scholarly journals The effect of susceptible and resistant potato cultivars on bacterial communities in the tuberosphere of potato in soil suppressive or conducive to common scab disease

2018 ◽  
Author(s):  
Jan Kopecky ◽  
Zuzana Samkova ◽  
Ensyeh Sarikhani ◽  
Martina Kyselková ◽  
Marek Omelka ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Common Scab ◽  
Resistant Cultivar ◽  
Susceptible Cultivar ◽  
Cultivar Resistance ◽  
Soil Suppressiveness ◽  
Suppressive Soil ◽  
Conducive Soil

ABSTRACTConnections between the structure of bacterial communities in suppressive soils and potato resistance to common scab (CS) are not well understood. In this study, one resistant and one susceptible cultivar were grown in a conducive and suppressive field to assess cultivar resistance × soil suppressiveness interactions. The resistant cultivar had a higher Mg content in periderm compare to susceptible cultivar, while suppressive soil had lower pH (5.3 vs 5.9), N, C, P, Ca contents but higher Fe and S compared with the conducive soil. Bacteria and actinobacteria numbers were higher in the conducive soil. Copy numbers oftxtBgene (coding for a pathogenicity determinant) were similar in both soils but were higher in the conducive soil (for periderm samples) and in the susceptible cultivar (for conducive soil samples). Taxonomic microarray analysis and Illumina sequencing of 16S rRNA genes amplicon showed that bacterial community differed between resistant vs susceptible cultivar and to a lesser extend between suppressive vs conducive soil. Bacteria participating in soil suppression belonged toPseudomonadaceae, Bradyrhizobiaceae, AcetobacteraceaeandPaenibacillaceae, while resistant cultivars selected a bacterial community resembling that of the suppressive soil, which was enriched inNitrospiraeandAcidobacteria. Thus, the analysis of soil suppressiveness×cultivar resistance interactions enabled to gain new insight to CS control in the field.IMPORTANCEIt was demonstrated that potato cultivars susceptible and resistant to common scab select differing bacterial community and above that this trait is further modified in suppressive and conducive soil. Common scab severity was diminished by either resistant cultivar or suppressive soil but without additive effect between them. Out of the two factors, potato cultivar had a more significant influence on tuberosphere bacterial community composition than soil. Results highlighted the usefulness of both cultivar resistance and soil suppressiveness traits in understanding and managing disease control of crops.

scholarly journals Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jan Kopecky ◽  
Zuzana Samkova ◽  
Ensyeh Sarikhani ◽  
Martina Kyselková ◽  
Marek Omelka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Common Scab ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Susceptible Cultivar ◽  
Soil Suppressiveness ◽  
Nutrient Contents ◽  
Copy Numbers ◽  
18S Rrna Genes ◽  
Conducive Soil

Abstract Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

scholarly journals Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

Plant Disease ◽  
2012 ◽  
Vol 96 (5) ◽  
pp. 718-725 ◽  
Author(s):  
Noah Rosenzweig ◽  
James M. Tiedje ◽  
John F. Quensen ◽  
Qingxiao Meng ◽  
Jianjun J. Hao
Keyword(s):  
Microbial Communities ◽  
Common Scab ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Suppressive Soil ◽  
Streptomyces Spp ◽  
Potato Common Scab ◽  
Order Of Magnitude ◽  
Disease Suppressive Soil ◽  
Conducive Soil

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.

scholarly journals High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12105
Author(s):  
Fangnan Xiao ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Yaling He ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Soil Bacteria ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Tarim River ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

scholarly journals Calcium Nutrition Affects Resistance of Tomato Seedlings to Bacterial Wilt

HortScience ◽  
1995 ◽  
Vol 30 (1) ◽  
pp. 91-93 ◽  
Author(s):  
Hiromichi Yamazaki ◽  
Tsuguo Hoshina
Keyword(s):  
Bacterial Wilt ◽  
Resistant Cultivar ◽  
Susceptible Cultivar ◽  
Cultivar Resistance ◽  
Pseudomonas Solanacearum ◽  
Tomato Seedlings ◽  
Pathogen Populations ◽  
Moderately Resistant ◽  
The Relationship ◽  
Nutrient Solutions

The relationship between Ca nutrition and bacterial wilt development was studied on three tomato (Lycopersicon esculentum Mill.) cultivar seedlings with various degrees of resistance to the disease. Seedlings were transplanted into nutrient solutions with Ca at 0.4, 4.4, or 20.4 mm. One week after initiating the Ca treatment, tomato seedlings were inoculated by wounding the stem with scissors dipped in a suspension of the pathogen (Pseudomonas solanacearum E.F. Smith). Disease development was rapid in `Ponderosa' (a susceptible cultivar) at all Ca concentrations. Increased Ca concentration in the nutrient solution reduced disease severity in `Zuiei' (a moderately resistant cultivar). Resistance was negated at the low Ca concentration in `Hawaii 7998' (a highly resistant cultivar). Pathogen populations in stems decreased with increased Ca concentrations and degrees of resistance.

Interactions among Gaeumannomyces graminis var. tritici, Trichoderma koningii, and soil bacteria

1988 ◽  
Vol 34 (7) ◽  
pp. 871-876 ◽  
Author(s):  
A. Simon ◽  
K. Sivasithamparam
Keyword(s):  
Pure Culture ◽  
Soil Bacteria ◽  
Gaeumannomyces Graminis ◽  
Suppressive Soil ◽  
Trichoderma Koningii ◽  
Gaeumannomyces Graminis Var Tritici ◽  
Conducive Soil

Interactions among Gaeumannomyces graminis var. tritici, Trichoderma koningii, and soil bacteria were studied in vitro and in soils suppressive and conducive of the saprophytic growth of G. graminis var. tritici. Fifty-four percent of bacteria isolated from the suppressive soil and 10% from the conducive soil were antagonistic to G. graminis var. tritici in vitro. The reduction in the growth of T. koningii in vitro by metabolite(s) produced in pure culture by soil bacteria was 14 and 28% for the bacteria isolated from the suppressive and conducive soil, respectively. Metabolite(s) produced by T. koningii in pure culture inhibited the growth in vitro of 8 and 65% of the bacteria isolated from the suppressive and conducive soils, respectively. All isolates of Trichoderma tested produced metabolite(s) that inhibited growth of G. graminis var. tritici in pure culture. The metabolite(s) produced by one isolate of T. koningii inhibited growth of all isolates of Trichoderma in vitro. Trichoderma koningii suppressed saprophytic growth of G. graminis var. tritici in irradiated conducive soil in the absence but not in the presence of bacteria isolated from the same soil. The results suggest that the suppressive soil may be more suppressive of the saprophytic growth of G. graminis var. tritici and less suppressive of the growth of T. koningii than the conducive soil.

scholarly journals Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 659
Author(s):  
Geon Seung Lee ◽  
Mahesh Adhikari ◽  
Jae E. Yang ◽  
Hyuck Soo Kim ◽  
Kyu Suk Han ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Soil Samples ◽  
Metagenomic Sequencing ◽  
Potato Varieties ◽  
Bacterial Phyla ◽  
Streptomyces Spp ◽  
The Common ◽  
Spatial Locations

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Co-Occurrence of Regulated and Emerging Mycotoxins in Corn Silage: Relationships with Fermentation Quality and Bacterial Communities

Toxins ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 232
Author(s):  
Antonio Gallo ◽  
Francesca Ghilardelli ◽  
Alberto Stanislao Atzori ◽  
Severino Zara ◽  
Barbara Novak ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Kojic Acid ◽  
Corn Silage ◽  
Fungal Metabolites ◽  
Fusarium Mycotoxins ◽  
Low Concentrations ◽  
Fermentation Quality ◽  
Low Levels

Sixty-four corn silages were characterized for chemicals, bacterial community, and concentrations of several fungal metabolites. Silages were grouped in five clusters, based on detected mycotoxins, and they were characterized for being contaminated by (1) low levels of Aspergillus- and Penicillium-mycotoxins; (2) low levels of fumonisins and other Fusarium-mycotoxins; (3) high levels of Aspergillus-mycotoxins; (4) high levels of non-regulated Fusarium-mycotoxins; (5) high levels of fumonisins and their metabolites. Altersetin was detected in clusters 1, 3, and 5. Rugulusovin or brevianamide F were detected in several samples, with the highest concentration in cluster 3. Emodin was detected in more than 50.0% of samples of clusters 1, 3 and 5, respectively. Kojic acid occurred mainly in clusters 1 and 2 at very low concentrations. Regarding Fusarium mycotoxins, high occurrences were observed for FB3, FB4, FA1, whereas the average concentrations of FB6 and FA2 were lower than 12.4 µg/kg dry matter. Emerging Fusarium-produced mycotoxins, such as siccanol, moniliformin, equisetin, epiequisetin and bikaverin were detected in the majority of analyzed corn silages. Pestalotin, oxaline, phenopirrozin and questiomycin A were detected at high incidences. Concluding, this work highlighted that corn silages could be contaminated by a high number of regulated and emerging mycotoxins.

scholarly journals Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1465
Author(s):  
Chao Shen ◽  
Liuyan Huang ◽  
Guangwu Xie ◽  
Yulai Wang ◽  
Zongkai Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Diversity Index ◽  
Plastic Substrate ◽  
Simpson Index ◽  
Plastic Debris ◽  
Plastic Substrates ◽  
Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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