Challenges and Approaches in Microbiome Research: From Fundamental to Applied

被引:102
作者
Sergaki, Chrysi [1 ]
Lagunas, Beatriz [1 ]
Lidbury, Ian [1 ]
Gifford, Miriam L. [1 ,2 ]
Schafer, Patrick [1 ,2 ]
机构
[1] Univ Warwick, Sch Life Sci, Coventry, W Midlands, England
[2] Univ Warwick, Warwick Integrat Synthet Biol Ctr, Coventry, W Midlands, England
基金
英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会;
关键词
microbial community; root interactions; cropping systems; gnotobiotic; omics; microbial function; RHIZOSPHERE MICROBIOME; BACTERIAL COMMUNITY; ROOT MICROBIOME; CARBON FLOW; CROP PRODUCTIVITY; PLANT MICROBIOME; SOIL MICROBIOMES; HUMAN GENOME; DIVERSITY; ARABIDOPSIS;
D O I
10.3389/fpls.2018.01205
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
引用
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页数:12
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共 158 条
[21]   The rhizosphere microbiome and plant health [J].
Berendsen, Roeland L. ;
Pieterse, Corne M. J. ;
Bakker, Peter A. H. M. .
TRENDS IN PLANT SCIENCE, 2012, 17 (08) :478-486
[22]   The frequency of mutators in populations of Escherichia coli [J].
Boe, L ;
Danielsen, M ;
Knudsen, S ;
Petersen, JB ;
Maymann, J ;
Jensen, PR .
MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS, 2000, 448 (01) :47-55
[23]   Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities [J].
Bonilla, Nuria ;
Vida, Carmen ;
Martinez-Alonso, Maira ;
Landa, Blanca B. ;
Gaju, Nuria ;
Cazorla, Francisco M. ;
de Vicente, Antonio .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2015, 81 (10) :3405-3418
[24]   Root microbiome relates to plant host evolution in maize and other Poaceae [J].
Bouffaud, Marie-Lara ;
Poirier, Marie-Andree ;
Muller, Daniel ;
Moenne-Loccoz, Yvan .
ENVIRONMENTAL MICROBIOLOGY, 2014, 16 (09) :2804-2814
[25]   Human alteration of the global nitrogen and phosphorus soil balances for the period 1970-2050 [J].
Bouwman, A. F. ;
Beusen, A. H. W. ;
Billen, G. .
GLOBAL BIOGEOCHEMICAL CYCLES, 2009, 23
[26]   Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria [J].
Bruto, Maxime ;
Prigent-Combaret, Claire ;
Muller, Daniel ;
Moenne-Loccoz, Yvan .
SCIENTIFIC REPORTS, 2014, 4
[27]   Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley [J].
Bulgarelli, Davide ;
Garrido-Oter, Ruben ;
Muench, Philipp C. ;
Weiman, Aaron ;
Droege, Johannes ;
Pan, Yao ;
McHardy, Alice C. ;
Schulze-Lefert, Paul .
CELL HOST & MICROBE, 2015, 17 (03) :392-403
[28]   Structure and Functions of the Bacterial Microbiota of Plants [J].
Bulgarelli, Davide ;
Schlaeppi, Klaus ;
Spaepen, Stijn ;
van Themaat, Emiel Ver Loren ;
Schulze-Lefert, Paul .
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64, 2013, 64 :807-838
[29]   Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota [J].
Bulgarelli, Davide ;
Rott, Matthias ;
Schlaeppi, Klaus ;
van Themaat, Emiel Ver Loren ;
Ahmadinejad, Nahal ;
Assenza, Federica ;
Rauf, Philipp ;
Huettel, Bruno ;
Reinhardt, Richard ;
Schmelzer, Elmon ;
Peplies, Joerg ;
Gloeckner, Frank Oliver ;
Amann, Rudolf ;
Eickhorst, Thilo ;
Schulze-Lefert, Paul .
NATURE, 2012, 488 (7409) :91-95
[30]   Application of metatranscriptomics to soil environments [J].
Carvalhais, Lilia C. ;
Dennis, Paul G. ;
Tyson, Gene W. ;
Schenk, Peer M. .
JOURNAL OF MICROBIOLOGICAL METHODS, 2012, 91 (02) :246-251