scholarly journals Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions

2006 ◽  
Vol 72 (1) ◽  
pp. 212-220 ◽  
Author(s):  
Silke Langenheder ◽  
Eva S. Lindström ◽  
Lars J. Tranvik
Keyword(s):  
Environmental Conditions ◽  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Scale Functions ◽  
And Function ◽  
Different Sources ◽  
The 16S Rrna Gene

ABSTRACT The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.

scholarly journals Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

2022 ◽  
Author(s):  
Juanita C. Rodríguez-Rodríguez ◽  
Yves Bergeron ◽  
Steven W. Kembel ◽  
Nicole J. Fenton
Keyword(s):  
Environmental Conditions ◽  
Host Species ◽  
Bacterial Communities ◽  
Forest Type ◽  
Bacterial Community Composition ◽  
Tree Canopy ◽  
Rrna Gene ◽  
Eastern Canada ◽  
Spruce Forests ◽  
Α Diversity

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.

scholarly journals 16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene

1998 ◽  
Vol 36 (6) ◽  
pp. 1761-1764 ◽  
Author(s):  
U. Reischl ◽  
K. Feldmann ◽  
L. Naumann ◽  
B. J. M. Gaugler ◽  
B. Ninet ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Fragment Length Polymorphism ◽  
Direct Sequencing ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
The 16S Rrna Gene

Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

scholarly journals Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252242
Author(s):  
Abasiofiok M. Ibekwe ◽  
Selda Ors ◽  
Jorge F. S. Ferreira ◽  
Xuan Liu ◽  
Donald L. Suarez
Keyword(s):  
Bacterial Communities ◽  
Spinacia Oleracea ◽  
Saline Water ◽  
Bacterial Community Composition ◽  
Seasonal Effects ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Illumina Platform ◽  
Functional Capabilities ◽  
And Function

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

scholarly journals Phytoplasma occurrence in apple trees in the Czech Republic

2011 ◽  
Vol 39 (No. 1) ◽  
pp. 7-12 ◽  
Author(s):  
R. Fialová ◽  
M. Navrátil ◽  
P. Válová
Keyword(s):  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Apple Proliferation ◽  
Chain Reaction ◽  
Apple Trees ◽  
The Czech Republic ◽  
High Incidence ◽  
Phytoplasma Infection ◽  
Polymerase Chain

The presence of phytoplasmas in apple trees with proliferation symptoms, rubbery wood symptoms and no symp&shy;toms was determined by using polymerase chain reaction assays with primers amplifying phytoplasma 16S rRNA gene. Phytoplasmas were detected in all trees with proliferation symptoms. Positive tests for phytoplasma in the group of trees with rubbery wood symptoms and of those without symptoms revealed a relatively high incidence of latent phytoplasma infection. Using restriction fragment length polymorphism analysis, phytoplasma of the same identity &ndash; apple proliferation phytoplasma (subgroup 16SrX-A) &ndash; was recorded in all positively tested trees. &nbsp;

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.

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