scholarly journals Linking Tree Health, Rhizosphere Physicochemical Properties, and Microbiome in Acute Oak Decline

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1153 ◽  
Author(s):  
Diogo Pinho ◽  
Cristina Barroso ◽  
Hugo Froufe ◽  
Nathan Brown ◽  
Elena Vanguelova ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Health Conditions ◽  
Soil Conditions ◽  
Oak Decline ◽  
Rhizosphere Ph ◽  
Microbial Composition ◽  
Tree Health ◽  
Microbiome Composition ◽  
Oak Trees ◽  
Rhizosphere Properties

Forest decline diseases are complex processes driven by biotic and abiotic factors. Although information about host–microbiome–environment interactions in agricultural systems is emerging rapidly, similar studies on tree health are still in their infancy. We used acute oak decline (AOD) as a model system to understand whether the rhizosphere physicochemical properties and microbiome are linked to tree health by studying these two factors in healthy and diseased trees located in three sites in different AOD stages—low, mid and severe. We found significant changes in the rhizosphere properties and microbiome composition across the different AOD sites and between the tree health conditions. Rhizosphere pH correlated with microbiome composition, with the microbial assemblages changing in more acidic soils. At the severe AOD site, the oak trees exhibited the lowest rhizosphere pH and distinct microbiome, regardless of their health condition, whereas, at the low and mid-stage AOD sites, only diseased trees showed lower pH and the microbial composition differed significantly from healthy trees. On these two sites, less extreme soil conditions and a high presence of host-beneficial microbiota were observed in the healthy oak trees. For the first time, this study gathers evidence of associations among tree health conditions, rhizosphere properties and microbiome as well as links aboveground tree decline symptoms to the belowground environment. This provides a baseline of rhizosphere community profiling of UK oak trees and paves the way for these associations to be investigated in other tree species suffering decline disease events.

scholarly journals Biochar and Rhizobacteria Amendments Improve Several Soil Properties and Bacterial Diversity

2020 ◽  
Vol 8 (4) ◽  
pp. 502
Author(s):  
Han Ren ◽  
Baoling Huang ◽  
Víctor Fernández-García ◽  
Jessica Miesel ◽  
Li Yan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Physicochemical Properties ◽  
Water Content ◽  
Soil Water ◽  
Soil Water Content ◽  
Community Composition ◽  
Soil Conditions ◽  
Microbial Composition ◽  
Total N ◽  
Total P

In the current context, there is a growing interest in reducing the use of chemical fertilizers and pesticides to promote ecological agriculture. The use of biochar and plant growth-promoting rhizobacteria (PGPR) is an environmentally friendly alternative that can improve soil conditions and increase ecosystem productivity. However, the effects of biochar and PGPR amendments on forest plantations are not well known. The aim of this study is to investigate the effects of biochar and PGPR applications on soil nutrients and bacterial community. To achieve this goal, we applied amendments of (i) biochar at 20 t hm−2, (ii) PGPR at 5 × 1010 CFU mL−1, and (iii) biochar at 20 t hm−2 + PGPR at 5 × 1010 CFU mL−1 in a eucalyptus seedling plantation in Guangxi, China. Three months after applying the amendments, we collected six soil samples from each treatment and from control plots. From each soil sample, we analyzed several physicochemical properties (pH, electrical conductivity, total N, inorganic N, NO3−-N, NH4+-N, total P, total K, and soil water content), and we determined the bacterial community composition by sequencing the ribosomal 16S rRNA. Results indicated that co-application of biochar and PGPR amendments significantly decreased concentrations of soil total P and NH4+-N, whereas they increased NO3-N, total K, and soil water content. Biochar and PGPR treatments increased the richness and diversity of soil bacteria and the relative abundance of specific bacterial taxa such as Actinobacteria, Gemmatimonadetes, and Cyanobacteria. In general, the microbial composition was similar in the two treatments with PGPR. We also found that soil physicochemical properties had no significant influence on the soil composition of bacterial phyla, but soil NH4+-N was significantly related to the soil community composition of dominant bacterial genus. Thus, our findings suggest that biochar and PGPR amendments could be useful to maintain soil sustainability in eucalyptus plantations.

scholarly journals Rhizosphere properties of maize genotypes with contrasting phosphorus efficiency

2011 ◽  
Vol 35 (1) ◽  
pp. 171-181
Author(s):  
Edilson Carvalho Brasil ◽  
Vera Maria Carvalho Alves ◽  
Ivanildo Evódio Marriel ◽  
Gilson Villaça Exel Pitta ◽  
Janice Guedes de Carvalho
Keyword(s):  
Functional Diversity ◽  
Root Hairs ◽  
Phosphorus Efficiency ◽  
Experimental Unit ◽  
Rhizosphere Ph ◽  
P Use Efficiency ◽  
Nodal Roots ◽  
Maize Genotypes ◽  
Use Efficiency ◽  
Rhizosphere Properties

An experiment was conducted in a growth chamber to evaluate characteristics of the rhizosphere of maize genotypes contrasting in P-use efficiency, by determining length and density of root hairs, the rhizosphere pH and the functional diversity of rhizosphere bacteria. A sample of a Red Oxisol was limed and fertilized with N, K and micronutrients. In the treatment with the highest P level, 174 mg kg-1 P was added. Each experimental unit corresponded to a PVC rhizobox filled with 2.2 dm-3 soil. The experiment was completely randomized with three replications in a 5 x 2 factorial design, corresponding to five genotypes (H1, H2 and H3 = P-efficient hybrids, H4 and H5 = P-inefficient hybrids) and two P levels (low = 3 mg dm-3, high = 29 mg dm-3). It was found that 18 days after transplanting, the nodal roots of the hybrids H3 and H2 had the longest root hairs. In general, the pH in the rhizosphere of the different genotypes was higher than in non-rhizosphere soil, irrespective of the P level. The pH was higher in the rhizosphere of lateral than of nodal roots. At low P levels, the pH variation of the hybrids H2, H4 and H5 was greater in rhizospheric than in non-rhizospheric soil. The functional microbial activity in the rhizosphere of the hybrids H3 and H5 was highest. At low soil P levels, the indices of microbial functional diversity were also higher. The microbial metabolic profile in the rhizosphere of hybrids H1, H2, H3, and H5 remained unaltered when the plants were grown at low P. The variations in the rhizosphere properties could not be related to patterns of P-use efficiency in the tested genotypes.

scholarly journals Influence of Tillage on the Mollisols Physicochemical Properties, Seed Emergence and Yield of Maize in Northeast China

Agriculture ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 939
Author(s):  
Qiang Chen ◽  
Xingyi Zhang ◽  
Li Sun ◽  
Jianhua Ren ◽  
Yaru Yuan ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Physicochemical Properties ◽  
Northeast China ◽  
Soil Structure ◽  
Aggregate Stability ◽  
Maize Yield ◽  
Conventional Tillage ◽  
Soil Conditions ◽  
Emergence Period

Tillage practices are critical for sustaining soil quality necessary for successful crop growth and productivity, but there are only few studies for strip tillage (ST) in the Mollisols region of Northeast China at present. A long-term (≥10-year) study was carried out to investigate the influence of within the tilled row (IR) and between rows (BR) in ST (10-year), conventional tillage (CT, 14-year) and no tillage (NT, 14-year) treatments on soil physicochemical properties. Soil samples were taken in May of 2019 at 0–5, 5–10, 10–20 and 20–30 cm depths and used to analyze bulk density (BD), soil aggregate distribution and stability, and soil organic carbon (SOC). Meanwhile, our study also explored the differences in seed emergence, soil moisture, and temperature during the seed emergence period, and yield of maize (Zea mays L.) among the different treatments. Similar soil properties were observed between ST-BR and NT, which showed they had a significantly greater BD, >0.25 mm water stable aggregate content (WR0.25) (especially in the amount of >2 mm and 1–2 mm size proportion), aggregate stability, and SOC than ST-IR and CT-IR at a depth of 0–20 cm. By improving soil conditions of seedbed, ST-IR and CT-IR increased soil temperature above NT by 1.64 °C and 1.80 °C, respectively, and ST-IR had a slight greater soil moisture than CT-IR in the top 10 cm layer during the seed emergence period. Late maize seed emergence was observed NT in than ST-IR and CT-IR and the average annual yields in ST were slightly greater than NT and CT, but the differences were not significant. Our results also showed that CT-BR had a poor soil structure and lower SOC than other treatments at 0–30 cm depth. We conclude from these long-term experimental results that ST could improve soil water-heat conditions to promote seed germination, maintain soil structure, and increase the maize yield and it should be applied in the Mollisols region of Northeast China.

Modulation of instinal microbiom in the formation and progression of ulterative colitis.

2020 ◽  
Vol 75 (6) ◽  
pp. 577-584
Author(s):  
G. R. Bikbavova ◽  
M. A. Livzan
Keyword(s):  
Ulcerative Colitis ◽  
Short Chain Fatty Acids ◽  
Intestinal Wall ◽  
Intestinal Microbiome ◽  
Industrial Society ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Available Information ◽  
Post Industrial

In recent decades, an increase in the incidence of ulcerative colitis has been observed throughout the world. The purpose of this review is to generalize the available information on the influence of environmental factors and intestinal microbiome on the occurrence and development of ulcerative colitis, the role of bacteria metabolism products in the pathogenesis of the disease. Studied literature, we came to the conclusion that lifestyle in the era of post-industrial society has a significant impact on the microbial composition of the intestine and leads to changes in its diversity in patients suffering from ulcerative colitis. The changes include a decrease in the number of residential flora with anti-inflammatory activity, which synthesize short-chain fatty acids, and an increase in the number of potentially pathogenic and pathogenic microorganisms. Within the phylums Firmicutes and Proteobacteria, the proportional ratio changes. The combination of aggression factors (deterioration of the intestinal microbiome composition, the presence of aggressive intestinal metabolites) leads to intestinal mucosa permeability disfunction, impairing its barrier function. Food and bacterial agents can penetrate deeper layers of the intestinal wall through mucosal defects, which then stimulate the development of inflammatory and immune responses.

scholarly journals The Effects of Glucosamine and Chondroitin Sulfate on Gut Microbial Composition: A Systematic Review of Evidence from Animal and Human Studies

Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 294 ◽  
Author(s):  
Anna Shmagel ◽  
Ryan Demmer ◽  
Daniel Knights ◽  
Mary Butler ◽  
Lisa Langsetmo ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gut Microbiota ◽  
Chondroitin Sulfate ◽  
Gut Microbiome ◽  
Human Studies ◽  
Journal Articles ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Search Terms ◽  
Quality Evidence

Oral glucosamine sulfate (GS) and chondroitin sulfate (CS), while widely marketed as joint-protective supplements, have limited intestinal absorption and are predominantly utilized by gut microbiota. Hence the effects of these supplements on the gut microbiome are of great interest, and may clarify their mode of action, or explain heterogeneity in therapeutic responses. We conducted a systematic review of animal and human studies reporting the effects of GS or CS on gut microbial composition. We searched MEDLINE, EMBASE, and Scopus databases for journal articles in English from database inception until July 2018, using search terms microbiome, microflora, intestinal microbiota/flora, gut microbiota/flora and glucosamine or chondroitin. Eight original articles reported the effects of GS or CS on microbiome composition in adult humans (four articles) or animals (four articles). Studies varied significantly in design, supplementation protocols, and microbiome assessment methods. There was moderate-quality evidence for an association between CS exposure and increased abundance of genus Bacteroides in the murine and human gut, and low-quality evidence for an association between CS exposure and an increase in Desulfovibrio piger species, an increase in Bacteroidales S24-7 family, and a decrease in Lactobacillus. We discuss the possible metabolic implications of these changes for the host. For GS, evidence of effects on gut microbiome was limited to one low-quality study. This review highlights the importance of considering the potential influence of oral CS supplements on gut microbiota when evaluating their effects and safety for the host.

scholarly journals Molecular Reconstruction of the Diet in Human Stool Samples

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Frank Maixner
Keyword(s):  
Human Subjects ◽  
Human Microbiome ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Diet Surveys ◽  
Dna Metabarcoding ◽  
Microbiome Research ◽  
Dietary Records ◽  
Stool Samples ◽  
Chloroplast Dna Markers

ABSTRACT Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition. The article by Reese et al. [A. T. Reese, T. R. Kartzinel, B. L. Petrone, P. J. Turnbaugh, et al., mSystems 4(5):e00458-19, 2019, https://doi.org/10.1128/mSystems.00458-19] in a recent issue of mSystems describes a DNA metabarcoding strategy targeting chloroplast DNA markers in stool samples from 11 human subjects consuming both controlled and freely selected diets. The aim of this study was to evaluate the efficiency of this molecular method in detecting plant remains in the sample compared to the written dietary records. This study displays an important first step in implementing molecular dietary reconstructions in stool microbiome studies which will finally help to increase the accuracy of dietary metadata.

scholarly journals Rethinking Invasion Impacts across Multiple Field Sites Using European Swallowwort (Vincetoxicum rossicum) as a Model Invader

2018 ◽  
Vol 11 (3) ◽  
pp. 109-116 ◽  
Author(s):  
Grant L. Thompson ◽  
Terrence H. Bell ◽  
Jenny Kao-Kniffin
Keyword(s):  
Enzyme Activities ◽  
New York State ◽  
Extracellular Enzyme ◽  
Growth Patterns ◽  
Soil Microbiome ◽  
Microbial Composition ◽  
Similar Time ◽  
Microbiome Composition ◽  
Extracellular Enzyme Activities ◽  
Vincetoxicum Rossicum

AbstractEuropean swallowwort [Vincetoxicum rossicum (Kleopow) Barbarich] is found in the northeastern United States and southeastern Canada. It forms dense growth patterns that reduce plant and insect biodiversity, and lab assays show that it produces allelopathic compounds that affect microbial activity. Consequently, we hypothesized that V. rossicum alters soil microbiome composition and activity in invaded habitats, which may impact ecosystem properties and processes. We sampled soil from a similar time point within a growing season at each of five sites in New York State where V. rossicum was both present and absent. We measured bacterial and fungal microbiome composition, available soil nitrogen (N), soil respiration (CO2 flux), and soil extracellular enzyme activities. Microbial composition varied across field sites, but only fungal composition was affected by invasion. No significant differences were found between the invaded and uninvaded plots at any of the sites for available soil ammonium, nitrate, or respiration, though extractable N varied greatly between sites. Microbial hydrolytic extracellular enzyme activities suggest decreased protein degradation and increased oxidative enzyme activity with V. rossicum invasion, which is relevant to soil N and carbon cycling processes. Although V. rossicum impacted rhizosphere microbial composition and activity, it was not associated with large perturbations in ecosystem function when examined across multiple invasion sites during this short-term study.

scholarly journals Phytophthora cinnamomi as a Contributor to White Oak Decline in Mid-Atlantic United States Forests

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 319-327 ◽  
Author(s):  
M. E. McConnell ◽  
Y. Balci
Keyword(s):  
United States ◽  
Fine Roots ◽  
Phytophthora Cinnamomi ◽  
United States Department ◽  
Oak Decline ◽  
White Oak ◽  
Phytophthora Spp ◽  
Oak Trees ◽  
Root Health ◽  
The Impact

To evaluate Phytophthora cinnamomi as a cause of white oak (Quercus alba) decline in mid-Atlantic forests, sampling was conducted at 102 sites from 2011 to 2012. Soil and roots from healthy and declining white oak trees were collected. Phytophthora spp. were isolated using baiting and CFU of P. cinnamomi quantified using wet-sieving. Fine roots were scanned and measured. Phytophthora spp. were isolated from 43% of the sites. P. cinnamomi was common; six other species were isolated infrequently. Little difference in lesion size existed on white oak seedlings inoculated with 32 isolates of P. cinnamomi; only 13 isolates caused significant mortality. Soils from white oak versus nine other hosts did not have significantly different CFU. P. cinnamomi was restricted to United States Department of Agriculture hardiness zones six and seven and never found in zone five. The presence of Phytophthora spp. in soil can be associated with white oak fine root health. When Phytophthora spp. were present, white oak trees in zones five and six had less fine roots. In mid-Atlantic oak forests, however, environmental conditions appear to play a key role in determining the impact of P. cinnamomi on the root system. P. cinnamomi alone does not appear to be a causal factor of white oak decline.

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