title: Niche and host-associated functional signatures of the root surface microbiome.
abstract: Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.
authors.affiliation: 1] Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel [2] Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
authors.forename: Maya
authors.initials: M
authors.lastname: Ofek-Lalzar
authors.affiliation: Department of Plant Pathology and Weed Research, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Sela
authors.affiliation: Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel.
authors.forename: Milana
authors.initials: M
authors.lastname: Goldman-Voronov
authors.affiliation: 1] DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60612, USA [2] Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, USA.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: Green
authors.affiliation: Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Hadar
authors.affiliation: Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel.
authors.forename: Dror
authors.initials: D
authors.lastname: Minz
mesh_terms: D018556:Crops, Agricultural / Q000382:microbiology*; D028462:Cucumis / Q000382:microbiology; D004247:DNA / Q000737:chemistry; D004777:Environment; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D015723:Gene Library; D005821:Genetic Techniques; D023281:Genomics; D005838:Genotype; D056186:Metagenomics; D064307:Microbiota; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D010944:Plants / Q000382:microbiology; D017422:Sequence Analysis, DNA; D012987:Soil; D012988:Soil Microbiology; D014908:Triticum / Q000382:microbiology
chemical_list: D012987:Soil; D004247:DNA