scholarly journals Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Jia ◽  
Xiao Chang ◽  
Yuanyuan Fu ◽  
Wei Heng ◽  
Zhenfeng Ye ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Rhizosphere Soil ◽  
Bacterial Species ◽  
Distribution Patterns ◽  
Fe Deficiency ◽  
Mineral Concentration ◽  
Iron Deficiency Chlorosis ◽  
Soil Aeration ◽  
Rhizosphere Soils ◽  
Asian Pear

Abstract Background Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. Results The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. Conclusions It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.

scholarly journals Metagenomic Analysis of Rhizosphere Microbiome Provides Insights Into Occurrence of Iron Deficiency Chlorosis in Field of Asian Pears

2020 ◽  
Author(s):  
Bing Jia ◽  
Xiao Chang ◽  
Yuanyuan Fu ◽  
Wei Heng ◽  
Zhenfeng Ye ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Rhizosphere Soil ◽  
Bacterial Species ◽  
Distribution Patterns ◽  
Fe Deficiency ◽  
Mineral Concentration ◽  
Iron Deficiency Chlorosis ◽  
Rhizosphere Soils ◽  
Leaf Chlorosis ◽  
Inhibit Root Growth

Abstract Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the bacterial biogeography in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution have been analyzed. The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Water-impermeable tables reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. The rhizosphere soils of FDC plants have distinct composition, lower relative abundance, and unstable diversity of microbiome. Higher amounts of AFe in the rhizosphere soil of chlorotic plants demonstrated it was the Fe uptake that caused FDC in this study.

scholarly journals Effects of continuous cropping of Pinellia ternata (Thunb.) Breit. on soil physicochemical properties, enzyme activities, microbial communities and functional genes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yuan Zhao ◽  
Xiao–Meng Qin ◽  
Xue–Ping Tian ◽  
Tao Yang ◽  
Rong Deng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Soil Fertility ◽  
Phenolic Acids ◽  
Relative Abundance ◽  
Enzyme Activities ◽  
Rhizosphere Soil ◽  
Functional Genes ◽  
Continuous Cropping ◽  
Pinellia Ternata

Abstract Background Pinellia ternata (Thunb.) Breit. is a commonly used herb in traditional Chinese medicine, and the main raw material of various Chinese patent medicines. Continuous cropping obstacle (CCO) is the main factor leading to the decline of crop yields and quality. Methods Metagenomics sequencing technology was used to analyze the microbial community and functional genes of continuous cropping (CC) and control (CK) soils of P. ternata. In addition, differences in physicochemical properties, enzyme activities, microbial community composition and the abundance of functional genes in CC and CK were evaluated, as well as the relationship between these factors and CCO. Results Results indicated that CC of P. ternata led to the decline of rhizosphere soil pH, nutrient imbalance and enzyme activity reduction. Metagenomic analysis indicted that CC also changed the composition of the microbial community, causing an increase in the relative abundance of pathogenic microorganisms such as Fusarium, Klebsiella oxytoca and Pectobacterium carotovorum in the P. ternata rhizosphere. The relative abundance of potentially beneficial Burkholderia and Bradyrhizobium was recorded to decrease. Results also showed that there were considerable differences in CC and CK about the abundances of functional genes related to soil enzymes and the degradation of P. ternata allelochemicals, as well as the microbial groups which they belong. These results clarified the effects of CC on the microbial community structure and functional genes of soil. In addition, Burkholderia and Bradyrhizobium might play important roles in enhancing soil fertility and reducing the toxicity of phenolic acids in rhizosphere soil. Conclusions CC of P. ternata changed the physicochemical properties, microbial community and functional genes of rhizosphere soil. Burkholderia and Bradyrhizobium for enhancing soil fertility and reducing the toxicity of phenolic acids might be potentially beneficial. These results provide theoretical guidance for bioremediation of CCO soil of P. ternata and other staple crops. Graphic abstract

Association of the anorectal microbiome and patient-reported gastrointestinal outcomes in patients with anal cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15504-e15504
Author(s):  
Ramez Kouzy ◽  
Daniel Lin ◽  
Molly Blue El Alam ◽  
Joseph Abi Jaoude ◽  
Grace L. Smith ◽  
...  
Keyword(s):  
Anal Cancer ◽  
Relative Abundance ◽  
Effect Size ◽  
Bacterial Species ◽  
Alpha Diversity ◽  
Standard Of Care ◽  
Wilcoxon Test ◽  
Linear Discriminant ◽  
End Of Treatment ◽  
Patient Reported

e15504 Background: Among patients with anal cancer undergoing chemoradiotherapy, the association between the microbiome and toxicity is not well documented. We sought to quantify the gastrointestinal-related patient-reported outcomes (PROs) and local microbiome profiles of patients with anal cancer receiving chemoradiotherapy in order to check for potential profiles that can help in predicting toxicity during treatment. Methods: We prospectively followed patients with non-metastatic squamous cell carcinoma of the anal canal who received definitive chemoradiotherapy. Anorectal swab samples were collected before treatment initiation and at 4 subsequent timepoints. Consequently, PROs were collected using the bowel subdomain of the Expanded Prostate Cancer Index Composite (EPIC). Samples were sequenced using 16S rRNA of the V4 region. Sequence reads were grouped by amplicon sequence variants (ASV’s) representative of unique bacterial species. We then used Linear discriminant analysis Effect Size (LEfSe) with an effect size of 4 to identify taxa at baseline that were differentially enriched in patients with high vs. low toxicity by end of treatment. We compared the EPIC scores with the relative abundance of species identified in the LEfSe using a paired Wilcoxon test. Results: The study included 22 patients (18 women and 4 men), whose median age was 59 years. Most patients were Stage III (59%) with negative HIV status (94%). The majority of patients (91%) received standard of care chemoradiotherapy. Overall toxicity was the highest at week 5 of treatment. At all individual time points, alpha diversity of the microbiome did not correlate with patient-reported GI function, additionally overall baseline diversity was not predictive of eventual GI outcomes. The LEfSe identified that patients with low patient reported toxicity at week 5 had higher of abundance of Selenomonas at baseline, while patients with higher toxicity had high abundance of baseline Actinobacteria, Peptoniphilus, Clostridiales , and Clostridia. When comparing the relative abundance of bacterial species among patients with high and low toxicities, patients with higher relative abundance of Clostridia and Actinobacteria had significantly higher toxicity (p = 0.03). Conclusions: Certain microbiome profiles at baseline are associated with anal cancer patients’ gastrointestinal-related PROs during chemoradiation. Our data provide novel avenues to study the potential uses of the local microbiome as a biomarker in predicting treatment toxicities in anal cancer.

Mega- and meta-analyses of fecal metagenomic studies in predicting response to immune checkpoint inhibitors.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 2570-2570
Author(s):  
Alya Heirali ◽  
Bo Chen ◽  
Matthew Wong ◽  
Pierre H.H. Schneeberger ◽  
Victor Rey ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Immune Checkpoint ◽  
Statistical Power ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Bacterial Species ◽  
Metagenomic Data ◽  
Tumor Type ◽  
Meta Analyses ◽  
Clostridium Bolteae

2570 Background: A number of studies have demonstrated that the gut microbiome of responders to immune checkpoint inhibitors (ICI) is compositionally different compared to that of non-responders. However, differences in study design, patient cohorts and bioinformatic analyses make it challenging to identify bacterial species consistently associated with response to ICI across different cohorts and cancer types. Methods: We leveraged the statistical power of mega- and meta-analyses to identify bacterial species consistently associated with response to ICI using data from three published fecal metagenomic studies (Gopalakrishnan et al., Science 2018; Matson et al., Science 2018; Routy et al., Science 2018). Metagenomic data was uniformly processed and analyzed using Metaphlan v2.0. We conducted a two-part modelling approach of bacterial species present in at least 20% of samples to account for both prevalence and relative abundance differences between responders/non-responders. Results: A total of 190 patients (n = 103 responders; n = 87 non-responders) were included from the three studies. Data from Routy et al., was analyzed as subsets based on tumor type for a total of 4 analyzed cohorts. We identified five species including Bacteroides thetaiotaomicron, Clostridium bolteae, Holdemania filiformis, Clostridiaceae bacterium JC118 and Escherichia coli that were concordantly significantly different between responders and non-responders using both meta- and mega-analyses. B. thetaiotaomicron and Clostridium bolteae relative abundance (RA) were independently predictive of non-response to immunotherapy when data sets were combined and analyzed using mega-analyses (AUC 0.59 95% CI 0.51-0.68 and AUC 0.61 95% CI 0.52-0.69, respectively). Conclusions: Despite inter-cohort heterogeneity in tumor type, treatment regimens, and sequencing modalities, meta- and mega analysis of published metagenomic studies identified generalizable bacterial species associated with ICI response or lack thereof. B. thetaiotaomicron and C. bolteae were predictors of non-response to ICI suggesting the clinical potential of narrow spectrum anti-biotics targeting non-response associated bacterial species to improve outcomes in ICI recipients.

Occurrence of Fusarium spp. associated with root tissues and rhizosphere soils of forest trees and assessment of their pathogenicity on Prunus amygdalus seedlings

2010 ◽  
Vol 58 (8) ◽  
pp. 679 ◽  
Author(s):  
K. Chehri ◽  
B. Salleh ◽  
M. J. Soleimani ◽  
K. R. N. Reddy ◽  
L. Zakaria
Keyword(s):  
Rhizosphere Soil ◽  
Morphological Characteristics ◽  
Soil Samples ◽  
Forest Trees ◽  
Prunus Amygdalus ◽  
Fusarium Spp ◽  
The West ◽  
Rhizosphere Soils ◽  
Climatic Regions ◽  
Root Tissues

Occurrence, distribution and pathogenicity of Fusarium spp. associated with roots and rhizosphere soils of forest trees were studied. Fusarium spp. was isolated from phloem and sapwood of forest trees and composite rhizosphere soil samples collected from highly diversified geographical and climatic regions of the west of Iran and identified based on their morphological characteristics. Only three Fusarium spp. (F. oxysporum, F. solani and F. eumartii) was isolated from roots. F. nygamai, F. graminearum, F. scirpi, F. proliferatum, F. anthophilum, F. longipes and F. chlamydosporum were recovered from soil samples collected from warm and moderately warm regions, while F. culmorum, F. sporotrichioides, F. sambucinum and F. subglutinans were recovered from cold regions. F. solani, F. oxysporum, F. semitectum, F. equiseti, F. verticillioides, F. merismoides and F. avenaceum were present in all climatic regions. In the bark inoculation tests, selected Fusarium strains representing all species were evaluated for their pathogenicity on stems of healthy Prunus amygdalus under greenhouse conditions. Stem rot assessment revealed that F. oxysporum, F. solani and F. eumartii were the most damaging species.

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

2020 ◽  
Vol 71 (12) ◽  
pp. 1702
Author(s):  
Baohua Zhou ◽  
Zhaowen Liu ◽  
Guo Yang ◽  
Hui He ◽  
Haijun Liu
Keyword(s):  
Invasive Species ◽  
Rhizosphere Soil ◽  
Remote Sensing Data ◽  
Wetland Loss ◽  
Freshwater Wetlands ◽  
Total Carbon ◽  
Freshwater Wetland ◽  
Available Nitrogen ◽  
Zizania Latifolia ◽  
Rhizosphere Soils

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.

Relative efficiency of rhizobacteria for auxin biosynthesis in rhizosphere and non-rhizosphere soils

Soil Research ◽  
2004 ◽  
Vol 42 (8) ◽  
pp. 921 ◽  
Author(s):  
Azeem Khalid ◽  
Shermeen Tahir ◽  
Muhammad Arshad ◽  
Zahir Ahmad Zahir
Keyword(s):  
High Performance ◽  
Indole Acetic Acid ◽  
Microbial Population ◽  
Rhizosphere Soil ◽  
Root Exudation ◽  
Auxin Biosynthesis ◽  
Rhizosphere Soils ◽  
Auxin Synthesis ◽  
Plant Crop

Biosynthesis of auxins in the rhizosphere of different crops may vary because of quantitative and qualitative variations in microbial population and root exudation. A laboratory study was conducted to assess in vitro auxin biosynthesis, and biosynthesis in rhizosphere and non-rhizosphere soils of different crops (maize, sorghum, mungbean, cotton). Soils were inoculated with selected rhizobacteria with and without the auxin precursor L-tryptophan (L-TRP). Auxins were detected by colourimetry as indole acetic acid equivalents and confirmed by high performance liquid chromatography. Results revealed that 83% of the 60 rhizobacteria were capable of producing auxins in the absence of L-TRP. Auxin biosynthesis by the 8 most efficient rhizobacteria ranged from 5.0 to 12.1 mg/L broth medium. A comparison of rhizosphere v. non-rhizosphere soils indicated a greater accumulation of auxins in the rhizosphere soils than non-rhizosphere soils. Overall, inoculation of rhizosphere soils with selected rhizobacteria resulted in greater production of auxin (up to 10.4 mg/kg soil) than in inoculated non-rhizosphere soils (up to 5.76 mg/kg). Moreover, efficiency of these rhizobacteria for auxin biosynthesis in both rhizosphere and non-rhizosphere soils differed with crop and bacterial strain. Some rhizobacterial strains exhibited superiority over the indigenous microflora for auxin biosynthesis in soil. Application of L-TRP promoted auxin biosynthesis in both rhizosphere and non-rhizosphere soils. These findings imply that inoculation with suitable strains and/or amendment with L-TRP could promote auxin synthesis in the rhizosphere soil of a given crop, which may have consequences for better plant/crop growth.

scholarly journals Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michael J. LaMonte ◽  
Robert J. Genco ◽  
Michael J. Buck ◽  
Daniel I. McSkimming ◽  
Lu Li ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Relative Abundance ◽  
Multiple Testing ◽  
Statistical Significance ◽  
Bacterial Species ◽  
Age Groups ◽  
Later Life ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Age Range

Abstract Background The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood. Methods The 16S rRNA gene of subgingival plaque in 1219 women, aged 53–81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method. Results Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = − 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50–59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older. Conclusions We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.

Corrigendum to: Distribution and relative abundance of forest duikers in Dassioko Sud Forest Reserve (coastal Côte d'Ivoire)

2018 ◽  
Vol 45 (2) ◽  
pp. 194
Author(s):  
K. A. Yao ◽  
E. A. Bitty ◽  
K. B. Kassé ◽  
Y. C. Kouakou ◽  
K. H. Yaokokoré-Beibro ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Habitat Preferences ◽  
Habitat Type ◽  
Distribution Patterns ◽  
Encounter Rate ◽  
Line Transect ◽  
Habitat Types ◽  
Anthropogenic Pressures ◽  
Forest Reserve ◽  
Encounter Rates

Context Duikers play a vital role in maintaining forest ecosystems, as both seed dispersers and prey. In West Africa, duikers are also an important source of food and income; however, it is likely that some species are now being hunted at unsustainable levels. So as to contribute to duiker conservation, we used line-transect data and additional information on dung and track counts to estimate relative abundance and establish distribution patterns of forest duikers in Côte d'Ivoire's Dassioko Sud Forest Reserve (DSFR), a poorly known, remnant coastal rainforest. We also collected basic information on hunting pressure. Methods Forest duiker counts were made twice per month from July 2013 to March 2014 on six line transects of varying lengths (5.6–6.7km) and in different regions of the DSFR, representing different habitat types. The number of sightings per kilometre walked, defined as ‘encounter rate', was used to compute an index of relative abundance. We recorded all evidence of poachers and used these data to generate a poaching index (# poaching signs per kilometre) for different habitat types. Key results The DSFR has lost three of seven total forest duiker species and populations of the four remaining species are declining. Encounter rates were greatest for Philantomba maxwellii (0.46 indices km–1) and accounted for 68% of total encounters. Cephalophus niger, C. dorsalis and C. silvicultor were encountered at similar (0.07 indices km–1) but much lower rates. For all species, mean encounter rates were highest in degraded forest (0.38–0.73 indices km–1), followed by secondary (0.2–0.44 indices km–1) and primary (0.19–0.44 indices km–1) forest. Conclusions Of the four forest duiker species still present in the DSFR, the black, bay and yellow-backed duikers are the most affected by anthropogenic pressures. Duiker abundance in the DSFR varies with habitat type. This variation is apparently influenced by differences in forest structure, poaching pressure and proximity to villages. Implications The study provides baseline data for future managing of ungulate populations in the DSFR. We recommend that a biomonitoring study of duiker populations be initiated immediately to help determine population trends, investigate habitat preferences, and help curb illegal hunting activities in this important forest reserve.

MANOMETRIC STUDIES WITH RHIZOSPHERE AND NON-RHIZOSPHERE SOIL

1957 ◽  
Vol 3 (5) ◽  
pp. 673-678 ◽  
Author(s):  
H. Katznelson ◽  
J. W. Rouatt
Keyword(s):  
Amino Acids ◽  
Oxygen Consumption ◽  
Oxygen Uptake ◽  
Organic Acids ◽  
Metabolic Activity ◽  
Rhizosphere Soil ◽  
Rhizosphere Soils ◽  
Manometric Studies ◽  
Casamino Acids

Manometric studies were carried out on the metabolic activity of different rhizosphere and non-rhizosphere soils from the greenhouse and the field. Oxygen consumption was distinctly greater with the rhizosphere soils. On the addition of substrates such as casamino acids or a mixture of carbohydrates and organic acids, greater oxygen uptake again occurred with the rhizosphere soils and was particularly striking with the amino acids. Chromatographic studies of extracts of rhizosphere and non-rhizosphere soil incubated with casamino acids suggested that certain amino acids such as arginine, proline, and tyrosine may be preferentially utilized in the rhizosphere.

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