Rhizosphere Microbial Populations Research Articles

Assessing HCH isomer uptake in Alnus glutinosa: implications for phytoremediation and microbial response

Although the pesticide hexachlorocyclohexane (HCH) and its isomers have long been banned, their presence in the environment is still reported worldwide. In this study, we investigated the bioaccumulation potential of α, β, and δ hexachlorocyclohexane (HCH) isomers in black alder saplings (Alnus glutinosa) to assess their environmental impact. Each isomer, at a concentration of 50 mg/kg, was individually mixed with soil, and triplicate setups, including a control without HCH, were monitored for three months with access to water. Gas chromatography–mass spectrometry revealed the highest concentrations of HCH isomers in roots, decreasing towards branches and leaves, with δ-HCH exhibiting the highest uptake (roots—14.7 µg/g, trunk—7.2 µg/g, branches—1.53 µg/g, leaves—1.88 µg/g). Interestingly, α-HCH was detected in high concentrations in β-HCH polluted soil. Phytohormone analysis indicated altered cytokinin, jasmonate, abscisate, and gibberellin levels in A. glutinosa in response to HCH contamination. In addition, amplicon 16S rRNA sequencing was used to study the rhizosphere and soil microbial community. While rhizosphere microbial populations were generally similar in all HCH isomer samples, Pseudomonas spp. decreased across all HCH-amended samples, and Tomentella dominated in β-HCH and control rhizosphere samples but was lowest in δ-HCH samples.

Unique dissolved organic matter molecules and microbial communities in rhizosphere of three typical crop soils and their significant associations based on FT-ICR-MS and high-throughput sequencing analysis

Using cucumber, maize, and ryegrass as model plants, the diversity and uniqueness of the molecular compositions of dissolved organic matter (DOM) and the structures of microbial communities in typical crop rhizosphere soils, as well as their associations, were investigated based on high-resolution mass spectrometry combined with high-throughput sequencing. The results showed that the rhizosphere contained 2200 organic molecules that were not identified in the non-rhizosphere soils, as characterized by FT-ICR-MS. The rhizosphere DOM molecules generally contained more N, S, and P heteroatoms, stronger hydrophilicity, and more refractory organic matter, representing high and complex chemical diversity characteristics. 16SrRNA sequencing results demonstrated that Proteobacteria, Actinomycetes and Firmicutes were the dominant flora in the soils. Plant species could significantly change the composition and relative abundance of rhizosphere microbial populations. The microbial community structures of rhizosphere and non-rhizosphere soils showed significant differences at both the phylum and class levels. Multiple interactions between the microorganisms and DOM compositions formed a complex network of relationships. There were strong and remarkable positive or negative couplings between different sizes and categories of DOM molecules and the specific microbial groups (P < 0.05, |R| ≥ 0.9) in the rhizosphere soils as shown by network profiles. The correlations between DOM molecules and microbial groups in rhizosphere soils had plant species specificity. The results above emphasized the relationship between the heterogeneity of DOM and the diversity of microbial communities, and explored the molecular mechanisms of the biochemical associations in typical plant rhizosphere soils, providing a foundation for in-depth understanding of plant-soil-microbe interactions.

An Integrated Investigation of the Relationship between Two Soil Microbial Communities (Bacteria and Fungi) and Chrysanthemum Zawadskii (Herb.) Tzvel. Wilt Disease.

Chrysanthemum wilt is a plant disease that exerts a substantial influence on the cultivation of Chrysanthemum zawadskii (Herb.) for tea and beverage production. The rhizosphere microbial population exhibits a direct correlation with the overall health of plants. Therefore, studying the rhizosphere microbial community of Chrysanthemum zawadskii (Herb.) Tzvel. is of great significance for finding methods to control this disease. This study obtained rhizosphere soil samples from both diseased and healthy plant individuals and utilized high-throughput sequencing technology to analyze their microbial composition. The results showed that the rhizosphere microbial diversity decreased significantly, and the microbial community structure changed significantly. In the affected soil, the relative abundance of pathogenic microorganisms such as rhizospora and Phytophthora was greatly increased, while the relative abundance of beneficial microorganisms such as antagonistic fungi and actinomyces was greatly decreased. In addition, this study also found that soil environmental variables have an important impact on plant resistance; the environmental factors mainly include soil properties, content of major microorganisms, and resistance characteristics of samples. Redundancy analysis showed that the drug-resistant population had a greater impact on the 10 species with the highest abundance, and the environmental factors were more closely related to the sensitive population. In the fungal community, the resistant sample group was more sensitive to the influence of environmental factors and high-abundance fungi. These findings provide a theoretical basis for improving microbial community structure by optimizing fertilization structure, thus affecting the distribution of bacteria and fungi, and thus improving the disease resistance of chrysanthemum. In addition, by regulating and optimizing microbial community structure, new ideas and methods can be provided for the prevention and control of chrysanthemum wilt disease.

Rhizosphere microbial community changes due to weed-weed competition

Many species of weeds are present in agricultural areas, but weeds with greater competitive ability normally become dominant in the field. Rhizosphere soil microbiota can influence weed-weed interactions. However, the role of rhizosphere soil microorganisms in weed-weed interactions remains largely unexplored. In this study, we investigated the ecological relationships and microbial taxa present in the rhizosphere of weeds in monoculture and coexistence systems. The weed species Ageratum conyzoides, Ipomoea ramosissima, and Bidens pilosa were grown in monoculture and coexistence pairs under greenhouse conditions for 80 days. The ecological relationships between weeds were analyzed by calculating the Relative Interaction Index (RII) based on the total dry mass of the plants. The rhizosphere microbiome was analyzed after extracting the metagenomic DNA from rhizosphere microbial populations, followed by PCR amplification and sequencing of the 16S rDNA gene and ITS region, using the Illumina MiSeq platform. Competitive interactions were observed for all combinations of weed species. Ageratum conyzoides showed the greatest decrease in dry matter production due to competition. Weed-weed competition changed rhizosphere microbial community composition and bacterial diversity. The abundance of different bacterial genera in rhizosphere soil varied according to the treatments. When comparing the competition between A. conyzoides and B. pilosa and their respective monocultures, the abundances of Opitutus, Diplorickettisiales uncultured and Bdellovibrio increased in B. pilosa monoculture. When comparing the competition between A. conyzoides and I. ramosissima and their respective monocultures, the abundance of Pseudonocardia increased while the abundance of Fimbriiglobus decreased in A. conyzoides monoculture. Already the abundances of Actinospica, Chitinophaga, Gemmatirosa, 1921-2 and Hymenobacter decreased I. ramosissima monoculture. When comparing the competition between B. pilosa and I. ramosissima, and their respective monocultures, the abundances of Flexibacter and Candidatus Xiphinematobacter decreased I. ramosissima monoculture. The abundances of Clostridium and Rhodobacter increased in competition while the abundance of Pajaroellobacter increased in B. pilosa monoculture. The fungal genera that had their abundances significantly altered were Scytalidium, whose abundance decreased in competition of A. conyzoides and B. pilosa when compared to the respective monocultures, while the abundance of Robillarda increased in B. pilosa monoculture. Already the abundance of Myriodontium increased in B. pilosa monoculture when compared with I. ramosissima monoculture and competition between both plants. Weeds can recruit specific taxa depending on the competition situation in which they are involved. Such changes in the rhizobiome are possibly related to the lower competitive ability and dry matter production of A. conyzoides. B. pilosa have a greater capacity to determine the structure of the rhizobiome when in competition with A. conyzoides. I. ramosissima seem to be less affected by rhizobiome taxon-specific changes.

Nanoscale sulfur alters the bacterial and eukaryotic communities of the tomato rhizosphere and their interactions with a fungal pathogen

Nanoformulations of sulfur have demonstrated the potential to enhance plant growth and reduce disease incidence when plants are confronted with pathogens. However, the impact of nanoscale sulfur on microbial communities in close contact with the plant root, known as the rhizosphere, remain poorly characterized. In this study, we investigate the impact of three formulations of sulfur; bulk sulfur, uncoated (pristine) sulfur nanoparticles, and stearic acid coated sulfur nanoparticles, on the rhizosphere of tomato plants. Tomato plants were additionally challenged by the pathogenic fungus Fusarium oxysporum f. sp. Lycopersici. Employing bacterial 16S rRNA gene sequencing, along with recently in-house designed peptide nucleic acid clamps to facilitate the recovery of microeukaryote sequences, we performed a comprehensive survey of rhizosphere microbial populations. We found the largest influence on the composition of the rhizosphere microbiome was the presence of the fungal pathogen. However, sulfur amendments also drove state changes in the rhizosphere populations; for example, enriching the relative abundance of the plant-beneficial sulfur-oxidizing bacterium Thiobacillus. Notably, when investigating the response of the rhizosphere community to the different sulfur amendments, there was a strong interaction between the fungal pathogen and sulfur treatments. This resulted in different bacterial and eukaryotic taxa being enriched in association with the different forms of sulfur, which was dependent on the presence of the pathogen. These data point to nano formulations of sulfur exerting unique shifts in the rhizosphere community compared to bulk sulfur, particularly in association with a plant pathogen, and have implications for the sustainable use of nanoscale strategies in sustainable agriculture.

Effect of Microbial Inoculants on Leghemoglobin Content in Nodules and Microbial Populations in Rhizosphere of Soybean in a Vertisols

The present study was carried out during kharif season 2019-20 at the Research Farm, Department of Soil Science &amp; Agricultural Chemistry, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh (INDIA), to assess the effect of microbial inoculants on leghemoglobin content in nodules and microbial populations in rhizosphere of soybean in a Vertisols. The experiment was laid out under randomized block design with three replications. The fifteen treatments comprised of different beneficial microbial consortia in possible combinations applied as seed treatments. Besides these, two control plots were maintained as fertilized un-inoculated control (FUI) and unfertilized un-inoculated control (UFUI). The results revealed that the significant improvement were noticed by the application of consortia NPK+EM+PGPR in leghemoglobin content in nodules at 25, 45 &amp; 65 DAS over control. Similarly, the microbial populations of the diazotroph, PSB, KSB, PGPR, phototroph, Lactic bacterium, actinomycetes, fungus and yeast were maximum in NPK+EM+PGPR treatment and followed by PK+EM+PGPR treatments. Thus, it may be concluded that the consortium of NPK + EM + PGPR was superior for maximum nodulation and microbial population in rhizosphere of soybean in a Vertisol.

Differential Response of Rhizosphere Microbial Diversity and Activities to System of Rice Intensification and Conventional Cultivation

Rice holds a vital position among staple crops worldwide, serving as a primary source of essential nutrition for a significant portion of the global population. Rice production is currently plagued by several problems causing a decline in crop yields. System of Rice Intensification (SRI) is a set of farming practices designed to improve the productivity and sustainability of rice cultivation. One of the reasons for the sustainability of SRI has been attributed to enhanced below-ground soil microbial processes around the SRI plant root system. This study assessed the effect of SRI and Normal Transplanting (NTP) cultivation methods on rhizospheric soil microbial populations, phyto-hormones, soil enzyme activities under four different nitrogen (N) treatments under a station trial and in on-farms experiments farmer’s. Rhizosphere soils and root samples of SRI exhibited significantly higher microbial population, microbial diversity, phyto - hormone production, enzyme activities in station trail. Among different levels of nitrogen fertilizer applications, treatments receiving 50% organic + 50% inorganic N forms possessed significantly higher microbiota and their activities. On farm trials also exhibited similar trends as the station trial. In conclusion, the study highlights the positive effects of SRI cultivation combined with a balanced organic and inorganic nitrogen treatment on soil microbial populations and phyto-hormone production and soil enzyme activities which could have an influence of system sustainability.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, influence of different soil organic carbon, sulfate fertilization, and cultivation time, and contribution to arsenic mobility and speciation.

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Despite mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil, and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization, and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated little significant effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate reducing and sulfur oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere versus pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria as well as pore water iron-oxidizing bacteria in the lower organic carbon soil supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates, and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

Quantitative analysis of rhizosphere microbial population obtained from main-croplands in South Sulawesi

The study aims to investigate microbial species and quantify population richness associated with main crop rhizosphere in South Sulawesi. Survey was conducted in two areas including healthy and infected croplands. In each area about 1 ha, samples were collected to consist of 250 g bulk soil of rhizosphere in healthy and infected farms 1 month after transplanting. For analysis, those samples were carried out at the Plant pathology Lab, Department Plant Pest and Disease, Faculty of Agriculture. 10 g bulk soil separation out of 250 g obtained from rhizosphere was sterilized into water 25 mL and sieved 50-100 mesh prior to transfer to growth medium. After that, 4 % (g/mL) potato dextrose agar (PDA) in the petri dish was earlier prepared. The soil mixture (1g/10 mL) was diluted and transferred into a series dilution and parallelly loaded into solid media kept in dark room with at room temperature. Microbiota successfully growing in the solid media were split and transferred into petridish contained PDA for morphological identification and quantified through a series dilution. The study found 23 native fungal isolates consisting of Genera: Rhizopus sp. Phytophthora sp., Fusarium sp., Rhizoctonia sp., Geotrichum, Aspergillus sp., Gliocladium sp., Gongronella sp., and 14 unknown groups of fungi. Three bacterial isolates were discovered as gram-positive bacteria (GPB) in the infected cropland and the other two were gram-negative bacteria (GNB) found in healthy farm. The finding evidenced that population of microbiota ‘bacterial and fungal’ richness was twofold much higher in the healthy farm than infected farm. Bacterial population was the highest in both healthy and infected farms. There is a tendency of the higher fungal population richness, the lower rice disease incidence in croplands, vice versa.

Impact of Biochar on Fusarium Wilt of Cotton and the Dynamics of Soil Microbial Community

The effects of biochar on leaf and soil-borne diseases of plants can be seen in addition to its ability to sequester carbon, improve soil quality, and enhance plant performance. However, the mechanisms by which soil-borne pathogens are suppressed and plant performance is enhanced are not well understood. The present work aims to comprehensively establish the links between biochar-induced changes in the richness of the rhizosphere microbial population, in association with the reduction of soil-borne Fusarium wilt disease (Fusarium oxysporum f. sp. vasinfectum), in cotton (Gossypium hirsutum), with improved plant performance. Biochar made from organic waste significantly decreased the colonization and survival of Fusarium in soil, raised the culture-able counts of numerous microbes with biocontrol potential (microorganisms that boost plant growth and development), and inhibited Fusarium wilt of cotton. The biochar amendment significantly enhanced the cotton plant development and physiological parameters such as chlorophyll content, etc. Overall, 9% organic waste biochar had shown a significant impact on cotton growth as compared to other treatments with or without biochar. Compared to the soil-only control, the disease index was considerably reduced in all biochar-amended treatments. In terms of the plant’s resistance to Fusarium wilt, biochar-induced increases in the level of overall chlorophyll content and biochemicals such as phenolics, flavonoids, etc. Additionally, cotton plants grown with a 9% biochar composition had considerably greater NPK levels than other treatments with or without biochar. The biochar addition resulted in increased counts of Pseudomonas spp., Actinomycetes spp., and Trichoderma spp., while Acidobacteriales, Rhodospirillales, and Frankiales were less when compared with an un-amended (without biochar) soil control. Thus, the composition of rhizosphere bacteria in the treatments with and without modified biochar was found to differ significantly.

Effect of indigenous bio-inoculants and commercial biological inputs on soil microbial population, soil health dynamics and pepper (capsicum annum L.) production

ABSTRACT Overusage of chemical fertilizers by farmers had adversely impacted soil fertility and agricultural ecosystem sustainability. To explore safer alternatives, six bio-treatments based on two Bacillus spp. consortium and three biological inputs were investigated. Assessments, carried out over two consecutive cropping years, were focused on their effects on soil microbial traits, pepper production and health status as measured by fungal and nematode infection levels. Rhizosphere microbial populations were more abundant at the second cropping year than at the first one, thus indicating their cumulative effects. The two Bacillus spp. strains applied individually, and Acadian input had induced significant increments in pepper production by 22–25% over control. No significant differences were recorded between two Bacillus spp. and their consortium on the severity of pepper-associated soil-borne diseases. B. amyloliquefaciens subsp. plantarum SV65 performed 39.7 and 59.6% better than Acadian and Trianum-P® in reducing nematode galling index and foliar severity index, respectively. Interestingly, single treatment using B. amyloliquefaciens subsp. plantarum SV65 performed better than the three biological inputs based on the majority of tested parameters. Thus, this strain used individually or in combination with B. subtilis SV41 is a promising eco-friendly alternative for the enhancement of pepper health and production.

IMPACT OF PGPR ON THE SUSTAINABLE DEVELOPMENT OF AGRICULTURE: CURRENT AND FUTURE PROSPECTS

The quest for boosting agricultural yields due to increased stress on food production has inevitably brought about the indiscriminate use of chemical fertilizers and different agrochemicals. Biofertilizers facilitate the overall growth and yield of crops in an eco-friendly manner. They comprise residing or dormant microbes implemented in the soil or used for treating crop seeds. One of the most applicants in this respect is rhizobacteria. Plant growth-promoting rhizobacteria (PGPR) are an important group of beneficial, root-colonizing bacteria. They exhibit harmonious and divergent interactions with the soil microbiota and interact in an array of activities of ecological meaning. They encourage plant growth by facilitating biotic and abiotic stress tolerance and aid the nutrition of host plants. Due to their lively growth endorsing activities, PGPRs are considered an eco-friendly alternative to dangerous chemical fertilizers. Chemical fertilizers used in agriculture to improve yields and eradicate pathogens, however, negatively influence the ecosystem. The doubts over pesticide side effects, there is a growing interest in better thoughtfulhelpful interactions between plants and rhizosphere microbial populations. As a result, biological agents are in high demand around the world. The use of plant growth-promoting Rhizobacteria (PGPR). They have a crucial function in increasing soil fertility, promoting plant growth, and suppressing phytopathogens for the development of environmentally friendly sustainable agriculture.In this section, we try to devise a strategy for increasing crop output and health, developing sustainable agriculture, and commercialization through the use of plant growth-promoting rhizobacteria.

Response of rare and abundant rhizosphere microbial communities to inoculated rhizobium in cadmium-contaminated soil phytoremediation

Soil microorganisms play an important role in maintaining ecosystem balance and exerting ecological functions. The taxonomic and functional changes in rare and abundant communities during in bioremediation of cadmium-contaminated soils and their contributions to the remediation of ecosystem functions remain elusive despite the significance of rare and abundant microbial taxa in maintaining soil ecological function. Mesorhizobiumloti HZ76-inoculated seedlings of the Robinia pseudoacacia were used to create a symbiotic system. The effects of rhizobium inoculation on rare and abundant rhizosphere microbial populations were investigated in pot experiments. Despite having minimal effects on the α-diversity of rare and abundant microbial communities, inoculation altered microbial community composition and functional gene abundance. For example, abundant phyla such as Proteobacteria were enriched following inoculation, whereas rare phyla such as Ascomycota were depleted. After inoculation, the abundance of nifH gene increased, while the abundance of amoA, amoB, nirS, nirK and nosZ gene decreased. Rare bacterial populations were more susceptible to the inoculated rhizobium's environmental alterations. In rare communities compared to abundance communities, the α-diversity was higher. Stochastic processes predominated in the communities of uncommon and abundant microorganisms. Furthermore, keystone taxa, particularly rare bacterial taxa (Gemmatimonadaceae and Saprospiraceae) and rare fungal taxa (Ascomycota), more mediates nitrogen cycle processes and is directly associated to the abundance of nitrogen functional genes. Together, our findings demonstrate the different ways that rare and abundant microbial species react to rhizobia inoculation and their connections to the nitrogen cycle.

Evaluation of the Usefulness of Fermented Liquid Organic Formulations and Manures for Improving the Soil Fertility and Productivity of Brinjal (Solanum melongena L.)

The practice of incorporating organic manures and fermented liquid biofertilizers of different origins and compositions can supply valuable nutrients to the soil. To ascertain the effect of fermented liquid organic nutrient formulations (FLONFs) on the rhizospheric microbial population, growth characteristics, nutritional status, and yield of brinjal, a field experiment was conducted in consecutive seasons in 2017 and 2018. Fermented liquid biofertilizers (panchagavya and jeevamrut) were prepared and applied along with organic manures to brinjal plants in ten treatment combinations in three replications. The treatment (T4) involving the combined use of organics and FLONFs contributed significantly to the soil dehydrogenase enzyme activity (4.9 mg TPF h−1 g−1 soil), phosphatase enzyme activity (25.5 mmoles PNP h−1 g−1 soil), and urease enzyme activity (0.27 mg NH4+ g−1 soil). The mean bacterial count, fungal count, and actinomycete levels were 203.3 × 108 cfu g−1, 4.34 × 103 cfu g−1, and 3.41 × 102 cfu g−1 soil, respectively, along with a mean soil microbial biomass of carbon value of 66.1 mg g−1 soil. The brinjal yield was maximal under treatment T4 with values of 389.2 q ha−1 and 153.7 q ha−1 for 2017 and 2018, respectively. As a result, for higher yields and soil longevity, the combination of organics and FLONFs can be advocated.

Evaluating the Biocontrol potential of Indigenous Trichoderma spp. against soil borne pathogens of rice and their impact on rhizospheric functional microbial populations

Trichoderma spp. is naturally mycoparasite and the most widely used biocontrol agent (BCA). This Trichoderma spp. is also naturally growth enhancer in crop plants. However, their uses in rice plants are limited to few reports only. The use of excessive Trichoderma as BCA may have effect on soil or soil microflora. We have also characterized Trichoderma spp. biochemically especially for their chitinase and protease activity. The impact of Trichoderma spp. showed that Trichoderma inoculation increases the growth of specific bacterial population and decreases the soil fungal population in rice soil, which indicated that the isolates may the best potential strains to control the soil pathogens. Antagonism effect of isolated Trichoderma spp. was found effective against various soil borne pathogens like R. solani, S. oryzae than S. rolfsii.

Cation Exchange Resins for Predicting Available K on K-Deficient Soils: Extraction Capacity among Different Soil K Pools and First Insights on the Contribution of K Solubilized by Rhizosphere Microbes

The contribution of non-exchangeable soil K in the total K availability may be essential to K deficient soils; however, less attention has been paid so far for proposing soil tests that assess the bioavailable structural K that is solubilized by soil microbes during a growing season. The objectives of this study were to evaluate cation exchange resins for their performance in predicting K uptake by plants; to investigate the relationships between rhizosphere soil microbes, different soil K pools, and soil parameters; and to assess their exchange capacity with respect to K derived by feldspars. A pot experiment with winter wheat was conducted on K deficient soils, several soil tests were examined, and rhizosphere K solubilizing microbial population was assessed. Single and multiple regressions showed that cation resins performed better in predicting total plant K uptake than the other chemical extractants (r2 = 0.64, r2 = 0.85, respectively, p ≤ 0.001), whereas the PCA analysis and Pearson correlation tests revealed a positive correlation between K derived by feldspars, K uptake, and the K solubilizing rhizosphere microbial population. The above was further confirmed by the mapping of cation resins of extraction capacity, which showed a significant contribution of K derived by feldspars (15.6%).

Enzyme activities and microbial population status of soil as influenced by humic acid under doses of nitrogen in Spinach rhizosphere

The response of rhizospheric microbial population and enzymes activities to humic acid and N-fertilizer were acquaintly correlated with each other. Sustained level of crop nutrition requires, achieving the potential yield and maximum nutrient use efficiency. Hence through integrated use of fertilizers and humic acid, the microbial population and soil enzymes in rhizosphere soil could be build up for the efficient utilization of nutrients.

Changes in the population and functional profile of bacteria and fungi in the rhizosphere of Suaeda salsa is driven by invasion of Spartina alterniflora

Changes in rhizosphere microbial populations and their functions in response to Spartina alterniflora root invasion could potentially reveal part of the mechanism of Suaeda salsa degradation. In this study, rhizosphere soils were collected from regions where S. alterniflora (SA) and S. salsa (SS) grew independently as well as rhizosphere soil from mixed growth regions (namely MSA and MSS) before applying high-throughput sequencing technology to study the characteristics of microbial communities. The results showed that the physicochemical properties of the rhizosphere soils were different between the groups of samples. However, based on the multi-factor PERMANOVA analysis, only EC and NO3−-N were found to significantly influence the microbial communities’ composition. Furthermore, α diversity indices and β diversity analyses revealed that the diversity and structure of rhizosphere microbial community changed in varying degrees after invasion. Compared with SS, the most abundant bacteria phylum namely Tenericutes, Firmicutes, Proteobacteria and Actinobacteria in MSS were identified as major species that increased significantly in abundance in response to S. alterniflora root invasion, while the composition of fungal community did not change. Furthermore, PICRUSt analysis revealed that the higher abundance of signal transduction, membrane transport, cell motility and certain disease-related functional pathways of MSA and MSS could be conducive to the colonization and survival of bacterial pathogens. Additionally, the analysis of the FUNGuild database confirmed that a higher proportion of pathotroph and pathogen. This could very likely cause S. salsa to be more susceptible to soil pathogenic fungi in mixed growth region. In contrast, the increase of the saprotroph-symbiotroph could be beneficial for the colonization and expansion of S. alterniflora. This study provides a new perspective for elucidating the driving mechanism by microorganisms behind S. salsa’s degradation following S. alterniflora’s invasion.

Insights into the deriving of rhizosphere microenvironments and its effects on the growth of authentic Angelica sinensis seedlings under continuous monoculture

PurposeContinuous monoculture leads to deterioration of soil microenvironment, which can severely threat the quality and efficiency of Angelica sinensis (A. sinensis), especially for seedlings production. However, little attention has been paid to investigate how continuous monocropping affects the growth of A. sinensis seedling, rhizosphere microbial populations, and nutrient status.MethodsA field experiment consisting of two different planting patterns — raising A. sinensis seedlings in reclamation alpine uncultivated meadow (RW) and 1-year continuous monoculture (CC), was carried out at Min County, Gansu province, China.ResultThe results showed that compared with RW, the growth rate and valid quantity of A. sinensis seedlings were significantly reduced by 195.4% and 36.7% in CC, respectively. Continuous monocropping significantly increased the rhizosphere soil pH value during the growing season, ranging from 6.18 to 7.10, while reducing the content of SOM, total N, and available P and K. Glomalin, AMF spore densities, and the number of actinomycetes, ammonifiers, and azotobacter were also decreased by CC. The CC treatment significantly increased the abundance of fungi. The diversity and richness of bacteria in CC were lower than RW. Furthermore, the composition and structure of bacterial and fungal flora also changed and that the abundance of beneficial bacteria decreased, while the abundance of pathogens increased in CC. Thus, CC appeared to completely upend the relationship between soil nutrient availability and microbial activity.ConclusionThe results illustrated that continuous monoculture led the flora of bacteria and fungi to changed dramatically, with the abundance of beneficial bacteria decreased and the abundance of harmful microbes, such as Lasiosphaeriaceae, Vishniacozyma, Myrmecridium, and Hypocreales, increased. The function of microbial population has changed from “beneficial bacteria dominated” to “harmful microbes dominant.” We concluded that continuous monoculture significantly reduced the growth and the efficiency of A. sinensis seedlings and deteriorated the rhizosphere soil microenvironment by increasing pH and decreasing nutrient availability, as well as altering the function of interactions between soil nutrients and microbial populations, thereby resulting in an unsuitable microenvironment for A. sinensis seedlings growth.

The Pattern Recognition Receptor FLS2 Can Shape the Arabidopsis Rhizosphere Microbiome β-Diversity but Not EFR1 and CERK1

Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) is the first line of plant defense. We hypothesized that the absence of pattern recognition receptors (PRRs) in plants could influence the rhizosphere microbiome. Here, we report sequencing of the 16S ribosomal RNA gene and the fungal ribosomal RNA internal transcribed spacer region of rhizosphere DNA from three Arabidopsis PRR mutants involved in plant innate immunity (efr1, fls2, and cerk1). We conducted experiments in a growth chamber using native soil from the Red River Farm (Terral, OK, USA) to detect microbial community shifts in the rhizosphere that may occur in the absence of PRR receptors compared to wild-type (WT; Col-0) plants. No difference in the α-diversity of the rhizosphere microbial population was observed between the PRR mutants tested and the WT. Plant host genotype had a significant impact in bacterial β-diversity only between the fls2 mutant and the WT. Surprisingly, no significant changes in fungal β-diversity were observed between the PRR mutants and WT, although we observed an increase in relative abundance for the cup fungi (Pezizaceae) in the cerk1 mutant. This finding suggests that the FLS2 receptor can modulate the rhizosphere-associated microbiome β-diversity and expands the list of current known genotypes that can modulate the rhizosphere microbiota.