Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition

Biotechnology for Biofuels
Cheng WangWeixiang Wu

Abstract

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofura...Continue Reading

References

Jun 1, 1987·Journal of Bacteriology·F J Stutzenberger
Jan 1, 1997·Critical Reviews in Biotechnology·A Sunna, G Antranikian
Aug 1, 1997·Phytochemistry·K HayashiS Hara
May 20, 2000·Biotechnology & Genetic Engineering Reviews·R A PradeA J Mort
Oct 17, 2001·Bioresource Technology·A HassenA Boudabous
Mar 6, 2003·Bioresource Technology·Des Raj KashyapRupinder Tewari
May 4, 2004·Nature Biotechnology·Diego MartinezDaniel Rokhsar
Jun 25, 2004·The Biochemical Journal·Alisdair B BorastonGideon J Davies
Jul 15, 2005·International Journal of Systematic and Evolutionary Microbiology·D P Labeda, R M Kroppenstedt
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Feb 8, 2006·Applied and Environmental Microbiology·Dhaval M NanavatiKenneth M Noll
Dec 13, 2006·Microbiology and Molecular Biology Reviews : MMBR·Josef DeutscherPieter W Postma
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Nov 13, 2007·Methods in Molecular Biology·Victor M Markowitz, Nikos C Kyrpides
Jan 9, 2008·Nature Reviews. Microbiology·Harry J FlintBryan A White
Feb 9, 2008·Nature Biotechnology·Lee R LyndCharles E Wyman
Apr 24, 2008·Molecular Microbiology·Girbe BuistOscar P Kuipers
May 20, 2008·Current Opinion in Plant Biology·Debra Mohnen
Jun 10, 2008·Annual Review of Microbiology·Christopher J LawDa-Neng Wang
Nov 14, 2008·Nucleic Acids Research·J R ColeJ M Tiedje
Feb 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer M BrulcBryan A White
Jun 12, 2009·Current Opinion in Biotechnology·Mark MorrisonChristopher S McSweeney
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Jul 6, 2010·Bioresource Technology·Gurdeep RastogiRajesh K Sani
Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·P B PopeM Morrison
Nov 13, 2010·Current Opinion in Biotechnology·Timothy D H BuggRahul Singh
Jan 29, 2011·Science·Matthias HessEdward M Rubin
Jan 1, 2009·Standards in Genomic Sciences·Chris MunkHans-Peter Klenk
Jan 1, 2009·Standards in Genomic Sciences·Rüdiger PukallPhilip Hugenholtz
Feb 11, 2011·Bioscience, Biotechnology, and Biochemistry·Kohsuke HashimotoKeiji Hasumi
Mar 12, 2011·Proceedings of the National Academy of Sciences of the United States of America·Joana L A BrásHarry J Gilbert
Oct 19, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lifeng ZhuFuwen Wei
Jan 4, 2012·Biotechnology for Biofuels·André SchusterMonika Schmoll
Feb 3, 2012·The ISME Journal·Tom O DelmontTimothy M Vogel
May 31, 2012·Nucleic Acids Research·Yanbin YinYing Xu
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Jun 20, 2012·Proceedings of the National Academy of Sciences of the United States of America·Philipp EngelNancy A Moran
Jun 23, 2012·PloS One·Iain AndersonNatalia Ivanova

❮ Previous
Next ❯

Citations

Oct 13, 2016·Frontiers in Microbiology·María-Eugenia DeCastroMaría-Isabel González-Siso
Feb 22, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Nathálya FariasCarlos Meneses
Nov 8, 2017·Extremophiles : Life Under Extreme Conditions·Jonathan BothaDon A Cowan
Jan 4, 2018·BMC Evolutionary Biology·Alexey Sergeevich RozanovSergey Evgenievich Peltek
Feb 3, 2018·Microbial Ecology·Pilar Eliana Puentes-Téllez, Joana Falcao Salles
Oct 8, 2019·3 Biotech·Nurshafika Abd KhalidAdibah Yahya
May 19, 2019·Folia Microbiologica·Kalpana SahooEnketeswara Subudhi
Jun 28, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Carlos MenesesDavid Johnston-Monje
May 26, 2017·Scientific Reports·Anna M AlessiNeil C Bruce
Aug 18, 2017·Applied Biochemistry and Biotechnology·Aravind MadhavanAshok Pandey
Jun 25, 2019·Canadian Journal of Microbiology·Yu FangJichen Chen
Sep 29, 2020·Frontiers in Microbiology·Cheng LongKoen Venema
Nov 14, 2019·Biotechnology for Biofuels·Rahul SinghSyed Shams Yazdani
May 5, 2017·Frontiers in Microbiology·Leandro N LemosJoão C Setubal
Jul 10, 2018·Applied Microbiology and Biotechnology·Hao ZhouAnthony G Hay
Jun 23, 2018·Applied Microbiology and Biotechnology·Marie-Ève Lacombe-HarveyCarole Beaulieu
Sep 24, 2020·Biotechnology Reports·Dixita ChettriAnil Kumar Verma
Jan 9, 2021·Environmental Science and Pollution Research International·Guilin DuBaoguo Zhang
Mar 9, 2021·International Microbiology : the Official Journal of the Spanish Society for Microbiology·Xiaoshen ZhaoHe Li

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRR1292608

Methods Mentioned

BETA
RSA
phosphotransferase
454
PCR

Software Mentioned

MetaPhlAn
MG
SOAPdenovo assembler
MEGAN
SortMeRNA
RAST
BLASTP
mOTU
mOTUs
Mothur

Related Concepts

Related Feeds

Biofuels (ASM)

Biofuels are produced through contemporary processes from biomass rather than geological processes involved in fossil fuel formation. Examples include biodiesel, green diesel, biogas, etc. Discover the latest research on biofuels in this feed.