Journal ArticleDOI
Direct cellular lysis/protein extraction protocol for soil metaproteomics.
Karuna Chourey,Janet K. Jansson,Nathan C Verberkmoes,Manesh B Shah,Krystle L. Chavarria,Lauren M. Tom,Eoin L. Brodie,Robert L. Hettich +7 more
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TLDR
To the authors' knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures.Abstract:
We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.read more
Citations
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Journal ArticleDOI
Soil enzymes in a changing environment: Current knowledge and future directions
Richard G. Burns,Jared L. DeForest,Juergen Marxsen,Robert L. Sinsabaugh,Mary E. Stromberger,Matthew D. Wallenstein,Michael N. Weintraub,Annamaria Zoppini +7 more
TL;DR: The collective vision of the future of extracellular enzyme research is offered: one that will depend on imaginative thinking as well as technological advances, and be built upon synergies between diverse disciplines.
Journal ArticleDOI
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
Jenni Hultman,Jenni Hultman,Mark P. Waldrop,Rachel Mackelprang,Rachel Mackelprang,Maude M. David,Jack W. McFarland,Steven J. Blazewicz,Jennifer W. Harden,Merritt R. Turetsky,A. David McGuire,Manesh B Shah,Manesh B Shah,Nathan C Verberkmoes,Lang Ho Lee,Konstantinos Mavrommatis,Konstantinos Mavrommatis,Janet K. Jansson +17 more
TL;DR: The combination of several molecular ‘omics’ approaches is used to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog.
Journal ArticleDOI
Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future
Sharon Huws,Christopher J. Creevey,Linda Oyama,Itzhak Mizrahi,Stuart E. Denman,Milka Popova,Rafael Muñoz-Tamayo,Evelyne Forano,Sinead M. Waters,Matthias Hess,Ilma Tapio,Hauke Smidt,Sophie J. Krizsan,David R. Yáñez-Ruiz,Alejandro Belanche,Le Luo Guan,Robert J. Gruninger,Tim A. McAllister,C. Jamie Newbold,Rainer Roehe,Richard J. Dewhurst,Timothy J. Snelling,Mick Watson,Garret Suen,Elizabeth H. Hart,Alison H. Kingston-Smith,Nigel D. Scollan,Rodolpho Martin do Prado,Eduardo Jorge Pilau,Hilário Cuquetto Mantovani,Graeme T. Attwood,Joan E. Edwards,Neil R. McEwan,Steven Morrisson,O. L. Mayorga,Christopher T. Elliott,Diego P. Morgavi +36 more
TL;DR: Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize the understanding of the rumen microbiome, which will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
Journal ArticleDOI
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.
TL;DR: The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information as discussed by the authors.
Journal ArticleDOI
Soil metaproteomics – Comparative evaluation of protein extraction protocols
Katharina M. Keiblinger,Inés C. Wilhartitz,Thomas Schneider,Bernd Roschitzki,Emanuel Schmid,Leo Eberl,Kathrin Riedel,Kathrin Riedel,Sophie Zechmeister-Boltenstern +8 more
TL;DR: This study demonstrates that a critical evaluation of the extraction protocol is crucial for the quality of the metaproteomics data, especially in highly complex samples like natural soils, where extraction with SDS–phenol resulted in “high” numbers of proteins.
References
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