scholarly journals Streptomyces strains modulate dynamics of soil bacterial communities and their efficacy in disease suppression caused by Phytophthora capsici

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abbasi Sakineh ◽  
Spor Ayme ◽  
Sadeghi Akram ◽  
Safaie Naser
Keyword(s):  
Bacterial Communities ◽  
Phytophthora Capsici ◽  
Illumina Miseq ◽  
Disease Suppression ◽  
Positive Interactions ◽  
Alpha And Beta Diversity ◽  
Operational Taxonomic Units ◽  
Soil Bacterial Communities ◽  
Phosphate Solubilizing ◽  
And Control

AbstractThe responses of rhizosphere bacterial communities of Streptomyces (SS14 and IT20 stains) treated-pepper plants following inoculation by Phytophthora capsici (PC) was investigated using Illumina MiSeq sequencing. Distinct modulation of the bacteriome composition was found for PC samples with the highest relative abundance (RA) of Chitinophaga (22 ± 0.03%). The RA of several bacterial operational taxonomic units (OTUs) was affected and caused changes in alpha and beta-diversity measures. In IT20, the RA of Cyanobacteria was enriched compared to SS14 (72%) and control samples (47%). Phylotypes belonging to Devosia, Promicromonospora, Kribbella, Microbacterium, Amylocolatopsis, and Pseudomonas genera in the rhizosphere were positively responding against the pathogen. Our findings show that the phosphate solubilizing strain IT20 has higher microbial community responders than the melanin-producing strain SS14. Also, positive interactions were identified by comparing bacterial community profiles between treatments that might allow designing synthetic bio-inoculants to solve agronomic problems in an eco-friendly way.

scholarly journals Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils

2006 ◽  
Vol 72 (11) ◽  
pp. 6965-6971 ◽  
Author(s):  
David K. Oline
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Regional Scale ◽  
Serpentine Soils ◽  
Operational Taxonomic Units ◽  
Microbial Biogeography ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Control Community ◽  
16S Rrna Clone Libraries

ABSTRACT I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

scholarly journals Termites Are Associated with External Species-Specific Bacterial Communities

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Patrik Soukup ◽  
Tomáš Větrovský ◽  
Petr Stiblik ◽  
Kateřina Votýpková ◽  
Amrita Chakraborty ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Negative Effects ◽  
Termite Species ◽  
Positive Effects ◽  
Operational Taxonomic Units ◽  
Wide Range ◽  
Species Specific ◽  
And Control

ABSTRACT All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. The abundance of several bacterial OTUs, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus, was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities. IMPORTANCE As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on Rhizobiales and Actinobacteria abundance and negative effects on the abundance of several ubiquitous genera, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus. Our results demonstrate that termite galleries harbor unique bacterial communities.

scholarly journals Metabarcoding Analysis of Bacterial Communities Associated with Media Grow Bed Zones in an Aquaponic System

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Nasser Kasozi ◽  
Horst Kaiser ◽  
Brendan Wilhelmi
Keyword(s):  
Bacterial Communities ◽  
Root Zone ◽  
Illumina Miseq ◽  
Effluent Water ◽  
Environmentally Sustainable ◽  
Operational Taxonomic Units ◽  
Dry Zone ◽  
Total Community ◽  
Mineralized Zone

The development of environmentally sustainable plant and fish production in aquaponic systems requires a complete understanding of the systems’ biological components. In order to better understand the role of microorganisms in this association, we studied the bacterial communities in the dry, root, and mineralized zones of a flood-and-drain media bed aquaponic system. Bacterial communities were characterized using metabarcoding of the V3-V4 16S rRNA regions obtained from paired-end Illumina MiSeq reads. Proteobacteria, Actinobacteria, and Bacteroidetes accounted for more than 90% of the total community in the dry zone and the effluent water. These phyla also accounted for more than 68% of the total community in the root and mineralized zones. The genera Massilia, Mucilaginibacter, Mizugakiibacter, and Rhodoluna were most dominant in the dry, root, and mineralized zones and in the effluent water, respectively. The number of shared operational taxonomic units (OTUs) for the three zones was 241, representing 7.15% of the total observed OTUs. The number of unique OTUs in samples from dry zone, root zone, mineralized zone, and effluent water was 485, 638, 445, and 383, respectively. The samples from the root zone harbored more diverse communities than either the dry or mineralized zones. This study is the first to report on the bacterial community within the zones of a flood-and-drain media bed. Thus, this information will potentially accelerate studies on other microbial communities involved in the bioconversion of nitrogen compounds and mineralization within these types of aquaponic systems.

Duration of continuous cropping with straw return affects the composition and structure of soil bacterial communities in cotton fields

2018 ◽  
Vol 64 (3) ◽  
pp. 167-181 ◽  
Author(s):  
Lei Yang ◽  
Lanlan Tan ◽  
Fenghua Zhang ◽  
William Jeffrey Gale ◽  
Zhibo Cheng ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
Continuous Cropping ◽  
Cotton Production ◽  
Positive Effects ◽  
Soil Bacterial Communities ◽  
Composition And Structure ◽  
Straw Return ◽  
Soil Bacterial

Salinized land in the China’s Xinjiang Region is being reclaimed for continuous cotton production. The specific objectives of this field study were (i) to compare bacterial composition and diversity in unfarmed (i.e., unreclaimed) and continuously (5, 10, 15, and 20 years) cropped soils and (ii) to explore correlations between soil properties and the bacterial communities identified by Illumina MiSeq sequencing. The results showed that bacterial species richness and diversity increased for 10–15 years and then declined when salinized land was reclaimed for cotton production. Proteobacteria and Firmicutes were the dominant phyla in unfarmed soil. Continuous cropping reduced the abundance of Firmicutes but increased that of Chloroflexi, Acidobacteria, and Actinobacteria. Cluster analyses showed that the greatest similarities in bacterial communities were between the 5- and 10-year treatments and between the 15- and 20-year treatments. Soil pH, electrical conductivity, alkali-hydrolyzable N, and available P were significantly correlated with bacterial community distribution. Overall, cotton production improved soil physicochemical properties and altered the structure and composition of soil bacterial communities compared with unfarmed soil. These positive effects began to decrease after 10–15 years of continuous cotton production.

scholarly journals Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Xiaoning Gao ◽  
Zilin Wu ◽  
Rui Liu ◽  
Jiayun Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Community Characteristics ◽  
Dynamic Changes ◽  
Operational Taxonomic Units ◽  
Total Bacterial Community ◽  
Rhizosphere Bacterial Community ◽  
Rhizosphere Bacterial Communities

To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.

PSIV-5 Characterization of the Fecal Bacterial Communities of Grass-fed and Grain-fed Bison Heifers

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 212-213
Author(s):  
Anlly M Fresno Rueda ◽  
Carter Kruse ◽  
Jason Griffin ◽  
Benoit St-Pierre
Keyword(s):  
North American ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Poor Quality ◽  
Rank Test ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
The North ◽  
Blue Creek

Abstract In comparison to the rumen, the bacterial communities of the hindgut have remained largely unexplored in ruminants. They not only strongly influence host health, but also efficiency, notably by continuing fermentation of feed that escaped foregut digestion. In non-domesticated ruminants, such as the North American bison, they are thought to contribute to the higher efficiency of their host on feed of poor quality. To gain further insight on this gut microbial ecosystem, fecal bacterial community composition of bison heifers raised at two locations [Standing Butte (n=17), SD, and Blue Creek (n=17), NE] were investigated. Each animal was sampled once while on pasture, then after 100 days on a grain-based diet. Data generated from Illumina MiSeq (2×300) sequencing of PCR amplicons targeting the V1-V3 region of the 16S rRNA gene were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). A total of 26,379 and 13,294 species-level operational taxonomic units (OTUs) were identified from Standing Butte and Blue Creek samples, respectively, with 446 and 281 OTUs shared between diets at each respective location. Further analysis of the most highly represented OTUs from each ranch revealed that the abundance of six OTUs differed between diets in Standing Butte heifers compared to nine OTUs in Blue Creek heifers (Kruskal-Wallis sum-rank test; P < 0.05). These included OTUs SD_Bb-00727 (µgrass = < 0.01% vs µgrain = 13.13%) and SD_Bb-00728 (µgrass = 5.62% vs µgrain = < 0.01%) from the Standing Butte samples, as well as OTUs SD_Bb-00730 (µgrass = 0.01% vs µgrain = 10.21%) and SD_Bb-00745 (µgrass = < 0.01% vs µgrain = 3.5%) from the Blue Creek samples. Together, these results indicate that the composition of hindgut bacterial communities of the North American bison are greatly affected by changes in diet.

scholarly journals Isolation of a Substantial Proportion of Forest Soil Bacterial Communities Detected via Pyrotag Sequencing

2013 ◽  
Vol 79 (6) ◽  
pp. 2096-2098 ◽  
Author(s):  
David VanInsberghe ◽  
Martin Hartmann ◽  
Gordon R. Stewart ◽  
William W. Mohn
Keyword(s):  
Forest Soil ◽  
Forest Soils ◽  
Bacterial Communities ◽  
Growth Characteristics ◽  
Substantial Proportion ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Ecological Traits ◽  
Operational Taxonomic Units ◽  
Soil Bacterial Communities

ABSTRACTWe isolated 1,264 bacterial strains from forest soils previously surveyed via pyrosequencing of rRNA gene amplicons. Conventional culturing techniques recovered a substantial proportion of the community, with isolates representing 22% of 98,557 total pyrotags. Growth characteristics of isolates indicated that ecological traits were associated with relative abundances of corresponding pyrotag operational taxonomic units.

scholarly journals Characteristics of Soil Bacterial Community in the Decomposition Process Inside and Outside Moso Bamboo Stumps

2022 ◽  
Author(s):  
Fengna Liang ◽  
Xiao Huang ◽  
Huixin Zheng ◽  
Xiangqing Ma ◽  
Yonglai Huang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Degradation Process ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Operational Taxonomic Units ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Map Analysis

Abstract Purpose: Soil bacteria comprise the largest number of soil microorganisms and play an important role in moso bamboo (Phyllostachys edulis) stump decay; however, the characteristics of soil bacterial communities inside and outside these stumps remain unclear. Methods: The characteristics of soil bacterial communities inside and outside Phyllostachys edulis bamboo stumps were analyzed under three different levels of decay using high-throughput sequencing technology. Results: The abundance of operational taxonomic units inside and outside the bamboo stumps increased as the decay progressed; Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, and Verrucomicrobia were the most abundant phyla in the soil inside and outside the bamboo stumps. In the outside bamboo stumps, there was a very significant positive correlation of Acidobacteria and Planctomycetes with the decaying degree of bamboo stumps. At the class level, Alphaproteobacteria, Gammaproteobacteria, and Planctomycetacia were the most abundant bacteria in the bamboo stumps. Inside the stumps, the decaying degree of bamboo stumps was significantly positively correlated with Alphaproteobacteria and significantly negatively correlated with Gammaproteobacteria and Bacilli. Principal component analysis and the heat map analysis at the genus level indicated similarities among soil bacterial communities inside the moderately and severely decayed bamboo stumps and among the communities outside the mildly and moderately decayed bamboo stumps. Conclusion: Our results augment our understanding of the expeditious degradation process of bamboo stumps, and provide a theoretical basis and reference for microbiological research, sustainable bamboo stump operations, and degradation methods of bamboo forests.

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