Abstract
To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
GENOME ANNOUNCEMENT
Plant-microbe interactions within the rhizosphere have been shown to have important roles in plant health and productivity (1, 4, 8, 20). As part of an ongoing effort to better understand the microbial communities associated with native Populus deltoides (Eastern cottonwood), we have under taken both cultivation-independent and cultivation-dependent assessments of microbial communities from the P. deltoides rhizosphere and endosphere (3, 5, 25). Our goal is to understand the diversity of the Populus microbiome and to elucidate the metabolic and molecular mechanisms responsible for shaping Populus-microbe root interactions.
We sampled P. deltoides at sites along the Caney Fork River in central Tennessee and at the Yadkin River in North Carolina. These sites represent ecotypes and soil conditions that are common to this region. Approximately 1,100 diverse bacterial strains were collected to investigate phylogenetic and functional diversity. The isolates comprise 7 classes and 85 genera of bacteria, including Actinobacterium (14%), Bacillus (17%), Flavobacterium (6%), Sphingobacterium (3%), Alphaproteobacteria (22%), Betaproteobacteria (16%), and Gammaproteobacteria (22%). A number of our isolates were Pseudomonas species, which have considerable genetic and phenotypic variability and include pathogenic, biocontrol, and plant growth-promoting bacteria (14, 21). Pseudomonads were also found to be one of the most common operational taxonomic units (OTUs) using direct rRNA gene sequencing of P. deltoides endosphere and rhizosphere samples (5). While representatives were chosen for genome sequencing based on overall phenotypic traits and phylogeny, a special emphasis was placed on sequencing P. fluorescens-like organisms. In all, 23 strains of Gammaproteobacteria, 5 of Betaproteobacteria, 8 of Alphaproteobacteria, 2 of Bacteroidetes, and 2 of Firmicutes were sequenced.
Paired-end DNA libraries with an average insert size of 500 bp were created and draft genome data were generated using Illumina (2) HiSeq2000 technology. CLC Genomics Workbench (version 4.7.1) and FASTQC (13) were applied to trim reads for quality sequence data. Trimmed Illumina data were assembled mostly using the CLC Genomics Workbench (version 4.9), although better assemblies for isolates AP49, BC25, CF314, GM16, and GM49 were generated with Velvet (version 1.2) (26). Draft genome sequences were annotated using the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) integrated microbial genomes database and comparative analysis system (IMG) (15), and contigs of 500 bp or greater were deposited at the National Center for Biotechnology Information GenBank database. The median value for the largest contig in each genome was 249,964 bp, and key attributes for the genome sequences are summarized in Table 1.
Table 1.
Summary of genome sequences for 40 rhizosphere and endosphere bacteria
| Organism | Origina | Coverage (fold) | No. of contigs | % GC | N50 | No. of CDS | Genome size (bp) | Accession no. |
|---|---|---|---|---|---|---|---|---|
| Acidovorax sp. strain CF316 | E | 310 | 315 | 67 | 37,104 | 7,206 | 7,086,227 | AKJX00000000 |
| Bradyrhizobium sp. strain YR681 | E | 250 | 351 | 64 | 37,719 | 8,302 | 7,831,714 | AKIY00000000 |
| Brevibacillus sp. strain CF112 | E | 560 | 172 | 54 | 76,367 | 5,272 | 5,271,824 | AKKB00000000 |
| Brevibacillus sp. strain BC25 | E | 650 | 140 | 47 | 68,877 | 6,021 | 6,279,079 | AKIX00000000 |
| Caulobacter sp. strain AP07 | R | 390 | 326 | 69 | 30,563 | 5,373 | 5,615,958 | AKKF00000000 |
| Chryseobacterium sp. strain CF314 | E | 1,200 | 119 | 37 | 80,113 | 4,125 | 4,484,672 | AKJY00000000 |
| Flavobacterium sp. strain CF136 | E | 2,721 | 113 | 34 | 89,762 | 4,366 | 5,102,016 | AKJZ00000000 |
| Herbaspirillum sp. strain CF444 | E | 520 | 125 | 60 | 82,125 | 5,004 | 5,594,732 | AKJW00000000 |
| Herbaspirillum sp. strain YR522 | E | 530 | 168 | 63 | 54,530 | 4,949 | 5,113,042 | AKJA00000000 |
| Novosphingobium sp. strain AP12 | R | 430 | 187 | 66 | 54,713 | 5,532 | 5,611,617 | AKKE00000000 |
| Pantoea sp. strain GM01 | R | 680 | 102 | 54 | 91,591 | 4,998 | 5,320,548 | AKIU00000000 |
| Pantoea sp. strain YR343 | R | 700 | 128 | 55 | 94,033 | 4,900 | 5,314,049 | AKIT00000000 |
| Phyllobacterium sp. strain YR531 | E | 990 | 41 | 53 | 257,533 | 4,901 | 4,997,302 | AKIZ00000000 |
| Polaromonas sp. strain CF318 | E | 620 | 159 | 65 | 61,518 | 4,828 | 5,008,816 | AKIV00000000 |
| Pseudomonas sp. strain GM16 | E | 2,300 | 128 | 59 | 122,673 | 5,888 | 6,550,518 | AKJV00000000 |
| Pseudomonas sp. strain GM84 | R | 256 | 384 | 63 | 24,795 | 5,295 | 5,818,772 | AKJC00000000 |
| Pseudomonas sp. strain GM24 | E | 3,200 | 399 | 59 | 32,656 | 5,885 | 6,517,063 | AKJR00000000 |
| Pseudomonas sp. strain GM102 | E | 440 | 159 | 59 | 88,165 | 6,039 | 6,657,346 | AKJB00000000 |
| Pseudomonas sp. strain GM33 | E | 440 | 205 | 60 | 61,913 | 6,102 | 6,727,223 | AKJO00000000 |
| Pseudomonas sp. strain GM78 | E | 469 | 235 | 60 | 57,174 | 6,724 | 7,287,561 | AKJF00000000 |
| Pseudomonas sp. strain GM80 | E | 474 | 282 | 59 | 39,805 | 6,245 | 6,786,162 | AKJD00000000 |
| Pseudomonas sp. strain GM17 | E | 480 | 280 | 63 | 44,590 | 6,105 | 6,786,964 | AKJU00000000 |
| Pseudomonas sp. strain GM79 | E | 486 | 126 | 59 | 96,213 | 6,062 | 6,707,010 | AKJE00000000 |
| Pseudomonas sp. strain GM67 | E | 509 | 183 | 60 | 68,050 | 6,003 | 6,502,113 | AKJH00000000 |
| Pseudomonas sp. strain GM74 | R | 512 | 180 | 60 | 75,201 | 5,562 | 6,104,277 | AKJG00000000 |
| Pseudomonas sp. strain GM30 | E | 520 | 180 | 60 | 59,627 | 5,611 | 6,140,967 | AKJP00000000 |
| Pseudomonas sp. strain GM41 | E | 520 | 164 | 59 | 75,073 | 6,066 | 6,615,479 | AKJN00000000 |
| Pseudomonas sp. strain GM50 | E | 520 | 155 | 59 | 68,220 | 6,068 | 6,692,143 | AKJK00000000 |
| Pseudomonas sp. strain GM25 | R | 530 | 91 | 61 | 137,130 | 5,758 | 6,350,607 | AKJQ00000000 |
| Pseudomonas sp. strain GM49 | R | 530 | 345 | 60 | 31,212 | 6,253 | 6,589,890 | AKJL00000000 |
| Pseudomonas sp. strain GM60 | E | 540 | 181 | 60 | 62,804 | 5,911 | 6,424,244 | AKJI00000000 |
| Pseudomonas sp. strain GM21 | E | 570 | 210 | 58 | 57,752 | 6,072 | 6,609,272 | AKJS00000000 |
| Pseudomonas sp. strain GM55 | E | 574 | 163 | 60 | 77,637 | 5,985 | 6,489,331 | AKJJ00000000 |
| Pseudomonas sp. strain GM18 | E | 580 | 140 | 60 | 106,048 | 5,711 | 6,297,618 | AKJT00000000 |
| Pseudomonas sp. strain GM48 | R | 580 | 200 | 59 | 59,542 | 5,902 | 6,443,787 | AKJM00000000 |
| Rhizobium sp. strain CF142 | E | 445 | 150 | 60 | 85,172 | 7,240 | 7,457,089 | AJWE00000000 |
| Rhizobium sp. strain CF122 | E | 543 | 130 | 60 | 117,778 | 6,090 | 6,142,299 | AKKA00000000 |
| Rhizobium sp. strain AP16 | E | 555 | 96 | 60 | 123,519 | 6,143 | 6,497,619 | AJVM00000000 |
| Sphingobium sp. strain AP49 | E | 665 | 99 | 63 | 89,526 | 4,585 | 4,479,274 | AJVL00000000 |
| Variovorax sp. strain CF313 | E | 2,200 | 173 | 67 | 65,214 | 5,674 | 6,029,174 | AKIW00000000 |
| Median | 530 | 166 | 60 | 68,549 | 5,895 | 6,387,426 |
E, endosphere; R, rhizosphere.
Recently, a number of genome sequences for plant growth-promoting and biocontrol bacteria have been reported (6, 7, 9–12, 16–19, 22–24, and 27). The genome sequences reported in this study will facilitate comprehensive comparisons of bacteria involved in plant-microbe interactions.
Nucleotide sequence accession numbers.
The nucleotide sequences have been deposited in DDBJ/EMBL/GenBank under the accession numbers provided in Table 1, and the versions described in this paper are the first versions. The entire DNA sequence data set has been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (accession number SRA050017).
ACKNOWLEDGMENTS
This research was sponsored by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological and Environmental Research, as part of the Plant Microbe Interfaces Scientific Focus Area (http://pmi.ornl.gov). Oak Ridge National Laboratory is managed by UT-Battelle LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.
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