scholarly journals Dehydrated pork manure by-product: effect of a chitosan amendment on bacterial community and common scab incidence

2011 ◽  
Vol 90 (3) ◽  
pp. 107-115
Author(s):  
Julie Roy ◽  
Pierre J. Lafontaine ◽  
Rock Chabot ◽  
Carole Beaulieu
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Seed Treatment ◽  
Common Scab ◽  
Disease Incidence ◽  
Anaerobic Bacteria ◽  
Field Trials ◽  
Potato Seed ◽  
Rrna Gene

Chitosan amendment modified the composition of a microbial community associated with dehydrated pork manure by-product. The amended product (biosolid PC) contained a lower number of anaerobic bacteria than the non-amended product (biosolid P). Chitosan also significantly reduced the fungal population. A 16S rRNA gene bank constructed from DNA extracted from the bacterial community associated with both P and PC biosolids revealed that bacterial ordersXanthomonodales,Pseudomonadales,Enterobacteriales,Burkholderiales,Actinomycetales,Bacillales,ClostridialesandLactobacillaleswere found in both biosolids. Bacteria from theStenotrophomonasgenus were abundant in both biosolids. However, the addition of chitosan appeared to induce changes in the population of some bacterial genera. For example, clones carrying a 16S rRNA gene corresponding to theBacillusgenus were doubled in biosolid PC. In field trials carried out to test their effect on common scab incidence, biosolids P and PC were applied as potato seed treatment. Biosolid P increased disease incidence by a factor of 1.33 and 2.85 in two independent experiments. However, when chitosan was added to the seed treatment, the stimulating effect of biosolid P on common scab was cancelled out.

scholarly journals First Report of Streptomyces stelliscabiei Causing Potato Common Scab in Guizhou Province, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Utpal Handique ◽  
Ruofang Zhang ◽  
Zhxin Zhang ◽  
Zhiwen Feng ◽  
Qinghua Sun ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Common Scab ◽  
Disease Incidence ◽  
Guizhou Province ◽  
Rrna Gene ◽  
Potato Tubers ◽  
First Report ◽  
Potato Common Scab

Potato (Solanum tuberosum L.) common scab can be caused by multiple pathogenic Streptomyces spp. worldwide. Potato tubers (cv. Favorita) with severe pitted common scab symptoms were observed at a small farm (2 hectares) during harvest in Anshun, Guizhou province in early May 2020. The disease incidence was around 10%, and symptomatic samples were collected to isolate the pathogen. Two isolates, ZR-IMU141 and ZR-IMU146 (Accession number MW995958 and MW995959 respectively), showed more than 99% sequence identity to S. stelliscabiei sequences (Accession No. HM018085). Five house-keeping genes for multi-locus sequence analyze (MLSA) of Streptomycetaceae were amplified, sequenced and uploaded to NCBI: atpD (MZ343164 and MZ343165), gyrB (MZ343162 and MZ343163), recA (MZ343166 and MZ343167), rpoB (MZ343168and MZ343169) and trpB (MZ343170 and MZ343171). All the genes show over 98% identity with S. stelliscabiei. Phylogenetic trees of 16S rRNA gene sequence and multi-locus sequence analysis (MLSA) were constructed. The two isolates contain pathogenicity genes txtAB, nec1, and tomA, which was confirmed by PCR. To complete Koch’s postulates, 9 potato seedlings (cv. Favorita, 15 centimeters high), were transferred to new pots and inoculated with spore suspensions of ZR-IMU141 and ZR-IMU146 (104 CFU/ml), or water as a negative control. Two months later, potato tubers inoculated with either ZR-IMU141 or ZR-IMU146 exhibited typical symptoms of potato common scab, such as superficial or deep, raised, pitted, or polygonal lesions like the field symptoms, but the negative controls remained asymptomatic. The pathogens were reisolated from the lesions and confirmed identical to the original isolate by 16s rRNA gene sequences. To our knowledge, this is the first report of S. stelliscabiei causing potato common scab in Guizhou province, China. We believe that this report will draw attention to the study and management of the increased pool of scab pathogens in China.

scholarly journals Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding

2020 ◽  
Vol 11 ◽  
Author(s):  
Pasquale Alibrandi ◽  
Sylvia Schnell ◽  
Silvia Perotto ◽  
Massimiliano Cardinale
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Plant ◽  
Bacterial Communities ◽  
Reproductive Organs ◽  
Distribution Model ◽  
Rrna Gene ◽  
Orchid Species ◽  
Core Microbiota

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

Streptomyces rhizophilus Causes Potato Common Scab Disease

Plant Disease ◽  
2021 ◽  
Author(s):  
Qi Wei ◽  
Jie Li ◽  
Shuai Yang ◽  
Wenzhong Wang ◽  
Fanxiang Min ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Common Scab ◽  
Bacterial Species ◽  
Economic Losses ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Heilongjiang Province ◽  
Epidemic Disease ◽  
Genus Streptomyces

Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.

Insights into Bacterial Community Structure of a Commercial Copper Bioheapleaching Plant: Growth of Heterotrophic Bacteria in the System

2013 ◽  
Vol 825 ◽  
pp. 50-53 ◽  
Author(s):  
Xing Yu Liu ◽  
Bo Wei Chen ◽  
Jian Kang Wen
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Heterotrophic Bacteria ◽  
Outer Part ◽  
Gene Clone ◽  
Rrna Gene ◽  
Liquid Samples ◽  
Lower Depth

The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.

Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

2018 ◽  
Vol 64 (12) ◽  
pp. 954-967 ◽  
Author(s):  
Liqiang Zhong ◽  
Daming Li ◽  
Minghua Wang ◽  
Xiaohui Chen ◽  
Wenji Bian ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Channel Catfish ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Integration System ◽  
Nursery Pond ◽  
Site Variation

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

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