Microbial Diversity In Rhizosphere Soil Research Articles

Nanoselenium integrates soil-pepper plant homeostasis by recruiting rhizosphere-beneficial microbiomes and allocating signaling molecule levels under Cd stress

Most studies have focused on regulation in a metabolic pathway in response to exogenous selenium under cadmium stress, rather than the change of key factors in soil and pepper plants. In this study, the correlations in environmental variables, microorganisms, metabolic pathways, Se and Cd morphology under nano-Se intervention were examined using metabolomics and microbial diversity in rhizosphere soil and pepper plants. The principal forms of Se in the soils were Se (VI) and SeCys, while SeMet and MeSeCys were the main components in the root, stem, leaves, and fruits in the treatment of nano-Se (5 and 20 mg/L) relative to the control. Soil enzymes,metabolites (fluorescein diacetate, urease, brassinolide, and p-hydroxybenzonic acid), and plant metabolites (rutin, luteolin, brassinolide, and abscisic acid) were remarkably enhanced by nano-Se fortification. The bio-enhancement of nano-Se can boost the beneficial microorganisms of Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Gemmatimonadetes, Deltaproteobacteria, and Anaerolineae in rhizosphere soil. Changes in microbial community were found to be strongly linked to the environment index, enzymes, soil metabolites, Se forms, which reduced Cd bioavailability and Cd accumulation in pepper plants. In conclusion, the nano-Se application integrates soil-plant balance by improving soil qualities and assigning signaling molecule levels in rhizosphere soil and pepper plants.

Microbial Diversity Analysis of Bupleurum latissimum Nakai from Ulleung-Do of South Korea Using Next-Generation Sequencing.

ABSTRACTBupleurum latissimum Nakai is a rare endemic species native to Ulleung-do in South Korea. This study aimed to report on the rhizosphere soil microbial diversity of B. latissimum. Proteobacteria, Actinobacteria, and Verrucomicrobia were identified in relative abundances of 27.77%, 21.70%, and 15.27%, respectively.

Effects of Plant Fine Root Functional Traits and Soil Nutrients on the Diversity of Rhizosphere Microbial Communities in Tropical Cloud Forests in a Dry Season

The composition and diversity of rhizosphere microbial communities may be due to root–soil–microbial interactions. The fine root functional traits and rhizosphere soil environmental factors of 13 representative plants in the Bawangling tropical cloud forest of Hainan Island were measured, to assess the key factors driving plant rhizosphere microbial communities. Illumina MiSeq sequencing technology was used to sequence the v3-V4 region of the 16SrDNA gene of 13 plant rhizosphere soil bacteria and the ITS1 region of the fungal ITSrDNA gene. Results showed that there were 355 families, 638 genera, and 719 species of rhizosphere soil bacteria as well as 29 families, 31 genera, and 31 species of rhizosphere soil fungi in the tropical cloud forests. The fine root traits, such as root phosphorus content, the specific root length and specific root area, were significantly negatively correlated with the Faith-pd indices of the bacterial community but were not correlated with the diversity of fungi communities. The soil pH was significantly and positively correlated with the Chao1 index, OTUs, Faith-pd and Simpson indices of the bacteria and fungi communities. The soil available phosphorus content was significantly and negatively correlated with the bacteria Simpson and the fungus Faith-pd indices. ABT analysis showed that soil pH and soil available phosphorus were the most important environmental conditions contributing to the rhizosphere bacterial and fungi communities, respectively. Our findings demonstrate that the soil environments had more influence on rhizosphere soil microbial diversity than the fine root functional traits.

Changes in Bulk and Rhizosphere Soil Microbial Diversity and Composition Along an Age Gradient of Chinese Fir (Cunninghamia lanceolate) Plantations in Subtropical China.

Soil microorganisms play key roles in biogeochemical cycling in forest ecosystems. However, whether the responses of microbial community with stand development differed in rhizosphere and bulk soils remains unknown. We collected rhizosphere and bulk soil in Chinese fir plantations with different stand ages (7a, 15a, 24a, and 34a) in subtropical China, and determined bacterial and fungal community variation via high-throughput sequencing. The results showed that soil bacterial, but not fungal, community diversity significantly differed among stand ages and between rhizosphere and bulk soils (p < 0.05). The differences in Shannon–Wiener and Simpson’s indices between rhizosphere and bulk soil varied with stand age, with significant higher soil bacterial diversity in rhizosphere than bulk soils in 7a and 34a plantations (p < 0.05), but there were no significant difference in soil bacterial diversity between rhizosphere and bulk soils in 15a and 24a plantations (p > 0.05). Soil microbial community composition varied significantly with stand age but not between the rhizosphere and bulk soil. The dominant bacterial phyla at all ages were Acidobacteria and Proteobacteria, while the dominant fungal phyla were Ascomycota and Basidiomycota in both rhizosphere and bulk soil. They showed inconsistent distribution patterns along stand age gradient (7–34a) in the rhizosphere and bulk soil, suggesting distinct ecological strategy (r-strategist vs. k-strategist) of different microbial taxa, as well as changes in the microenvironment (i.e., nutrient stoichiometry and root exudates). Moreover, bacterial and fungal community composition in rhizosphere and bulk soil were governed by distinct driving factors. TP and NH4+–N are the two most important factors regulating bacterial and fungal community structure in rhizosphere soil, while pH and NO3––N, DON, and TN were driving factors for bacterial and fungal community structure in bulk soil, respectively. Collectively, our results demonstrated that the changes in microbial diversity and composition were more obvious along stand age gradients than between sampling locations (rhizosphere vs. bulk soil) in Chinese fir plantations.

Succession Pattern in Soil Micro-Ecology Under Tobacco (Nicotiana tabacum L.) Continuous Cropping Circumstances in Yunnan Province of Southwest China.

Continuous cropping obstacle (CCO) is a common phenomenon in agricultural production and extremely threatens the sustainable development of agriculture. To clarify the potential keystone factors causing tobacco (Nicotiana tabacum L.) CCO, tobacco plants, topsoil, and rhizosphere soil were sampled from the fields with no, slight, and severe tobacco disease in Dali and Yuxi of Yunnan province in China. The physicochemical properties of topsoil and rhizosphere soil, the phenolic acids (PAs) contents in rhizosphere soil, and elemental contents in topsoil, rhizosphere soil, and tobacco plants were analyzed. Microbial diversity in rhizosphere soil was determined by the metagenomic sequencing method. The results showed that soil pH, texture, cation exchange capacity, organic matter, TC, TN, and available K contents showed a significant difference (p < 0.05) in soil physicochemical properties. There was a deficiency of B, K, Mg, and Mn contents in soil and/or tobacco plants. The contents of PAs, especially syringic acid in rhizosphere soil, varied significantly among the three sampling groups (p < 0.05). Meanwhile, microbial communities and functional genes changed from beneficial to harmful, showing an intimate correlation with soil pH and syringic acid content. It can be concluded that tobacco CCO could be allocated to the imbalance of soil micro-ecology, which possessed a regional feature at the two sampling sites.

Microbial Diversity Characteristics of Areca Palm Rhizosphere Soil at Different Growth Stages.

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the areca palm’s developmental stages on the rhizosphere microbiota, the rhizosphere microbiota of areca palm (Areca catechu) grown in its main producing area were examined in Wanning, Hainan province, at different vegetation stages by an Illumina Miseq sequence analysis of the 16S ribosomal ribonucleic acid and internal transcribed spacer genes. Significant shifts of the taxonomic composition of the bacteria and fungi were observed in the four stages. Burkholderia-Caballeronia-Paraburkholderia were the most dominant group in stage T1 and T2; the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were decreased significantly from T1 to T2; and the genera Acidothermus and Bacillus were the most dominant in stage T3 and T4, respectively. Meanwhile, Neocosmospora, Saitozyma, Penicillium, and Trichoderma were the most dominant genera in the stage T1, T2, T3, and T4, respectively. Among the core microbiota, the dominant bacterial genera were Burkholderia-Caballeronia-Paraburkholderia and Bacillus, and the dominant fungal genera were Saitozyma and Trichoderma. In addition, we identified five bacterial genera and five fungal genera that reached significant levels during development. Finally, we constructed the OTU (top 30) interaction network of bacteria and fungi, revealed its interaction characteristics, and found that the bacterial OTUs exhibited more extensive interactions than the fungal OTUs. Understanding the rhizosphere soil microbial diversity characteristics of the areca palm could provide the basis for exploring microbial association and maintaining the areca palm’s health.

Microbial Diversity in Tobacco Rhizosphere Soil at Different Growth Stages

Rhizosphere microorganisms are the main participants of material transformation and energy cycle in soil. To further explore its composition and variation, the tobacco rhizosphere soil were sequenced by Illumina MiSeq, the microbial community at different growth stages were analyzed and compared. The analysis of Alpha diversity showed that, the Chao1 index, Shannon index of bacteria and Chao1 index of fungi in rhizosphere soil were the highest in tobacco budding stage, while the peak of Shannon index of fungi appeared in tobacco material stage. Principal component analysis (PCA) further showed that at different growth stages, Proteobacteria was the dominant, followed by Actinobacteria, Acidobacteria and Gemmatimonadetes for bacterials; Ascomycota was the dominant, followed by Zygomycota and Basidiomycota for fungi. Under field conditions, the microbial abundance changed with the growth of tobacco, and the microbial diversity reached the peak at budding stage. The bacterial community and abundance between budding and mature stages was highly similar, while the bacterial community in vigorous growth stage is quite different. The similarity of fungal community in budding stage was very low, compared with the other stages; while in other stages was high. This study provides a theoretical basis for further understanding the relationship between tobacco rhizosphere soil microbial diversity and variation, tobacco growth and soil diseases.

Heavy metals uptake and translocation of typical wetland plants and their ecological effects on the coastal soil of a contaminated bay in Northeast China

Heavy metal pollution in coastal zone is a global environment problem concerning the international society. As an eco-friendly and economical method, phytoremediation is a promising strategy for improving heavy metal pollution in coastal soil. In order to alleviate the ecological risk of heavy metal pollution in Jinzhou Bay, a typical and important heavy industrial area in China, three local wetland plants (Scirpus validus, Typha orientalis and Phragmites australis) were selected and planted in the field. The plants showed strong tolerance of high concentrations of heavy metals. Stressed by the heavy metals, the root weight of S. validus and P. australis increased 114.74% and 49.91%, respectively. The concentrations of heavy metals (Cd, Cr, Cu, Ni, Pb, Zn, As, Hg) accumulated in the plant roots were 4–60 times higher than that in plant shoots. The SEM analysis found that abundant heavy metals were adhered to the root surface closely. Bioconcentration factor of heavy metals on the plant roots were 0.08–0.89 (except Cr, Ni), while the translocation factor from roots to above ground of plants were 0.02–0.27. Furthermore, the wetland plants improved the regional ecological environment quality. The concentrations of heavy metals in the rhizosphere soil decreased significantly. Compared with the bulk soil, the potential ecological risk index in the rhizosphere soil reduced 26.51%–69.14%. Moreover, the microbial diversity in rhizosphere soil increased significantly, and the abundances of Proteobacteria and Bacteroidetes also increased in rhizosphere soil. Pearson correlations indicated that Hg, As, Ni and Cr were negatively correlated with Proteobacteria (p < 0.05), and Cu was significantly negative correlated with Bacteroidetes (p < 0.05). The results support that using suitable local plants is a promising approach for repairing heavy metal contaminated costal soil, not only because it can improve the regional ecological environment quality, but also because it can enhance the landscape value of coastal zone.

A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils.

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

小蓬竹根际土壤微生物及内生真菌多样性分析

为了解喀斯特典型物种-小蓬竹根际土壤微生物及不同部位内生真菌多样性，采用沿等高线等距离取样法采集小蓬竹根际土壤及健康植株，通过可培养对根际土微生物及内生菌进行分离，利用分子技术对其进行鉴定，根据鉴定结果构建系统发育树，并计算小蓬竹根际土壤微生物和根茎叶内生真菌多样性。结果如下：（1）共从根际土壤、根、茎、叶分离得到139个真菌菌株，隶属于27属，其中根际土壤分离得到34个真菌菌株隶属于12属，根部分离得到的63个内生真菌菌株隶属于17个属，茎部分离得到的14个内生真菌菌株隶属于8个属，叶部分离得到28个内生真菌菌株隶属于9个属；（2）根际土壤共分离得到41株细菌菌株，隶属于7个属26个种，20株放线菌菌株，隶属于1属15种；从Shannon-Wiener多样性指数、均匀度指数、Simpson指数排序来看，真菌主要表现为根 > 根际土壤 > 茎 > 叶，细菌和放线菌多样性均较低。（3）按层次聚类分析可分别将真菌、细菌、放线菌聚为3支。小蓬竹根际土壤、根、茎和叶具有丰富的微生物多样性，不同部位菌群组成存在差异性（P<0.05），且存在以假单胞菌属、芽孢杆菌属等为优势属的抗盐耐旱菌群，这有助于揭示小蓬竹对喀斯特生境的适应性，以及为微生物-植物群落之间相互关系提供一定基础数据，为后期寻找小蓬竹相关耐性功能菌奠定基础。;To understand the diversity of the rhizosphere soil microbial and endophytic fungi from the typical karst species-A. luodianensis, rhizosphere soil and healthy plants were collected through Isometric sampling method, then the soil microbial and endophytic fungi were isolated by culturable cultivation, and identified using the molecular technology. Finally, we constructed a phylogenetic tree, and calculated the diversity index according to the results, which reveal the conclusion:(1)Totally, there are 139 fungal isolates was obtained from rhizosphere soil, root, stem and leaf, belonging to 27 genera. Among them, 34 fungi strains were isolated from rhizosphere soil, belonging to 12 genera; 63 endophytic fungi strains were isolated from the roots, belonging to 17 genera; 14 endophytic fungi strains were isolated from the stems, belonging to 8 genera, 28 endophytic fungi strains were isolated from the leaves, belong to 9 genera. (2)There are 41 bacteria strains were isolated from rhizosphere soil, belonging to 7 genera and 26 species totally; 20 actinomycetes strains, belonging to 1 genus and 15 species. According to the order of microorganism diversity index, there was a significant difference in fungal diversity:root > rhizosphere soil > stem > leaf, but it was not significant in the diversity of bacteria and actinomycetes. (3)Fungi, bacteria and actinomycetes were divided into 3 branches by hierarchical cluster analysis. We found that the microbial diversity in rhizosphere soil, root, stem and leaf of A. luodianensis was abundant, and there was a significant difference in microbial community composition in different parts (P < 0.05), salt-tolerant and drought-tolerant bacteria groups with pseudomonas and bacillus were the dominant genera here. This study laid a foundation for searching for functional bacteria related to A. luodianensis, which would help to reveal the adaptability of A. luodianensis to karst habitat and provide some basic data for the relationship between microorganism and plant community.

Intercropping Alters the Soil Microbial Diversity and Community to Facilitate Nitrogen Assimilation: A Potential Mechanism for Increasing Proso Millet Grain Yield.

Intercropping of cereals and legumes has been used in modern agricultural systems, and the soil microorganisms associated with legumes play a vital role in organic matter decomposition and nitrogen (N) fixation. This study investigated the effect of intercropping on the rhizosphere soil microbial composition and structure and how this interaction affects N absorption and utilization by plants to improve crop productivity. Experiments were conducted to analyze the rhizosphere soil microbial diversity and the relationship between microbial composition and N assimilation by proso millet (Panicum miliaceum L.) and mung bean (Vigna radiata L.) from 2017 to 2019. Four different intercropping row arrangements were evaluated, and individual plantings of proso millet and mung bean were used as controls. Microbial diversity and community composition were determined through Illumina sequencing of 16S rRNA and internal transcribed spacer (ITS) genes. The results indicated that intercropping increased N levels in the soil–plant system and this alteration was strongly dependent on changes in the microbial (bacterial and fungal) diversities and communities. The increase in bacterial alpha diversity and changes in unique operational taxonomic unit (OTU) numbers increased the soil N availability and plant N accumulation. Certain bacterial taxa (such as Proteobacteria) and fungal taxa (such as Ascomycota) were significantly altered under intercropping and showed positive responses to increased N assimilation. The average grain yield of intercropped proso millet increased by 13.9–50.1% compared to that of monoculture proso millet. Our data clearly showed that intercropping proso millet with mung bean altered the rhizosphere soil microbial diversity and community composition; thus, this intercropping system represents a potential mechanism for promoting N assimilation and increasing grain yield.

Effects of Rhizobium Inoculation on N2 Fixation, Phytochemical Profiles and Rhizosphere Soil Microbes of Cancer Bush Lessertia frutescens (L.)

Plant-beneficial microorganisms are determinants of plant health and productivity. However, the effects associated with secondary plant metabolism and interactions in the rhizosphere for Cancer bush Lessertia frutescens (L.) is unclear. The study was conducted to understand the mechanism of rhizobium inoculation for L. frutescens, variations in phytochemicals, soluble sugars, and soil–plant interactions in the rhizosphere. Four rhizobium inoculation levels (0, 100, 200, and 400 g) were evaluated under the field conditions to establish the antioxidant properties, soluble sugars, and rhizosphere soil microbial diversity at 150, 240, and 330 days after planting (d.a.p). Although inoculation did not significantly affect plant biomass and N2 fixation of L. frutescens, total phenolics and flavonoids were enhanced with the application of 200 g at 240 days after planting. The antioxidant values analyzed through FRAP (Ferric reducing power assay) were highest with 100 g inoculation at 240 days after planting. Water-soluble sugars such as fructose, sucrose, and glucose increased with the application of 400, 200, and 100 g rhizobium inoculation. The rhizosphere′s carbon source utilization profiles (CSUP) did not vary significantly, depicting the weaker ability in converting C, P, and N profiles. The lowest ß glucosidase activity was observed in the bulk soil with the lowest alkaline and acid phosphatase activities. Soil microbial populations present in the bulk sample demonstrated the smallest overall enzyme activities. The variation of different variables studied indicate the potential of rhizobium inoculation. However, further studies are required to ascertain the inoculation′s effectiveness for plant growth and rhizosphere microbial populations of L. frutescens.

Effects of Continuous Nitrogen Fertilizer Application on the Diversity and Composition of Rhizosphere Soil Bacteria.

Little has been reported on the effects of long-term fertilization on rhizosphere soil microbial diversity. Here, we investigated the effects of long-term continuous nitrogen (N) fertilization on the diversity and composition of soil bacteria using data from a 10-year field experiment with five N application rates (0, 120, 180, 240, and 360 kg N hm–2). The results revealed varying degrees of reduction in the numbers of bacterial operational taxonomic units (OTUs) in response to the different N application rates. The highest wheat yield and number of proprietary bacterial OTUs were found in the N input of 180 kg N hm–2. In terms of average relative richness, the top seven phyla of soil bacteria in the rhizosphere of wheat after long-term nitrogen application were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Gemmatimonadetes, and Patescibacteria. Among these, Proteobacteria and Gemmatimonadetes were found to be unaffected by the nitrogen fertilizer and soil environmental factors (pH, C/N ratio, and NO3– concentration), whereas Acidobacteria and Actinobacteria showed significant positive and negative correlations, respectively, with soil pH. The richness of Actinobacteria significantly increased in the N180 treatment. Patescibacteria and Bacteroidetes showed significant positive correlations with soil NO3– and wheat yield, and the average relative richness of these two phyla was high under long-term application of the N180 treatment. These findings indicate that the relative richness of Patescibacteria and Bacteroidetes can affect wheat yield. In conclusion, the results of our 10-year field experiments clearly show that long-term N fertilization can significantly affect most of the dominant soil bacterial species via changing the soil pH. The richness of Actinobacteria can serve as an indicator of a decreased soil pH caused by long-term N fertilization.

Rhizosphere soil affects pear fruit quality under rain-shelter cultivation

The use of rain shelters in pear cultivation has been shown to improve yields and the appearance and quality of fruit, as well as reduce diseases and pests; however, how rain shelters affect soil chemical properties, soil enzyme activity, and soil microbial diversity remains unknown. Here, we studied pear trees under rain-shelter cultivation and open-field cultivation in the same orchard and compared fruit quality, soil chemical characteristics, soil enzyme activity, and soil microbial diversity. Results showed that rain shelters can significantly (p &lt; 0.05) increase the sugar content (sweetness) of pear fruits and decrease the content of acids. The levels of available phosphorus, available potassium, organic matter, and water in soils under rain shelters were significantly (p &lt; 0.05) lower than in soils in open fields. Rain-shelter treatment increased soil polyphenol oxidase activity and decreased phosphomonoesterase, urease, and sucrase activity. Analysis of microbial carbon-source utilization rates and microbial diversity showed that open-field cultivation is beneficial for microbial carbon-source utilization and microbial diversity in rhizosphere soil. Our study found that rain-shelter cultivation is not beneficial to soil fertility, microbial carbon-source metabolism and utilization, matter cycling, or microbial diversity and that the use of rain shelters may require appropriate nutrient and organic matter supplementation to maintain long-term cultivation of crops; whereas, the effects of environmental factors on open-field cultivation are greater, and more refined water and fertilizer management is required to improve fruit quality.

Biotransformation of the herbicide nicosulfuron residues in soil and seven sulfonylurea herbicides by Bacillus subtilis YB1: A climate chamber study

Bacillus subtilis YB1 is a strain that can efficiently transform nicosulfuron. In order to study its remediation ability and effects on other microorganisms in the soil, indoor biological remediation experiments and rhizosphere microbial diversity analysis were performed. B. subtilis YB1 granules were prepared and applied to the nicosulfuron contaminated soil. The concentration of nicosulfuron was detected by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and changes in the physiological indicators of wheat were measured. At the same time, the changes in the rhizosphere soil microbial diversity were determined by 16S RNA sequencing. Results showed that the YB1 granules made a contribution to the transformation of nicosulfuron (0.05 mg kg−1) in the soil within 55 days. The physiological indicators of wheat also showed consistent result about nicosulfuron transformation. Rhizosphere soil microbial diversity results indicated the relative abundance of Firmicutes decreased (3.0%–0.35%) and Acidobacteria first decreased (25.82%–22.38%) and then increased (22.3%–26.1%) with nicosulfuron added (N group). The relative abundance of Acidobacteria first decreased (25.8%–15.3%) and then increased (15.3%–21.7%) while Proteobacteria increased (26.5%–38.08%). At the same time, Firmicutes first increased (2.6%–12.3%) and then decreased to original level (12.3%–0.7%) in the N group with YB1 granules (NYB1 group). Members of the genus Bacillus initially increased and then decreased to the original level as the Control group, therefore, they did not become dominant in the rhizosphere soil. Alpha diversity analyses showed no obvious differences in species diversity among the N, NYB1 and Control groups. So YB1 did not have obvious influence on the rhizosphere microbial community structure during nicosulfuron transformation, which only had some effect on species abundance. This study revealed the successful indoor bioremediation of nicosulfuron in the soil, providing a potential strategy for solving the problem of nicosulfuron contamination.

Microbial activity and diversity in the rhizosphere soil of the invasive species Zizania latifolia in the wetland of Wuchang Lake, China

Information about the consequences of invasive species overgrowing freshwater wetlands is limited. According to remote sensing data, the invasive species Zizania latifolia spreads at an annual rate of 1.78km2 in the freshwater wetland of Wuchang Lake, China, resulting in wetland loss and degradation due to the overgrowth. This species not only increases soil organic matter, total carbon, total nitrogen, total sulfate, available nitrogen and the C/N ratio in the rhizosphere soil, but also results in increased urease, sucrose and catalase activity, as well as fluorescein diacetate hydrolysis. In this study, we have analysed microbial diversity in rhizosphere soils among different habitat types of Z. latifolia. Microbial communities in different habitats invaded by Z. latifolia differed considerably at the genus level, although all soil samples were predominated by the phyla Proteobacteria, Acidobacteria and Chloroflexi. The dominant bacterial taxa in the rhizosphere soil from the floating blanket included Acidimicrobiales, Thiomonas, Alicyclobacillus, Acetobacteraceae and Acidocella, whereas those in rhizosphere soils from the lake sludge were Acidobacteria, Anaerolineaceae, Bacteroidetes and Nitrospirae. The bacterial community in the rhizosphere soil differed significantly from that in the non-rhizosphere soil. Z. latifolia potentially creates suitable habitats and provides substrate for a unique set of microbes, further facilitating the succession of this species.

Changes of Microbial Diversity in Rhizosphere Soils of New Quality Varieties of Winter Wheat Cultivation in Organic Farming

The aim of this paper was to evaluation functional diversity in rhizosphere soils of new quality varieties of winter wheat cultivation in organic farming. Field experiments were carried out in 2017 and 2018. Twelve commercial winter wheat varieties were selected for testing: Arktis, Bellisa, Estivus, Fidelius, Hondia, Jantarka, KWS Ozon, Linus, Markiza, Ostka Strzelecka, Pokusa, and Rokosz. Winter wheat cultivars were chosen for their high yielding potential and good tolerance to fungal diseases. In the plant production conducted in accordance with the principles of organic farming, the selection of the best quality varieties is a key element of agrotechnics. The samples of rhizosphere soils were collected each year in two seasons: spring and summer. The basic parameters of soil biological activities and microbial biodiversity indicators were determined. The high variability of biological activity and functional diversity of rhizosphere soils in the growing season between particular varieties of winter wheat was observed. The rhizosphere soils from varieties such as Bellisa, Arktis, Jantarka, Fidelius, Ostka Strzelecka, Pokusa, Rokosz and KWS Ozon were characterized by high biological activity and functional biodiversity. On the other hand, the soils collected from the varieties Estivus, Fidelius, Jantarkaand Hondia were characterized by medium and low biological activity and biodiversity indices. The highest yield was found in winter wheat varieties such as Bellisa, Fidelius and Jantarka. The results of these analyses allows for a more complete characterization of the yield potential of the tested varieties and their suitability for cultivation in the conditions of organic farming, taking into account the biological activity of soils.

“Delineating bacterial community structure of rhizosphere metagenome from Kansal Forest”

Rhizosphere bacteria play crucial role in numerous biochemical and ecological processes ranging from biomass disintegration, mineralization, biological nitrogen fixation and de nitrification. The present investigation was carried out to delineate the microbial diversity of rhizosphere soil using metagenomic approach. Extraction of metagenomic DNA, PCR amplification and cloning of 16S rRNA genes resulted in library consisting of ~2000 clones. Sequencing of randomly selected 400 clones resulted in 352 unique sequences of 16S rRNA. Analysis of recovered sequences using BlastN (NCBI) revealed that ~47% of these sequences had uncultured representatives, uncultured Proteobacteria constituted ~8% of the total sequence diversity, uncultured acidobacteria comprised 5% of the total diversity among recovered clones. Other minor groups represent 2–5% of the total sequence diversity and include Bacillus and Pseudomonas . In addition, 1–2% of the total sequences also include uncultured Commensalibacter sp., Streptomyces sp., uncultured Gemmatimonadales , Halomonas (Gram-negative), uncultured Burkholderia sp., uncultured Pelomonas and other uncultured species. Phylogeny tree revealed that all sequence can be clustered into twelve main clusters indicating their diverse origin. Further clustering of these clones using QIIME resulted in 300 unique OTUs that constitutes 83.57% of the total sequence diversity, 52 clones were clustered as single OTU making a total 14.21%, while one sequence remain unclassified. At the Genus level, Bacillus, Pseudomonas and Staphylococcus demonstrated abundant presence in this soil. At species level Flavisolibacter tropicus of phylum Bacteriodetes showed maximum abundance followed by Bacillus cereus of phylum Firmicutes and Betaproteobacteria bacterium GR16-43 of phylum Proteobacteria.

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato

Microbial diversity in rhizosphere soil considered as important factors for agricultural productivity. Proteomic approach in Fusarium wilt infected and healthy rhizosphere soils of tomato provided the role of microbial protein involved for the development of disease as well as resistance. In this study, two different rhizosphere soils of tomato were collected analyzed through metaproteomic approach to determine the microbial protein abundance. The result of 2D-PAGE from both the soils revealed that, totally 11 differentially proteins were expressed and they were identified through MALDI-TOF. The identified proteins were originated from bacteria, fungus and plant. The functions of proteins showed that they were involved in resistance of tomato plant. Quantification of fungal pathogen inoculums from the both soils were formed by qPCR analysis. The result of qPCR analysis in soils revealed that Fusarium wilts infected soil contained more amount of Fungal ITS, Fusarium genus and F. oxysporum inoculums than healthy soils. Hence, our result suggests that due to the activity of beneficial microbial proteins in healthy soil, protected the tomato plants from wilt disease under the field conditons. Likewise, qPCR analysis clearly demonstrated the requirement of pathogen inoculums for the development of Fusarium wilt disease in tomato. Thus, the current study concludes that exploitation of microbial protein functions unravels the role of microbes including unculturable bacteria's for the development of resistance in plants against pathogens. In the other hand, early detection of pathogen by qPCR at minimal population level helps to develop management strategies before infection.