An ecological function conceptual model for bacterial communities with high relative abundance in an unplanted and canola ( Brassica napus ) planted Podzol

Rhizosphere ◽  
2018 ◽  
Vol 5 ◽  
pp. 26-31 ◽  
Author(s):  
C.M. Monreal ◽  
J. Zhang
Keyword(s):  
Brassica Napus ◽  
Conceptual Model ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Ecological Function

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Stefanie P Glaeser ◽  
Iulian Gabur ◽  
Hossein Haghighi ◽  
Jens-Ole Bartz ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Quantitative Resistance ◽  
Bacterial Community Composition ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Host Genotype ◽  
Brassica Napus L ◽  
Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

scholarly journals Changes of Bacterial Communities in Response to Prolonged Hydrodynamic Disturbances in the Eutrophic Water-Sediment Systems

2019 ◽  
Vol 16 (20) ◽  
pp. 3868
Author(s):  
Haomiao Cheng ◽  
Ling Cheng ◽  
Liang Wang ◽  
Tengyi Zhu ◽  
Wei Cai ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Evolutionary Trend ◽  
Ecological Evaluation ◽  
Eutrophic Water ◽  
Rrna Gene Sequencing ◽  
Opposite Tendency

The effects of hydrodynamic disturbances on the bacterial communities in eutrophic aquatic environments remain poorly understood, despite their importance to ecological evaluation and remediation. This study investigated the evolution of bacterial communities in the water–sediment systems under the influence of three typical velocity conditions with the timescale of 5 weeks. The results demonstrated that higher bacterial diversity and notable differences were detected in sediment compared to water using the 16S rRNA gene sequencing. The phyla Firmicutes and γ-Proteobacteria survived better in both water and sediment under stronger water disturbances. Their relative abundance peaked at 36.0%, 33.2% in water and 38.0%, 43.6% in sediment, respectively, while the phylum Actinobacteria in water had the opposite tendency. Its relative abundance grew rapidly in static control (SC) and peaked at 44.8%, and it almost disappeared in disturbance conditions. These phenomena were caused by the proliferation of genus Exiguobacterium (belonging to Firmicutes), Citrobacter, Acinetobacter, Pseudomonas (belonging to γ-Proteobacteria), and hgcI_clade (belonging to Actinobacteria). The nonmetric multidimensional scaling (NMDS) and Venn analysis also revealed significantly different evolutionary trend in the three water-sediment systems. It was most likely caused by the changes of geochemical characteristics (dissolved oxygen (DO) and nutrients). This kind of study can provide helpful information for ecological assessment and remediation strategy in eutrophic aquatic environments.

scholarly journals Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Randall R. Jiménez ◽  
Gilbert Alvarado ◽  
José Sandoval ◽  
Simone Sommer
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Defense Mechanism ◽  
Anthropogenic Activities ◽  
Habitat Disturbance ◽  
Amphibian Declines ◽  
Stress Factors ◽  
Skin Microbiome ◽  
Disturbed Habitats

Abstract Background The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be “extinct” have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. Results We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. Conclusions Our findings support the microbial “Anna Karenina principle”, in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.

scholarly journals Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA

2012 ◽  
Vol 78 (9) ◽  
pp. 3495-3499 ◽  
Author(s):  
Alexandre B. de Menezes ◽  
James E. McDonald ◽  
Heather E. Allison ◽  
Alan J. McCarthy
Keyword(s):  
16S Rrna ◽  
Reverse Transcriptase ◽  
Quantitative Pcr ◽  
Lake Sediment ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Population ◽  
Freshwater Lakes ◽  
Content Type ◽  
Water Columns

ABSTRACTThe relative abundance of micromonosporas in the bacterial communities inhabiting cellulose baits, water columns, and sediments of two freshwater lakes was determined by quantitative PCR (qPCR) of reverse-transcribed 16S rRNA.Micromonosporaspp. were shown to be significant members of the active bacterial population colonizing cellulosic substrates in the lake sediment, and their increased prevalence with greater depth was confirmed by enumeration of CFU.

OBSERVATIONS ON DISTRIBUTION, SEASONAL LIFE HISTORY, AND ABUNDANCE OF FLEA BEETLES (COLEOPTERA: CHRYSOMELIDAE) THAT INFEST RAPE CROPS IN MANITOBA

1979 ◽  
Vol 111 (12) ◽  
pp. 1345-1353 ◽  
Author(s):  
H. G. Wylie
Keyword(s):  
Life History ◽  
Brassica Napus ◽  
Relative Abundance ◽  
Flea Beetle ◽  
Phyllotreta Cruciferae ◽  
Main Species ◽  
Phyllotreta Striolata ◽  
Flea Beetles ◽  
History Of

AbstractPhyllotreta cruciferae (Goeze) was usually the most abundant flea beetle on crops of Argentine rape, Brassica napus L., in Manitoba, followed in order by Phyllotreta striolata (F.) and Psylliodes punctulata Melsh. These three species and small numbers of Phyllotreta bipustulata (F.) were present on volunteer rape in the spring. A few specimens of a fifth rape-eating species, Phyllotreta robusta Lee, were trapped in April after hibernating. The three main species were recorded in all 16 localities in which samples of flea beetles on rape crops and/or volunteer rape were collected. Details of seasonal life history of each species are presented, as well as data on the abundance of the three main species throughout the year on rape crops, in overwintering habitats and on volunteer rape in spring. The relative abundance of P. cruciferae, P. striolata, and Ps. punctulata in different rape-growing areas of Manitoba is discussed.

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