Turkey fecal microbial community structure and functional gene diversity revealed by 16S rRNA gene and metagenomic sequences

2008 ◽  
Vol 46 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Jingrang Lu ◽  
Jorge Santo Domingo
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Gene Diversity ◽  
Functional Gene ◽  
Rrna Gene ◽  
Functional Gene Diversity

scholarly journals Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

2018 ◽  
Author(s):  
Lauren Gillies Campbell ◽  
J. Cameron Thrash ◽  
Nancy N. Rabalais ◽  
Olivia U. Mason
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of Mexico ◽  
Dissolved Oxygen ◽  
Microbial Community Structure ◽  
Rrna Gene ◽  
Hypoxic Zone ◽  
Low Do

AbstractRich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditioXSns. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with dissolved oxygen (DO) in both years and that low DO concentrations, and the high Thaumarchaeota abundances, influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially influence patterns in microbial community structure, with two years of data revealing that the annual nGOM hypoxic zone is emerging as a low DO adapted AOA hotspot.

scholarly journals Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0132253 ◽  
Author(s):  
Guoqin Yu ◽  
Doug Fadrosh ◽  
James J. Goedert ◽  
Jacques Ravel ◽  
Alisa M. Goldstein
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Nested Pcr ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

scholarly journals Distribution of Microbial Community Structure in Sediment from the Suyeong River and Bay of Busan, Republic of Korea, Determined by 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Ilwon Jeong ◽  
Junho Lee ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Sediment Samples

Here, we report a 16S rRNA gene amplicon sequence analysis presenting the microbial community in sediments from the Suyeong River and Suyeong Bay, Republic of Korea. The dominant phyla in all sediment samples were Proteobacteria (39.69 to 53.62%) and Bacteroidetes (29.78 to 33.89%).

scholarly journals Analysis of the Microbial Community Structure in Coastal Sediment of an Ascidian Farm in South Korea through 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Ilwon Jeong ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Styela Clava ◽  
Structure Changes

Aquaculture places contamination pressure on the coastal environment. We investigated the microbial community structure changes in sediment in an ascidian Styela clava farm. Data profiling of the 16S rRNA gene amplicon sequence shows that the microbial diversity of sediment in the Styela clava farm is dominated by Proteobacteria phyla (relative abundance, 95.34 to 97.85%).

scholarly journals Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping

2019 ◽  
Author(s):  
Xiumei Tang ◽  
Saiyun Luo ◽  
Zhipeng Huang ◽  
Haining Wu ◽  
Jin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Physicochemical Properties ◽  
Microbial Community Structure ◽  
Enzyme Activities ◽  
Southern China ◽  
Nutrient Content ◽  
Rrna Gene ◽  
Rhizospheric Soil

ABSTRACTCassava/peanut intercropping is a popular cultivation method in southern China and has the advantages of apparently increased yield and economic efficiency compared with monoculture, however, the ecological benefits of this method are poorly understood. This study aimed to investigate the effects of intercropping on the physicochemical properties and microbial community structures of soil. Field trials were performed to determine the effects of cassava/peanut intercropping on rhizospheric soil nutrient content, enzyme activities, microbial quantity and microbial community structure. The microbial community was characterized by 16S rRNA tag-based high-throughput sequencing on the Illumina MiSeq platform. Results showed that cassava/peanut intercropping could improve the physicochemical properties of rhizospheric soil by increasing the available nutrient content, pH, bacterial quantity, and some enzyme activities and by altering the microbial community structure. 16S rRNA gene sequencing demonstrated that the microbial community structure varied between the intercropping and monoculture systems. Nitrospirae, Verrucomicrobia and Gemmatimonadetes were more abundant in the intercropping system than in the monocultures. Redundancy analysis (RDA) revealed that the abundances ofDA101,PilimeliaandRamlibacterwere positively correlated with environmental parameters such as available nitrogen and pH, and these were dominant genera in the rhizospheric soil of the intercropped peanut plants.

scholarly journals Methane related changes in prokaryotic activity along geochemical profiles in sediments of Lake Kinneret (Israel)

2014 ◽  
Vol 11 (6) ◽  
pp. 9813-9852 ◽  
Author(s):  
I. Bar Or ◽  
E. Ben-Dov ◽  
A. Kushmaro ◽  
W. Eckert ◽  
O. Sivan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Community Structure ◽  
Iron Reduction ◽  
Lake Kinneret ◽  
Community Diversity ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Deep Sediments

Abstract. Microbial methane oxidation process (methanotrophy) is the primary control on the emission of the greenhouse gas methane (CH4) to the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are mainly responsible for oxidizing the methane. In marine sediments the coupling of the anaerobic oxidation of methane (AOM) with sulfate reduction, often by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria, was found to consume almost all the upward diffusing methane. Recently, we showed geochemical evidence for AOM driven by iron reduction in Lake Kinneret (LK) (Israel) deep sediments and suggested that this process can be an important global methane sink. The goal of the present study was to link the geochemical gradients found in the porewater (chemical and isotope profiles) with possible changes in microbial community structure. Specifically, we examined the possible shift in the microbial community in the deep iron-driven AOM zone and its similarity to known sulfate driven AOM populations. Screening of archaeal 16S rRNA gene sequences revealed Thaumarchaeota and Euryarchaeota as the dominant phyla in the sediment. Thaumarchaeota, which belongs to the family of copper containing membrane-bound monooxgenases, increased with depth while Euryarchaeota decreased. This may indicate the involvement of Thaumarchaeota, which were discovered to be ammonia oxidizers but whose activity could also be linked to methane, in AOM in the deep sediment. ANMEs sequences were not found in the clone libraries, suggesting that iron-driven AOM is not through sulfate. Bacterial 16S rRNA sequences displayed shifts in community diversity with depth. Proteobacteria and Chloroflexi increased with depth, which could be connected with their different dissimilatory anaerobic processes. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for iron-driven AOM in deep sediments.

scholarly journals The diversity of active microbial groups in an activated sludge process treating painting process wastewater

2020 ◽  
Vol 148 ◽  
pp. 01002
Author(s):  
Herto Dwi Ariesyady ◽  
Mentari Rizki Mayanda ◽  
Tsukasa Ito
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Biological Treatment ◽  
Rrna Gene ◽  
Activated Sludge Process ◽  
Painting Process ◽  
Process Wastewater

Activated sludge process is one of the wastewater treatment method that is applied for many wastewater types including painting process wastewater of automotive industry. This wastewater is well-known to have high heavy metals concentration which could deteriorate water environment if appropriate performance of the wastewater treatment could not be achieved. In this study, we monitored microbial community diversity in a Painting Biological Treatment (PBT) system. We applied a combination of cultivation and genotypic biological methods based on 16S rRNA gene sequence analysis to identify the diversity of active microbial community. The results showed that active microbes that could grow in this activated sludge system were dominated by Gram-negative bacteria. Based on 16S rRNA gene sequencing analysis, it was revealed that their microbial diversity has close association with Bacterium strain E286, Isosphaera pallida, Lycinibacillus fusiformis, Microbacterium sp., Orchobactrum sp., Pseudomonas guariconensis, Pseudomonas sp. strain MR84, Pseudomonas sp. MC 54, Serpens sp., Stenotrophomonas acidaminiphila, and Xylella fastidiosa with similarity of 86 – 99%. This findings reflects that microbial community in a Painting Biological Treatment (PBT) system using activated sludge process could adapt with xenobiotics in the wastewater and has a wide range of diversity indicating a complex metabolism mechanism in the treatment process.

scholarly journals Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2080-2091 ◽  
Author(s):  
Anne-Laure Michon ◽  
Fabien Aujoulat ◽  
Laurent Roudière ◽  
Olivier Soulier ◽  
Isabelle Zorgniotti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
Natural Populations ◽  
Variable Region ◽  
Housekeeping Gene ◽  
Single Copy ◽  
Population Based ◽  
Rrna Gene ◽  
Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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