Magma-To-Microbe Networks in the Context of Sulfide Hosted Microbial Ecosystems

2013 ◽  
pp. 233-258 ◽  
Author(s):  
Matthew O. Schrenk ◽  
James F. Holden ◽  
John A. Baross
Keyword(s):  
Microbial Ecosystems

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at YanartaÅŸ (Chimera), Turkey

2015 ◽  
Vol 5 ◽  
Author(s):  
D'Arcy R. Meyer-Dombard ◽  
Kristin M. Woycheese ◽  
Erin N. YargıçoÄŸlu ◽  
Dawn Cardace ◽  
Everett L. Shock ◽  
...  
Keyword(s):  
High Ph ◽  
Microbial Ecosystems

scholarly journals Towards Predictive Modeling of Information Processing in Microbial Ecosystems with Quorum Sensing Interactions

2016 ◽  
Vol 110 (3) ◽  
pp. 141a-142a ◽  
Author(s):  
Tahir Yusufaly ◽  
James Boedicker
Keyword(s):  
Information Processing ◽  
Quorum Sensing ◽  
Predictive Modeling ◽  
Microbial Ecosystems

Establishment of Defined Microbial Ecosystems in Germ-Free Rats

1972 ◽  
Vol 6 (3) ◽  
pp. 211-223 ◽  
Author(s):  
F.H.M. Mikx ◽  
J.S. van der Hoeven ◽  
K.G. König ◽  
A.J.M Plasschaert ◽  
B. Guggenheim
Keyword(s):  
Germ Free ◽  
Microbial Ecosystems

scholarly journals An equation‐free method reveals the ecological interaction networks within complex microbial ecosystems

2017 ◽  
Vol 8 (12) ◽  
pp. 1774-1785 ◽  
Author(s):  
Kenta Suzuki ◽  
Katsuhiko Yoshida ◽  
Yumiko Nakanishi ◽  
Shinji Fukuda
Keyword(s):  
Interaction Networks ◽  
Ecological Interaction ◽  
Microbial Ecosystems

Microbial Ecosystems, Protection of

2015 ◽  
pp. 480-487
Author(s):  
Paul L. E. Bodelier
Keyword(s):  
Microbial Ecosystems

Interactions between Environmental Microbial Ecosystems and Humans: the Case of the Water Environment and Antibiotic Resistance

2014 ◽  
pp. 81-92
Author(s):  
Chuanwu Xi ◽  
Kathleen Bush ◽  
Karen L. Lachmayr ◽  
Yongli Zhang ◽  
Timothy E. Ford
Keyword(s):  
Antibiotic Resistance ◽  
Water Environment ◽  
Microbial Ecosystems

scholarly journals Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem

2017 ◽  
Author(s):  
Arisa Tsuboi ◽  
Misao Itoga ◽  
Yuichi Hongoh ◽  
Shigeharu Moriya
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Taxonomic Composition ◽  
Rrna Genes ◽  
Reference Database ◽  
Similar Distribution ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Microbial Ecosystems ◽  
Sulfur Oxidizing

AbstractWe developed a new pipeline for simultaneous analyses of both rRNA profile as a taxonomic marker and mRNA profile as a functional marker, to understand microbial ecosystems in natural environments. Our pipeline, named All-RNA-Information sequencing (ARIseq), comprises a high-throughput sequencing of reverse transcribed total RNA and several widely used computational tools, and generates quantitatively reliable information on both community structures and gene expression patterns, which were verified by quantitative PCR analyses in this study. Particularly, correlation network analysis in the pipeline can reveal microbial taxa and expressed genes that share patterns of dynamics among different time and/or geographical points. The pipeline is primarily mapping-based, using a public database for small subunit rRNA genes and obtained contigs as the reference database for protein-coding genes. We applied this pipeline to biofilm samples, as examples, collected from an acidic spring water stream in the Chyatsubomi-goke Park in Gunma prefecture, Japan. Our analyses revealed the predominance of iron and sulfur-oxidizing bacteria and Pinnularia diatoms, and also indicated that the distributions of the iron-sulfur-oxidizing bacterial consortium and the Pinnularia diatoms largely overlapped but showed distinct patterns. In addition, our analyses showed that the iron-oxidizing bacterial genus Acidithiobacillus and co-occurring Acidiphilium shared similar distribution pattern whereas another iron-oxidizing genus Leptospirillum exhibited a distinct pattern. Our pipeline enables researchers to more easily capture the outline of microbial ecosystems based on the taxonomic composition, protein-coding gene expression, and their correlations.

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