Tomato endophyte bacteria diversity under long-term organic agricultural manipulation systems

Abstract Purpose: Differences were observed in both microbial structure and physicochemical properties were observed in the organic and conventional agricultural systems. However, very little is known about the diversity of endophytic bacterial communities in plants grown in separate manipulation systems. The goal of this work was to get a broader overview of the diversity and dynamics of the tomato endophytic bacteria in the different agricultural manipulation systems.Methods: The structure of endophyte bacterial communities under different growth periods (seeding stage, flowering stage, fruiting stage and harvesting stage), agricultural manipulation practices (organic and conventional systems) and organ-type (root or stem) were explored by using 16Sr RNA gene profiling in this study.Results: A total of 2,014,992 part 16 SRRNA gene sequences were obtained. These sequences revealed large-scale functional taxonomy units (OTUs). That is, there are 648 different OTUS in libraries, and 96 OTUs are common. Tomato endophytes consisted mainly of four phylloxera, of which Proteobacteria was the most represented, followed by Formigiotes, bacteriophages, Actinobacteria, Gamma proteobacteria, the most abundant class of proteobacteria, bacteriobacteria, and so on. Proteobacteria are low. General enterobacteriaceae, Vecella, Bacillus, Mesorizobium and Chrysobacterium were shared by all growth periods. Rich endophytic bacterial diversity was observed at the seedling stage (DI), and endophytic bacterial diversity at the flowering stage and fruiting stage was low. Significant difference in endophytic bacterial communities emerged from roots and different host biographical stages, and tomato exerts greater influence on endophyte bacteria compared to organ type (main) agricultural manipulation methods.Conclusions: Tomato endophyte microbiota have a distinct structure in different growth periods. Bacillus were enriched seeding stage and decreased in the fruiting stage while Mesorhizobium increased during in the fruiting stage. Tomato have distinct endosphere microbiota by comparing beta diversity of microbiota in different growth periods, compared with the manipulation resume and organ type. And a strong correlation was observed between the structure of the microbiota in the whole dataset and soil chemistry which indicated that the soil type and treatment affected the endosphere microbiota of tomato. Organ-type (niche) exert more influence on the tomato microbiota compared with manipulation treatments between organic-farming and conventional farming.

Download Full-text

Revealing the Tomato Endophyte Bacteria Communities Under Long-term Organic and Conventional Agricultural Practice System

10.21203/rs.3.rs-432178/v1 ◽

2021 ◽

Author(s):

Zeyu Zhang ◽

Yabin Zhan ◽

Zengqiang Zhang ◽

Youzhou Liu ◽

Ting Xu ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Plant Development ◽

Bacterial Communities ◽

Development Stage ◽

Rrna Gene ◽

Agricultural Practice ◽

Flowering Stage ◽

Organ Type ◽

Fruiting Stage

Abstract Purpose: Microorganisms associated with the plant can contribute to plant health. Discrepancy both soil microbial structure and physicochemical properties observed in the organic and conventional agricultural systems. However, very little is known about the diversity of endophytic bacterial communities in plants grown in separate manipulation systems. The goal of this work was to get a broader overview of the diversity and dynamics of the tomato endophytic bacteria in the different agricultural practice systems.Methods: The structure of tomato endophyte bacterial communities under different growing stage (seeding stage, flowering stage, fruiting stage and harvesting stage), agricultural manipulation practices (organic and conventional systems) and organ-type (root or stem) were explored by using 16S rRNA gene profiling in this study.Results: A total of 2,014,992 16S rRNA gene sequences were obtained. These sequences revealed large-scale functional taxonomy units (OTUs). That is, there are 648 different OTUs in libraries, and 96 OTUs are common. Tomato endophyte bacteria consisted mainly of four phyllum, of which Proteobacteria was the most represented, followed by Firmcutes, Bacteroides, Actinobacteria, Gamma proteobacteria, the most abundant class are proteobacteria, bacteriobacteria, and so on. Proteobacteria are low. Enterobacteriaceae, Vecella, Bacillus, Mesorizobium and Chrysobacterium were shared by all plant development stage. Rich endophytic bacterial diversity was observed at the seedling stage（TI）, and endophytic bacterial diversity at the flowering stage （T2）and fruiting stage （T4）was low. Significant difference in endophytic bacterial communities emerged from roots and different host biographical stages, and tomato exerts greater influence on endophyte bacteria compared to organ type (main) agricultural manipulation methods.Conclusions: Tomato endophyte microbiota have a distinct structure in different plant development stage. Bacillus.spp were enriched seeding stage (TI) and decreased in the fruiting stage while Mesorhizobium.spp increased during in the fruiting stage(T4). Tomato have distinct endosphere microbiota by comparing beta diversity of microbiota in all crop season, compared with the manipulation resume and organ niche. And a strong correlation was observed between the structure of the microbiota in the whole dataset and soil chemistry which indicated that the soil type and treatment affected the endosphere microbiota of tomato. Organ niche exert more influence on the tomato microbiota compared with agricultural treatments between organic-farming and conventional farming.

Download Full-text

Evaluation of Bacterial Diversity and Quality Features of Traditional Sichuan Bacon from Different Geographical Region

Applied Sciences ◽

10.3390/app11209738 ◽

2021 ◽

Vol 11 (20) ◽

pp. 9738

Author(s):

Song Wang ◽

Xingjie Wang ◽

Wanshu Pan ◽

Aiping Liu ◽

Shuliang Liu ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Physicochemical Characteristics ◽

Geographical Regions ◽

Significant Difference ◽

Geographic Regions ◽

Shared Otus ◽

Nitrite Content

Sichuan bacon is one of the most popular types of Chinese bacon in the domestic market. High-throughput sequencing was used to characterize the bacterial diversity of 39 Sichuan bacon samples collected from 3 geographical regions. The results showed that the bacterial diversity of Sichuan bacon in different regions demonstrated certain specificity as well as similarity, and the shared OTUs were close to 81% of the total number in the basin group, mountain group, and plateau group. At the genus level, Staphylococcus is the most dominant genus among the three groups, covering 26.7%, 20.6%, and 22.7%, respectively. Beta diversity shows significant differences in bacterial compositions in different geographic regions, especially for Pseudomonas, Brochothrix, Lactobacillus, Lactococcus, and Enterococcus. Meanwhile, some physicochemical characteristics were analyzed, and a significant difference (p < 0.05) among the three regions was shown in the Aw, pH, and nitrite content, which were significantly correlated with undesired bacteria. This study provides insights into the understanding of the role of bacterial communities in the microbial safety and quality improvement of Sichuan bacon.

Download Full-text

Global Comparison of the Bacterial Communities of Bilge Water, Boat Surfaces, and External Port Water

Applied and Environmental Microbiology ◽

10.1128/aem.01804-19 ◽

2019 ◽

Vol 85 (24) ◽

Cited By ~ 2

Author(s):

Laura G. Schaerer ◽

Ryan B. Ghannam ◽

Timothy M. Butler ◽

Stephen M. Techtmann

Keyword(s):

Invasive Species ◽

Microbial Community ◽

Microbial Communities ◽

Bacterial Communities ◽

Large Scale ◽

Water Discharge ◽

Global Comparison ◽

Bilge Water ◽

Significant Difference ◽

The World

ABSTRACT In the past, ballast water has been a key vector in the ship-mediated dispersal of invasive species. Here, we evaluate the potential for port microorganisms to enter and colonize the hull and bilge water of ships. Due to the small size and ubiquitous nature of bacteria, they also have the potential to be spread through hull fouling and bilge water discharge. The goal of this study was to identify the extent to which the boat microbial community is shaped by the microbial community in the port water where the boat spends most of its time. Here, we compared the microbial communities of the hull and bilge compartments of 20 boats to those of the port water in 20 different ports in five regions around the world. We found that there was a significant difference in microbial diversity between boat and port microbial communities. Despite these differences, we found that Cyanobacteria were present at high abundances in the bilge water of most vessels. Due to the limited light in the bilge, the presence of Cyanobacteria suggests that port microorganisms can enter the bilge. Using source-tracking software, we found that, on average, 40% of the bilge and 52% of the hull microbial communities were derived from water. These findings suggest that the bilge of a vessel contains a diverse microbial community that is influenced by the port microbial community and has the potential to serve as an underappreciated vector for dispersal of life. IMPORTANCE Invasive species have been a worldwide problem for many years. However, the potential for microorganisms to become invasive is relatively underexplored. As the tools to study bacterial communities become more affordable, we are able to perform large-scale studies and examine bacterial communities in higher resolution than was previously practical. This study looked at the potential for bacteria to colonize both boat surfaces and bilge water. We describe the bacterial communities on boats in 20 shipping ports in five regions around the world, describing how these microorganisms were similar to microorganisms found in port water. This suggests that the water influences the bacterial community of a boat and that microorganisms living on a boat could be moved from place to place when the boat travels.

Download Full-text

Bacterial diversity associated with subalpine fir (Abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central British Columbia

Canadian Journal of Microbiology ◽

10.1139/w02-056 ◽

2002 ◽

Vol 48 (7) ◽

pp. 611-625 ◽

Cited By ~ 18

Author(s):

Madhukar B Khetmalas ◽

Keith N Egger ◽

Hugues B Massicotte ◽

Linda E Tackaberry ◽

M Jill Clapperton

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Bacterial Communities ◽

Restriction Analysis ◽

Rrna Gene ◽

Abies Lasiocarpa ◽

Gram Positive ◽

Salvage Logging ◽

Gram Positive Bacteria ◽

Significant Difference

To assess the effect of fire and salvage logging on the diversity of mycorrhizalbacterial communities, bacteria associated with Cenococcum, Thelephora, Tomentella, Russulaceae, and E-strain ectomycorrhizae (ECM) of Abies lasiocarpa seedlings were characterized using two approaches. First, bacteria were isolated and characterized by Biolog©, gas chromatography fatty acid methyl ester (GC-FAME), and amplified 16S rDNA restriction analysis (ARDRA). The bacterial communities retrieved from ECM from both sites were dominated by Proteobacteria (groups gamma and beta). Pseudomonas was the most common genus isolated, followed by Variovorax, Burkholderia, and Xanthomonas. Gram-positive isolates (mostly high-G+C Gram-positive bacteria) were more frequently retrieved on the burned-salvaged site, many commonly associated with the two ascomycete ECM, Cenococcum and E-strain. Pseudomonas species were retrieved more frequently from Thelephora. Although actinomycetes were isolated from all sites, almost no actinomycetes or other Gram-positive bacteria were isolated from either Thelephora or Tomentella. Second, amplified 16S rRNA gene sequences were amplified directly from root tips and then cloned into the plasmid vector pAMP1, followed by restriction analysis. This technique distinguished more genotypes than isolates retrieved by culturing methods, but generally, results were similar in that the largest proportion of the bacteria were putatively Gram-negative; putative Gram-positive bacteria were fewer and most were from the burnedsalvaged site. Direct cloning resulted in many patterns that did not match any identified isolates, suggesting that a large proportion of clones were unique or not culturable by the methods used. Analysis for both protocols showed no significant difference in bacterial diversity between the burnedsalvaged and unburned sites. Key words: rhizosphere bacteria, ARDRA, 16S rDNA, Biolog©, GC-FAME.

Download Full-text

Effects of Imazapyr on Spartina alterniflora and Soil Bacterial Communities in a Mangrove Wetland

Water ◽

10.3390/w13223277 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3277

Author(s):

Xue Mo ◽

Panpan Dong ◽

Lumeng Xie ◽

Yujiao Xiu ◽

Yanqi Wang ◽

...

Keyword(s):

Bacterial Diversity ◽

Spartina Alterniflora ◽

Bacterial Communities ◽

Available Phosphorus ◽

Soil Bacterial Diversity ◽

Factors Affecting ◽

Soil Bacterial Communities ◽

Mangrove Wetland ◽

Significant Difference ◽

Soil Bacterial

The invasion of Spartina alterniflora (S. alterniflora) has caused serious damage to coastal wetland ecosystems in China, especially the mangrove wetlands in South China. This study aimed to validate the effect of imazapyr on S. alterniflora and soil. The controlled experiment was conducted in May 2021 at the Zhangjiangkou Mangrove Wetland Reserve. In the experiment, 25% (W) imazapyr was used, and six treatments were set up: 3035, 6070, and 9105 mL/acre 25% imazapyr and 1299, 2604, and 5202 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The results showed no side effects on mangrove plants in the spraying area. The highest control efficiency (95.9%) was given by 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The residues of imazapyr in different soils were reduced to 0.10–0.59 mg/kg. The sequencing results showed no significant difference in the overall bacterial communities under different treatments (p > 0.05). The soil bacterial diversity in the samples with adjuvant was higher than that in the samples without adjuvant, while the abundance values were the opposite. There were 10 main communities (>0.3%) at phylum level in all soil samples, among which Proteobacteria, Bacteroidetes, Acidobacteria, Chloflexi, and Actinobacteria were the dominant communities, and the latter four’s abundance changed significantly (p < 0.05). There were significant abundance differences between the groups of oligotrophic and eutrophic bacteria. The redundancy analysis and Monte Carlo tests showed that the total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), ammonia nitrogen, and total nitrogen were the main factors affecting soil bacterial diversity. At the same time, TOC, AP, and TP were the most critical factors affecting the overall characteristics of soil bacterial communities in different treatments, while soil residues had no significant effect on bacteria. This might be due to the addition and degradation of imazapyr and the coverage of S. alterniflora. The best recommendation is 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr to be applied in China’s mangrove wetland reserves and coastal wetlands.

Download Full-text

The impact of persistent bacterial bronchitis on the pulmonary microbiome of children

10.1101/181982 ◽

2017 ◽

Author(s):

Leah Cuthbertson ◽

Vanessa Craven ◽

Lynne Bingle ◽

William O.C.M. Cookson ◽

Mark L. Everard ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Healthy Children ◽

Significant Difference ◽

The Impact

AbstractPersistent bacterial bronchitis is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of persistent bacterial bronchitis.Blind, protected brushings were obtained from 20 healthy controls and 24 children with persistent bacterial bronchitis, with an additional directed sample obtained from persistent bacterial bronchitis patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing.No significant difference in bacterial diversity or community composition (R2 = 0.01, P = 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota. This has important implications for collecting lower respiratory samples from healthy children. A significant decrease in bacterial diversity (P < 0.001) and change in community composition (R2 = 0.08, P = 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated by Proteobacteria, and indicator species analysis showed that Haemophilus and Neisseria were significantly associated with the patient group. In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with persistent bacterial bronchitis were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.

Download Full-text

Effect of Bio and Organic Fertilizers on Pumpkin's (Cucurbita pepo L.) Leave Content of N, P, and K

Al-Qadisiyah Journal For Agriculture Sciences (QJAS) (P-ISSN 2077-5822 E-ISSN 2617-1479) ◽

10.33794/qjas.vol10.iss1.104 ◽

2020 ◽

Vol 10 (1) ◽

pp. 241-245

Author(s):

Ammar Hameed Madi ◽

Jawad A. Kamal Al-Shibani

Keyword(s):

Cucurbita Pepo ◽

Sandy Loam ◽

Block Design ◽

Organic Fertilizers ◽

Flowering Stage ◽

College Of Agriculture ◽

Significant Difference ◽

Randomized Complete Block Design ◽

Loam Soil ◽

Four Levels

This study was conducted to investigate the effect of bacterial bio-fertilization A. chroococcum and P. putide and four levels of compost (0, 1, 2, 3) tons.h-1 on the leaves content of N.P.K elements. The experiment was carried out in one of the greenhouses of the College of Agriculture - University of Al-Qadisiyah during fall season 2018-2019. It designed in accordance with the Randomized Complete Block Design (RCBD) with three replicates in sandy loam soil. The means of treatments were compared with the least significant difference (LSD) at (5)% probability level. The results present that the treatments of A. chroococcum, P. putide and compost at (3) tons.kg-1 significantly increases the leaves content of K.P.K compared to all other treatments in the flowering stage (4.970, 0.5000, and 4.930) mg.kg-1, respectively. This treatment was followed by the effect of the treatment of A. chroococcum and compost at (3) tons.kg-1, which increases the values of all traits except the leaf content of (P). Bio-fertilizer with P. putide + A. chroococcum significantly increases the leaves' content of P.

Download Full-text

Optimizing Manufacturing and Osseointegration of Ti6Al4V Implants through Precision Casting and Calcium and Phosphorus Ion Implantation? In Vivo Results of a Large-Scale Animal Trial

Materials ◽

10.3390/ma13071670 ◽

2020 ◽

Vol 13 (7) ◽

pp. 1670 ◽

Cited By ~ 2

Author(s):

Wölfle-Roos JV ◽

Katmer Amet B ◽

Fiedler J ◽

Michels H ◽

Kappelt G ◽

...

Keyword(s):

Ion Implantation ◽

Large Scale ◽

In Vivo Studies ◽

Control Group ◽

Implant Surface ◽

Precision Casting ◽

Pull Out ◽

Significant Difference ◽

Calcium And Phosphorus

Background: Uncemented implants are still associated with several major challenges, especially with regard to their manufacturing and their osseointegration. In this study, a novel manufacturing technique—an optimized form of precision casting—and a novel surface modification to promote osseointegration—calcium and phosphorus ion implantation into the implant surface—were tested in vivo. Methods: Cylindrical Ti6Al4V implants were inserted bilaterally into the tibia of 110 rats. We compared two generations of cast Ti6Al4V implants (CAST 1st GEN, n = 22, and CAST 2nd GEN, n = 22) as well as cast 2nd GEN Ti6Al4V implants with calcium (CAST + CA, n = 22) and phosphorus (CAST + P, n = 22) ion implantation to standard machined Ti6Al4V implants (control, n = 22). After 4 and 12 weeks, maximal pull-out force and bone-to-implant contact rate (BIC) were measured and compared between all five groups. Results: There was no significant difference between all five groups after 4 weeks or 12 weeks with regard to pull-out force (p > 0.05, Kruskal Wallis test). Histomorphometric analysis showed no significant difference of BIC after 4 weeks (p > 0.05, Kruskal–Wallis test), whereas there was a trend towards a higher BIC in the CAST + P group (54.8% ± 15.2%), especially compared to the control group (38.6% ± 12.8%) after 12 weeks (p = 0.053, Kruskal–Wallis test). Conclusion: In this study, we found no indication of inferiority of Ti6Al4V implants cast with the optimized centrifugal precision casting technique of the second generation compared to standard Ti6Al4V implants. As the employed manufacturing process holds considerable economic potential, mainly due to a significantly decreased material demand per implant by casting near net-shape instead of milling away most of the starting ingot, its application in manufacturing uncemented implants seems promising. However, no significant advantages of calcium or phosphorus ion implantation could be observed in this study. Due to the promising results of ion implantation in previous in vitro and in vivo studies, further in vivo studies with different ion implantation conditions should be considered.

Download Full-text

Cohesive Zone Model for the Interface of Multiwalled Carbon Nanotubes and Copper: Molecular Dynamics Simulation

Journal of Nanotechnology in Engineering and Medicine ◽

10.1115/1.4029462 ◽

2014 ◽

Vol 5 (3) ◽

Cited By ~ 8

Author(s):

Ibrahim Awad ◽

Leila Ladani

Keyword(s):

Carbon Nanotubes ◽

Normal Stress ◽

Multiwalled Carbon Nanotubes ◽

Cohesive Zone ◽

Large Scale ◽

Cohesive Zone Model ◽

Dynamics Simulation ◽

Zone Model ◽

Multiwalled Carbon ◽

Significant Difference

Due to their superior mechanical and electrical properties, multiwalled carbon nanotubes (MWCNTs) have the potential to be used in many nano-/micro-electronic applications, e.g., through silicon vias (TSVs), interconnects, transistors, etc. In particular, use of MWCNT bundles inside annular cylinders of copper (Cu) as TSV is proposed in this study. However, the significant difference in scale makes it difficult to evaluate the interfacial mechanical integrity. Cohesive zone models (CZM) are typically used at large scale to determine the mechanical adherence at the interface. However, at molecular level, no routine technique is available. Molecular dynamic (MD) simulations is used to determine the stresses that are required to separate MWCNTs from a copper slab and generate normal stress–displacement curves for CZM. Only van der Waals (vdW) interaction is considered for MWCNT/Cu interface. A displacement controlled loading was applied in a direction perpendicular to MWCNT's axis in different cases with different number of walls and at different temperatures and CZM is obtained for each case. Furthermore, their effect on the CZM key parameters (normal cohesive strength (σmax) and the corresponding displacement (δn) has been studied. By increasing the number of the walls of the MWCNT, σmax was found to nonlinearly decrease. Displacement at maximum stress, δn, showed a nonlinear decrease as well with increasing the number of walls. Temperature effect on the stress–displacement curves was studied. When temperature was increased beyond 1 K, no relationship was found between the maximum normal stress and temperature. Likewise, the displacement at maximum load did not show any dependency to temperature.

Download Full-text

Heterogeneity and effectiveness analysis of COVID-19 prevention and control in major cities in China through time-varying reproduction number estimation

Scientific Reports ◽

10.1038/s41598-020-79063-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Qing Cheng ◽

Zeyi Liu ◽

Guangquan Cheng ◽

Jincai Huang

Keyword(s):

Prevention And Control ◽

Large Scale ◽

Reproduction Number ◽

Correlation Method ◽

Control Measures ◽

Time Varying ◽

Short Period ◽

Significant Difference ◽

Prevention And Control Measures ◽

And Control

AbstractBeginning on December 31, 2019, the large-scale novel coronavirus disease 2019 (COVID-19) emerged in China. Tracking and analysing the heterogeneity and effectiveness of cities’ prevention and control of the COVID-19 epidemic is essential to design and adjust epidemic prevention and control measures. The number of newly confirmed cases in 25 of China’s most-affected cities for the COVID-19 epidemic from January 11 to February 10 was collected. The heterogeneity and effectiveness of these 25 cities’ prevention and control measures for COVID-19 were analysed by using an estimated time-varying reproduction number method and a serial correlation method. The results showed that the effective reproduction number (R) in 25 cities showed a downward trend overall, but there was a significant difference in the R change trends among cities, indicating that there was heterogeneity in the spread and control of COVID-19 in cities. Moreover, the COVID-19 control in 21 of 25 cities was effective, and the risk of infection decreased because their R had dropped below 1 by February 10, 2020. In contrast, the cities of Wuhan, Tianmen, Ezhou and Enshi still had difficulty effectively controlling the COVID-19 epidemic in a short period of time because their R was greater than 1.

Download Full-text