Journal ArticleDOI
Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure
TLDR
In this paper, the authors examined the composition and substrate utilization profiles of microbial communities at the Morrow plots in Illinois and assessed microbial community composition with 16S rRNA gene sequencing and subsequent bioinformatic analyses.Abstract:
Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois. Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community- level substrate utilization is characterized with the BIOLOG EcoPlate. Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not crop-rotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization. Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.read more
Citations
More filters
Journal ArticleDOI
Research priorities for harnessing plant microbiomes in sustainable agriculture.
Posy E. Busby,Chinmay Soman,Maggie R. Wagner,Maren L. Friesen,James M. Kremer,Alison E. Bennett,Mustafa Morsy,Jonathan A. Eisen,Jan E. Leach,Jeffery L. Dangl +9 more
TL;DR: In this paper, the authors identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, and (4) determine functional mechanisms of plant microbiome interactions.
Journal ArticleDOI
On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics.
TL;DR: Three major questions that must be answered are focused on to move from current Breeding 3.0 practices to Breeding 4.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes.
Journal ArticleDOI
Introducing the North American project to evaluate soil health measurements
Charlotte E. Norris,G. Mac Bean,Shannon Cappellazzi,Michael P. Cope,Kelsey L. H. Greub,Daniel Liptzin,Elizabeth L. Rieke,P. W. Tracy,Cristine L.S. Morgan,C. Wayne Honeycutt +9 more
Journal ArticleDOI
Effects of organic substitution for synthetic N fertilizer on soil bacterial diversity and community composition: A 10-year field trial in a tea plantation
TL;DR: In this paper, the effect of organic substitution ratio (OSR) on soil bacterial communities was investigated in a field experiment with six treatments, from pure synthetic fertilization (NPK) to 100% N substituted with organic fertilizer (OM100), and the results indicated the tradeoff effect between tea yield and soil bacterial diversity under different OSRs.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
vegan: Community Ecology Package
Jari Oksanen,F. Guillaume Blanchet,Roeland Kindt,Pierre Legendre,Peter R. Minchin,Robert B. O'Hara,Gavin Simpson,Péter Sólymos,M. Henry H. Stevens,Helene H. Wagner +9 more
Journal ArticleDOI
FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies
Tanja Magoc,Steven L. Salzberg +1 more
TL;DR: FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
Journal ArticleDOI
Species assemblages and indicator species:the need for a flexible asymmetrical approach
Marc Dufrêne,Pierre Legendre +1 more
TL;DR: A new and simple method to find indicator species and species assemblages characterizing groups of sites, and a new way to present species-site tables, accounting for the hierarchical relationships among species, is proposed.
Related Papers (5)
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