Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
Reads0
Chats0
TLDR
A metagenomic analysis of the rice straw-adapted microbial consortia enriched from compost ecosystems reveals a new benchmark for microbial enzymatic deconstruction of lignocelluloses, and suggests that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignOcellulosic enzymes in the biofuel industry.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, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.read more
Citations
More filters
Journal ArticleDOI
Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.
Gina R. Lewin,Camila Carlos,Camila Carlos,Marc G. Chevrette,Heidi A. Horn,Bradon R. McDonald,Bradon R. McDonald,Robert J. Stankey,Robert J. Stankey,Brian G. Fox,Cameron R. Currie,Cameron R. Currie +11 more
TL;DR: Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry.
Journal ArticleDOI
Biological valorization strategies for converting lignin into fuels and chemicals
Zhu Chen,Caixia Wan +1 more
TL;DR: This paper reviews the recent development in biological conversion of lignin into value-added products and covers potential catabolic pathways, exploration of new lIGNin degradation systems, and lignIn consolidated bioprocessing (Lignin CBP).
Journal ArticleDOI
Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics.
Luciana Principal Antunes,Layla Farage Martins,Roberta Verciano Pereira,Andrew Maltez Thomas,Deibs Barbosa,Leandro Nascimento Lemos,Gianluca Major Machado Silva,Livia Maria Silva Moura,George Willian Condomitti Epamino,Luciano Antonio Digiampietri,Karen Cristina Lombardi,Patrícia Locosque Ramos,Ronaldo Bento Quaggio,Julio Cezar Franco de Oliveira,Renata C. Pascon,João Batista da Cruz,Aline Maria Da Silva,João C. Setubal,João C. Setubal +18 more
TL;DR: Time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin.
Journal ArticleDOI
Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction.
TL;DR: The results suggest that decomposition of HS coupled to DIR and other anaerobic pathways could play an important role in soil and sediment OC metabolism.
Journal ArticleDOI
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
TL;DR: This review summarizes the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
References
More filters
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Journal ArticleDOI
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin,Ruiqiang Li,Jeroen Raes,Manimozhiyan Arumugam,Kristoffer Sølvsten Burgdorf,Chaysavanh Manichanh,Trine Nielsen,Nicolas Pons,Florence Levenez,Takuji Yamada,Daniel R. Mende,Junhua Li,Junming Xu,Shaochuan Li,Dongfang Li,Jianjun Cao,Bo Wang,Huiqing Liang,Huisong Zheng,Yinlong Xie,Julien Tap,Patricia Lepage,Marcelo Bertalan,Jean-Michel Batto,Torben Hansen,Denis Le Paslier,Allan Linneberg,H. Bjørn Nielsen,Eric Pelletier,Pierre Renault,Thomas Sicheritz-Pontén,Keith Turner,Hongmei Zhu,Chang Yu,Shengting Li,Min Jian,Yan Zhou,Yingrui Li,Xiuqing Zhang,Songgang Li,Nan Qin,Huanming Yang,Jian Wang,Søren Brunak,Joël Doré,Francisco Guarner,Karsten Kristiansen,Oluf Pedersen,Julian Parkhill,Jean Weissenbach,Peer Bork,S. Dusko Ehrlich,Jun Wang +52 more
TL;DR: The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Journal ArticleDOI
Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies,Michael Egholm,William E. Altman,Said Attiya,Joel S. Bader,Lisa A. Bemben,Jan Berka,Michael S. Braverman,Yi-Ju Chen,Zhoutao Chen,Scott Dewell,Lei Du,J. M. Fierro,Xavier V. Gomes,Brian C. Godwin,Wen He,Scott Edward Helgesen,Chun Heen Ho,Gerard P. Irzyk,Szilveszter C. Jando,Maria L. I. Alenquer,Thomas P. Jarvie,Kshama B. Jirage,Jong-Bum Kim,James R. Knight,Janna R. Lanza,John H. Leamon,Steven Lefkowitz,Ming Lei,Jing Li,Kenton Lohman,Hong Lu,Vinod Makhijani,Keith Mcdade,Michael P. McKenna,Eugene W. Myers,Elizabeth Nickerson,John Nobile,Ramona Plant,Bernard P. Puc,Michael T. Ronan,George T. Roth,Gary J. Sarkis,Jan Fredrik Simons,John Simpson,Maithreyan Srinivasan,Karrie R. Tartaro,Alexander Tomasz,Kari A. Vogt,Greg A. Volkmer,Shally H. Wang,Yong Wang,Michael P. Weiner,Pengguang Yu,Richard F. Begley,Jonathan M. Rothberg +55 more
TL;DR: A scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments with 96% coverage at 99.96% accuracy in one run of the machine is described.
Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Journal ArticleDOI
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
James R. Cole,Qiong Wang,Erick Cardenas,Jordan A. Fish,Benli Chai,Ryan J. Farris,A. S. Kulam-Syed-Mohideen,Donna M. McGarrell,Terry L. Marsh,George M. Garrity,James M. Tiedje +10 more
TL;DR: An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
Related Papers (5)
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Matthias Hess,Matthias Hess,Alexander Sczyrba,Alexander Sczyrba,Rob Egan,Rob Egan,Tae-Wan Kim,Harshal A. Chokhawala,Gary P. Schroth,Shujun Luo,Douglas S. Clark,Feng Chen,Feng Chen,Tao Zhang,Tao Zhang,Roderick I. Mackie,Len A. Pennacchio,Len A. Pennacchio,Susannah G. Tringe,Susannah G. Tringe,Axel Visel,Axel Visel,Tanja Woyke,Tanja Woyke,Zhong Wang,Zhong Wang,Edward M. Rubin,Edward M. Rubin +27 more
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more