managed to identify the main active molecule(s) produced by PA14H7. Cell-free supernatant (CFS) of PA14H7 cultures were extracted and analyzed using LC-MS, GC-MS, and NMR. We further correlated the biological activity against Dickeya solani of extracted CFS-PA14H7 to the presence of 7-hydroxytropolone (7-HT) complexed with iron. In a second time, we have synthesized this molecule and determined accurately using LC-UV, LC-MS, and GC-MS that, after 48 h incubation, PA14H7 released, in its CFS, around 9 mg/L of 7-HT. The biological activities of CFS-PA14H7 vs. synthetic 7-HT, at this concentration, were evaluated to have a similar bacteriostatic effect on the growth of Dickeya solani. Even if 7-HT is produced by other Pseudomonas species and is mostly known for its antibacterial and antifungal activities, this is the first description of its involvement as an effective molecule against pectinolytic bacteria. Our work opens the way for the comprehension of the mode of action of PA14H7 as a biocontrol agent against potato blackleg.

Diversity Temporal-Spatial Dynamics of Potato Rhizosphere Ciliates and Contribution to Nitrogen- and Carbon-Derived Nutrition in North-East China.

Ciliates are an important component of the rhizosphere microorganism community, but their nutritional contribution to plants has not been fully revealed. In this paper, we investigated the rhizosphere ciliate community of potatoes during six growth stages, illustrated the spatial-temporal dynamics of composition and diversity, and analyzed the correlation between soil physicochemical properties. The contributions of ciliates to the carbon- and nitrogen-derived nutrition of potatoes were calculated. Fifteen species of ciliates were identified, with higher diversity in the top soil, which increased as the potatoes grew, while they were more abundant in the deep soil, and the number decreased as the potatoes grew. The highest number of species of ciliates appeared in July (seedling stage). Among the five core species of ciliates, Colpoda sp. was the dominant species in all six growth stages. Multiple physicochemical properties affected the rhizosphere ciliate community, with ammonium nitrogen (NH4+-N) and the soil water content (SWC) greatly influencing ciliate abundance. The key correlation factors of ciliates diversity were NH4+-N, available phosphorus (AP), and soil organic matter (SOM). The annual average contribution rates of carbon and nitrogen by rhizosphere ciliates to potatoes were 30.57% and 23.31%, respectively, with the highest C/N contribution rates reaching 94.36% and 72.29% in the seedling stage. This study established a method for estimating the contributions of carbon and nitrogen by ciliates to crops and found that ciliates could be potential organic fertilizer organisms. These results might be used to improve water and nitrogen management in potato cultivation and promote ecological agriculture.

Microbiological Parameters of Sod-Podzolic Soil and Rhizosphere in a Half-Century Field Experiment with Different Fertilizer Systems

The regular application of mineral and organic fertilizers is one of the essential components of the agricultural intensification. The applied fertilizers lead to artificial enrichment of the soil environment with readily available substrates and biophilic elements, which can have a significant impact on the soil and rhizosphere microbiome. The aim of the study was to investigate the effect of different fertilizer systems on the quantitative parameters of various microbial groups in soddy-podzolic soil (Umbric Albic Retisol) and the rhizosphere of potatoes and barley. The study was carried out on a long-term field experiment, in which mineral (NPK), organic (manure) and mixed (NPK + manure) fertilizer systems have been applied since 1968. The application of organic fertilizers increased the microbial biomass carbon (Cmic) in the bulk soil and the rhizosphere by 25–100% compared to the soil without fertilizers, while the use of mineral fertilizers, on the contrary, decreased it by 10–30%. Basal respiration and respiratory coefficient (qСО2) increased in the row: without fertilizers NPK NPK + manure manure. The gene copies number of bacteria, archaea, and fungi significantly increased (1.5–2.5 times) under organic fertilizers and decreased (2–2.5 times) under NPK. The varied from 32 to 100 and from 0.10 to 0.92 by the luminescent microscopy and quantitative PCR, respectively. The lowest fungi/bacteria ratios were revealed for variants with NPK, and the highest fungi/bacteria ratios were in variants with manure. Thus, the applied doses of mineral fertilizers must be compensated by the introduction of fresh organic matter in order to maintain the stability of the soil-microbe-plant system.

Tare Soil Alters the Composition of the Developing Potato Rhizosphere Microbiome

Understanding the factors influencing microbial community composition in the rhizosphere is an important step toward managing the microbiomes of globally important crops such as potato ( Solanum tuberosum). Potato is vegetatively propagated and seed tubers are planted with tare soil, or soil adhering to the tuber surface, from their field of origin. Bulk soil is known to influence rhizosphere microbiome composition but whether tare soil additionally contributes to compositional variation is not known. We tested this hypothesis in a greenhouse experiment where tare soil was removed (or remained intact for controls) prior to planting in either soil from a potato field or soil from a previously uncultivated area next the potato field. We used internal transcribed spacer and 16S metabarcoding to characterize the fungal and bacterial rhizosphere communities of plants grown from the experimental seed tubers. We found that tare soil influenced rhizosphere microbial composition, more strongly for fungi than bacteria. As expected, bulk soil origin explained the greatest amount of variation in the rhizosphere microbiome overall but we found no evidence that the impact of tare soil on microbial community composition differed between bulk soil origins. However, the magnitude of the tare soil effect did depend, in part, on seed tuber origin. Our findings reveal that tare soil explains a significant, though modest, amount of variation in rhizosphere composition, and sets the stage for future work addressing functional consequences for plant health and productivity.

Sensitive or tolerant functional microorganisms under cadmium stress: suggesting potential specific interaction network characteristics in the rhizosphere system of karst potato.

The heavy metal cadmium (Cd) pollution in Chinese karst soils threatens food security, and microorganisms play an important role in regulating the migration and transformation of Cd in the soil-plant system. Nevertheless, the interaction characteristics between key microbial communities and environmental factors in response to Cd stress in specific crop environmental systems need to be explored. In this study, the soil (ferralsols)-microbe-crop (potato) system was taken as the object to explore the potato rhizosphere microbiome, using toxicology and molecular biology approaches, to explore the potato rhizosphere soil properties, microbial stress characteristics, and important microbial taxa under Cd stress. We hypothesized that different members of fungal and bacterial microbiome would regulate the resilience of potato rhizosphere and plants to Cd stress in the soil environment. Meanwhile, individual taxa will have different roles in the contaminated rhizosphere ecosystem. We found that soil pH was the main environmental factor affecting fungal community structure; urea-decomposing and nitrate-reducing functional bacteria as well as endosymbiotic and saprophytic functional fungi gradually decreased. In particular, Basidiomycota may play a key role in preventing the migration of Cd from the soil to plants (potato). These findings provide important candidates for screening the cascade of Cd inhibition (detoxification/regulation) from soil to microorganisms to plants. Our work provides an important foundation and research insights for the application of microbial remediation technology in the karst cadmium-contaminated farmland.

Deciphering differences in microbial community composition and multifunctionality between healthy and Alternaria solani-infected potato rhizosphere soils

Deciphering differences in microbial community composition and multifunctionality between healthy and Alternaria solani-infected potato rhizosphere soils

Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota.

The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota.

Inoculation With Azospirillum spp. Acts as the Liming Source for Improving Growth and Nitrogen Use Efficiency of Potato.

Nitrogen (N) is one of the limiting factors for plant growth, and it is mainly supplied exogenously by fertilizer application. It is well documented that diazotrophic rhizobacteria improve plant growth by fixing atmospheric N in the soil. The present study investigates the nitrogen-fixing potential of two Azospirillum spp. strains using the 15N isotope-dilution method. The two diazotrophic strains (TN03 and TN09) native to the rhizosphere of potato belong to the genus Azospirillum (16S rRNA gene accession numbers LN833443 and LN833448, respectively). Both strains were able to grow on an N-free medium with N-fixation potential (138–143 nmol mg−1 protein h−1) and contained the nifH gene. Strain TN03 showed highest indole acetic acid (IAA) production (30.43 μg/mL), while TN09 showed highest phosphate solubilization activity (249.38 μg/mL) while both diazotrophs showed the production of organic acids. A 15N dilution experiment was conducted with different fertilizer inputs to evaluate the N-fixing potential of both diazotrophs in pots. The results showed that plant growth parameters and N contents increased significantly by the inoculations. Moreover, reduced 15N enrichment was found compared to uninoculated controls that received similar N fertilizer levels. This validates the occurrence of N-fixation through isotopic dilution. Strain TN09 showed higher N-fixing potential than TN03 and the uninoculated controls. Inoculation with either strain also showed a remarkable increase in plant growth under field conditions. Thus, there were remarkable increases in N use efficiency, N uptake and N utilization levels. Confocal laser scanning and transmission electron microscopy showed that TN03 is an ectophyte, i.e., present outside root cells or within the grooves of root hairs, while TN09 is an endophyte, i.e., present within root cells, forming a strong association withroot it. This study confirms that diazotrophic Azospirillum spp. added to potato systems can improve plant growth and N use efficiency, opening avenues for improvement of potato crop growth with reduced input of N fertilizer.