TITLE

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

AUTHOR(S)
Kittelmann, Sandra; Seedorf, Henning; Walters, William A.; Clemente, Jose C.; Knight, Rob; Gordon, Jeffrey I.; Janssen, Peter H.
PUB. DATE
February 2013
SOURCE
PLoS ONE;Feb2013, Vol. 8 Issue 2, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.
ACCESSION #
87623354

 

Related Articles

  • Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces. Orsi, William; Biddle, Jennifer F.; Edgcomb, Virginia // PLoS ONE;Feb2013, Vol. 8 Issue 2, p1 

    The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an...

  • An all-taxon microbial inventory of the Moorea coral reef ecosystem. McCliment, Elizabeth A; Nelson, Craig E; Carlson, Craig A; Alldredge, Alice L; Witting, Jan; Amaral-Zettler, Linda A // ISME Journal: Multidisciplinary Journal of Microbial Ecology;Feb2012, Vol. 6 Issue 2, p309 

    The Moorea Coral Reef Long Term Ecological Research (LTER) Site (17.50°S, 149.83°W) comprises the fringe of coral reefs and lagoons surrounding the volcanic island of Moorea in the Society Islands of French Polynesia. As part of our Microbial Inventory Research Across Diverse Aquatic LTERS...

  • Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. Rodriguez-R, Luis M; Overholt, Will A; Hagan, Christopher; Huettel, Markus; Kostka, Joel E; Konstantinidis, Konstantinos T // ISME Journal: Multidisciplinary Journal of Microbial Ecology;Sep2015, Vol. 9 Issue 9, p1928 

    Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns...

  • Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. Pantos, Olga; Bongaerts, Pim; Dennis, Paul G; Tyson, Gene W; Hoegh-Guldberg, Ove // ISME Journal: Multidisciplinary Journal of Microbial Ecology;Sep2015, Vol. 9 Issue 9, p1916 

    Reef-building corals form complex relationships with a range of microorganisms including bacteria, archaea, fungi and the unicellular microalgae of the genus Symbiodinium, which together form the coral holobiont. These symbionts are known to have both beneficial and deleterious effects on their...

  • Physiological Status and Community Composition of Microbial Mats of the Ebro Delta, Spain, by Signature Lipid Biomarkers. Navarrete, A.; Peacock, A.; Macnaughton, S. J.; Urmeneta, J.; Mas-Castellà, J.; White, D. C.; Guerrero, R. // Microbial Ecology;Jan2000, Vol. 39 Issue 1, p92 

    Physiological status of microbial mats of the Ebro Delta (Tarragona, Spain) based on the extraction of lipids considered ``signature lipid biomarkers'' (SLB) from the cell membranes and walls of microorganisms has been analyzed. Data from a day–night cycle show significant differences in...

  • Primeval pools. Schmidt, Karen // New Scientist;7/2/2005, Vol. 187 Issue 2506, p40 

    The article presents a study of mountains' limestone layers and caves, as well as gushing up from deep and ancient aquifers, the pools, or pozas as the locals call them. Whatever their origins, though, the pozas contain a profusion of microbial communities, leaving biologists wondering how so...

  • Distinct Soil Bacterial Communities Revealed under a Diversely Managed Agroecosystem. Shange, Raymon S.; Ankumah, Ramble O.; Ibekwe, Abasiofiok M.; Zabawa, Robert; Dowd, Scot E. // PLoS ONE;Jul2012, Vol. 7 Issue 7, p1 

    Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to...

  • Coherent dynamics and association networks among lake bacterioplankton taxa. Eiler, Alexander; Heinrich, Friederike; Bertilsson, Stefan // ISME Journal: Multidisciplinary Journal of Microbial Ecology;Feb2012, Vol. 6 Issue 2, p330 

    Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these are largely unknown. We used 454 pyrosequencing of 16S rRNA genes to study associations of...

  • Metamorphosis of a Butterfly-Associated Bacterial Community. Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah // PLoS ONE;Jan2014, Vol. 9 Issue 1, p1 

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics