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

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2706
Author(s):  
Siyuan Ma ◽  
Yubin Lin ◽  
Yongqiang Qin ◽  
Xiaoping Diao ◽  
Peng Li
Keyword(s):  
Microbial Diversity ◽  
Developmental Stages ◽  
Rhizosphere Soil ◽  
Interaction Network ◽  
Illumina Miseq ◽  
Growth Stages ◽  
Dominant Group ◽  
Soil Microbial Diversity ◽  
Bacteria And Fungi ◽  
Stage T1

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

2021 ◽  
Vol 15 (5) ◽  
pp. 606-614
Author(s):  
Yanan Ruan ◽  
Shengguang Xu ◽  
Zuoxin Tang ◽  
Xiaolin Liu ◽  
Qirui Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Rhizosphere Soil ◽  
Principal Component ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Growth Stages ◽  
Soil Microbial Diversity ◽  
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.

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

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

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.

scholarly journals Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa

2021 ◽  
Author(s):  
Manoj Kaushal ◽  
Yao Kolombia ◽  
Amos Emitati Alakonya ◽  
Apollin Fotso Kuate ◽  
Alejandro Ortega-Beltran ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Smallholder Farmers ◽  
Central Africa ◽  
Illumina Miseq ◽  
Sub Saharan Africa ◽  
Plant Performance ◽  
Fungal Communities ◽  
Soil Microbial Diversity ◽  
Microbial Profile ◽  
Β Diversity

AbstractPlantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon–Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.

Rhizosphere soil affects pear fruit quality under rain-shelter cultivation

2020 ◽  
Vol 100 (6) ◽  
pp. 683-691
Author(s):  
Xiao-Ming Chen ◽  
Qi Zhang ◽  
Shao-Min Zeng ◽  
Yao Chen ◽  
Yong-Yan Guo ◽  
...  
Keyword(s):  
Carbon Source ◽  
Microbial Diversity ◽  
Open Field ◽  
Fruit Quality ◽  
Rhizosphere Soil ◽  
Soil Enzyme ◽  
Carbon Source Utilization ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Microbial Carbon

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 < 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 < 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.

scholarly journals Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes

2016 ◽  
Author(s):  
Andrew T. Nottingham ◽  
Noah Fierer ◽  
Benjamin L. Turner ◽  
Jeanette Whitaker ◽  
Nick J. Ostle ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Tropical Forest ◽  
Soil Ph ◽  
Soil Bacteria ◽  
Environmental Drivers ◽  
Future Climate Change ◽  
Soil Microbial Diversity ◽  
Tropical Mountains ◽  
Bacteria And Fungi

SummaryMore than 200 years ago, von Humboldt reported decreases in tropical plant species richness with increasing elevation and decreasing temperature. Surprisingly, co-ordinated patterns in plant, bacterial and fungal diversity on tropical mountains are yet to be observed, despite the central role of soil microorganisms in terrestrial biogeochemistry. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria and fungi can follow similar biogeographical patterns with shared environmental drivers. We found co-ordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional-dissimilarity of communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of co-ordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi and plants. These findings suggest that, across landscape scales of relatively constant soil pH, inter-related patterns of plant and microbial communities with shared environmental drivers can occur, with large implications for tropical forest communities under future climate change.

scholarly journals Microbial Structure and Diversity in Rhizosphere Soil under Different Forest Types in the Subtropical Zone of China

2021 ◽  
Author(s):  
Liuting Zhou ◽  
Jianjuan Li ◽  
Chen Zhang ◽  
Xinlai Guo ◽  
Wei Chu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Nutrients ◽  
Soil Microbial Community ◽  
Rhizosphere Soil ◽  
Forest Types ◽  
Soil Microbial Diversity ◽  
Subtropical Zone ◽  
Soil Microbial

Abstract The aim of this study was to explore the soil microbial variability within different forest ecosystems (evergreen broad-leaf forest (EBF), coniferous forest (CF), subalpine dwarf forest (SDF) and alpine meadow (AM) at different altitudes in mid-subtropics of China. The phospholipid fatty acid (PLFA) method was used to analyze the microbial communities in rhizosphere soil under different forest types. The relationships were also analyzed between the microbial diversity and soil nutrients. A total of 27 PLFA biomarkers were detected and the PLFA concentrations decreased in the sequence of bacteria > fungus > actinomycete > protozoa in all forest types. The microbial communities in the soil under all forest types were distinct. The predominant microflora in all soils were 18:1ω9c, 16:1ω7c, cy19:0, a17:0 and 18:0. The indexes of Simpson, Shannon-Wiener and Brillouin of soil microbial community diversity in these four forest types all showed a trend of EBF > CF > SDF > AM. According to principal component analyses (PCA), the variable variances of principal components 1 and 2, which were related to the PLFA biomarkers of soil microorganisms, were 67.67% and 17.91%, respectively. Furthermore, the total PLFAs of different soil microbial groups showed a correlation with soil nutrients and enzyme activities in all forest types. The soil microbial diversity gradually decreased in the order of EBF > CF > SDF > AM in the Daiyun Mountains. Different vegetation types affect soil microbial community composition and diversity by changing the soil physicochemical properties and enzyme activity.

scholarly journals The influence of genetically modified glyphosate-tolerant maize CC-2 on rhizosphere bacterial communities revealed by MiSeq sequencing

2020 ◽  
Vol 66 (No. 8) ◽  
pp. 387-394
Author(s):  
Xiaoli Zhou ◽  
Jingang Liang ◽  
Ying Luan ◽  
Xinyuan Song ◽  
Zhengguang Zhang
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Rhizosphere Soil ◽  
Genetically Modified ◽  
Economic Benefits ◽  
Growth Stages ◽  
Safety Issues

Genetically modified (GM) crops have brought huge economic benefits to mankind, however, at the same time, their safety issues are drawing growing attention. This investigation was conducted to assess whether the long-term cultivation of GM glyphosate resistant maize CC-2 effects bacterial communities in the rhizosphere soil. A 2-year follow-up trial was conducted, and soils were sampled at various plant developmental stages. The bacterial community structure of the rhizosphere soil was analysed by the high-throughput sequencing and compared with the near-isogenic non-GM maize Zheng 58. We showed here that long-term cultivation of CC-2 has no significant effect on the structure and diversity of bacterial communities, while different growth stages had significant effect. These results provided a reliable theoretical basis for the future cultivation and increased commercialisation of CC-2.  

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

2020 ◽  
Vol 11 ◽  
Author(s):  
Ke Dang ◽  
Xiangwei Gong ◽  
Guan Zhao ◽  
Honglu Wang ◽  
Aliaksandr Ivanistau ◽  
...  
Keyword(s):  
Grain Yield ◽  
Microbial Diversity ◽  
Mung Bean ◽  
Rhizosphere Soil ◽  
Potential Mechanism ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Proso Millet ◽  
N Assimilation

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.

scholarly journals Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation

2021 ◽  
Vol 9 (1) ◽  
pp. 100
Author(s):  
Alba C. Mayta-Apaza ◽  
Israel García-Cano ◽  
Konrad Dabrowski ◽  
Rafael Jiménez-Flores
Keyword(s):  
Microbial Diversity ◽  
Microbial Ecology ◽  
Illumina Miseq ◽  
Human Consumption ◽  
Fish Waste ◽  
Alpha And Beta Diversity ◽  
Analysis And Evaluation ◽  
Dynamic Variations ◽  
Acid Whey ◽  
By Products

The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.

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