Ensifer (syn. Sinorhizobium) meliloti U143 is an effective nitrogen-fixing strain isolated from Uruguayan soils. For decades, this strain has been used as an inoculant for different alfalfa ...cultivars. Here we report for the first time a characterization of the U143 elite strain that includes the preliminary genomic sequence, its annotation, and physiological parameters related to its symbiotic efficiency and nitrate respiration capacity. Through Illumina sequencing, the genome of the U143 strain was sequenced. The genome length was 6,801,966 bp, and it contained two megaplasmids, an average GC content of 62.15 %, and 6522 protein-coding sequences. In the symbiotic plasmid, we identified nap, nir, nor, and nos sequences that explain the ability of the U143 strain to respire NO3- in free-living and microaerobic conditions. Field assays performed in two locations for two years showed that alfalfa inoculated with the U143 strain produced 41 % more total shoot dry matter than the non-inoculated control, and between 61.3 % and 66.5 % of shoot N in alfalfa inoculated with strain U143 derived from nitrogen fixation.
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•Ensifer meliloti U143 strain was isolated from Medicago sativa nodules in Uruguayan soils. .•Elite U143 strain has been used as a commercial inoculant for alfalfa cultivars since 1991.•The genome length was 6,807,606 bp, with a GC average content of 62.14 % and 6522 protein-coding sequences.
The endemic spread of plastic in the environment requires urgent need of a sustainable approach. Marine microbes found to have vast bioactivity and play a central role in biogeochemical cycling in ...the ocean; however, very few of them had been explored for biochemical cycling or plastic degradation. In the present study, we report the draft genome sequence of marine Bacillus sp. AIIW2 which was found to utilize plastic as a carbon source. The Bacillus sonorensis SRCM101395 was used as a reference genome for mapping the reads. The genome size of strain AIIW2 was approximately 4.4 Mb and composed of 4737 coding sequences with 45.7% G + C contents. The whole genome comparison of strain AIIW2 with three closest Bacillus strains showed strain specificity, the 16S ribosomal RNA sequence shows 99.93% similarity with Bacillus paralicheniformis KJ‐16T (KY694465). This genome data would provide the genetic basis in developing plastic bioremediation approaches and discover the enzymes pertinent in the biodegradation processes.
The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting ...individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.
To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.
MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .
The fungal genus
, which causes a variety of crop diseases, is widely distributed in the world. Alternaria leaf blight, caused by
, is one of the most common and destructive diseases in carrot. The ...infection of
leads to dramatic decay on both foliage and taproot in severe cases, which results in significant yield losses. In this study, we sequenced and assembled the genome of
isolate CALB1, which isolated from the major carrot producing areas of China. A total of 65 contigs were assembled, and the estimated genome size was 34.9 Mb. The draft genome of
can be used for comparative genomic analysis of
species and provide genetic information for further research on plant-pathogen interactions.
, the carrot cyst nematode, is a significant pest affecting carrot globally. Here we present the draft genome of
, which was generated from short read libraries from Illumina HiSeq technology, and ...the corresponding genome annotation.
A urease-producing Gram-stain-positive actinobacterium, designated strain T5
T
, was isolated from a soil sample collected at a highway hillslope in Selangor, Malaysia. The strain was found to ...produce pale yellowish-pink aerial mycelia with smooth long chain spores and extensively branched light yellowish-pink substrate mycelia on oatmeal agar. Strain T5
T
grew at 15–37 °C, pH 6–11, and tolerated up to 9 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 6–9 and without NaCl. The whole-cell sugar hydrolysate of strain T5
T
contained galactose, glucose and ribose. The
ll
-diaminopimelic acid isomer was detected in the cell wall. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were found to be the predominant polar lipids. The main fatty acids were anteiso-C
17 : 0
, iso-C
16 : 0
, anteiso-C
15 : 0
and iso-C
14 : 0
. Comparative analysis of the 16S rRNA gene sequences indicated that strain T5
T
belonged to
Streptomyces
of the family
Streptomycetaceae
with the highest 16S rRNA gene sequence similarity to
Streptomyces lichenis
LCR6-01
T
(99.0 %). The overall genome relatedness indices revealed that the closest related species was
S. lichenis
LCR6-01
T
with 89.4 % average nucleotide identity and 33.7 % digital DNA–DNA hybridization. Phylogeny analyses showed that strain T5
T
was closely related to
Streptomyces fradiae
,
Streptomyces lavendofoliae
,
Streptomyces lichenis
,
Streptomyces roseolilacinus
and
Streptomyces somaliensis
. Based on these polyphasic data, strain T5
T
represents a novel species, for which the name
Streptomyces solincola
sp. nov. is proposed. The type strain is T5
T
(=TBRC 5137
T
= DSM 42166
T
).
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold ...sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).
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•The genes involving in nitrogen metabolism were identified from draft genome.•The change levels of pathway genes under organic and inorganic N were investigated.•Three types of ...nitrate reductase are present in SND strain Klebsiella sp. KSND.•Hydroxylamine reductase showed activity in NH2OH to generate NH4+.
Here, the draft genome of simultaneous nitrification-denitrification strain (SND) Klebsiella sp. KSND revealed possible existence of genes involved in N-assimilation and -dissimilation pathways. The change levels of genes under defined N-sources were analyzed by Quantitative Real-Time PCR. It suggested that NH4+-assimilation via NADP-glutamate dehydrogenase pathway would occur preferentially. NirBD genes were tightly regulated in a lower level, so that nitrite was rapidly consumed for detoxication by denitrification. Three types of nitrate reductase homologues are surprisingly present in KSND, whereas the dominant nitrate reduction for assimilation and denitrification processes mediates by NapA-type nitrate reductase. Nitric oxide reductase homologues FlRd and FlRd-red provide an adequate capacity for NO detoxification. The recombinant hydroxylamine reductase showed high activity in hydroxylamine to generate ammonium, which might contribute to detoxification mechanism in nitrogen cycling. Overall, this study firstly provides valuable insights into the genes expression and enzyme action, which helps understanding the mechanism of SND processes.
A novel yellow-pigmented catalase- and oxidase-positive bacterial strain (designated NA20
) was isolated from wetland soil and characterized. Results of 16S rRNA and draft genome sequence analysis ...placed strain NA20
within the genus
of the family
. Strain NA20
showed ≤97.1 % sequence similarity to members of the genus
and the highest sequence similarity was found to
DY
(97.1%). The draft genome of strain NA20
had a total length of 7 144 125 base pairs. A total of 5659 genes were identified, of which 5613 were CDS and 46 RNA genes were assigned a putative function. Mining the genomes revealed the presence of 225 carbohydrate genes out of 1334 genes. Strain NA20
contained iso-C
, iso-C
G, iso-C
3-OH and summed feature 3 (C
7
and/or C
6
) as major fatty acids. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unknown polar lipid and one unknown aminophospholipid. Additionally, the functional analysis of NA20
showed the conversion of protopanaxatriol-mix type major ginsenosides (Rb1, Rc and Rd) to minor ginsenosides F2 and weak conversion of Rh2 and C-K within 24 h. As a result, the genotypic, phenotypic and taxonomic analyses support the affiliation of NA20
within the genus
, for which the name
sp. nov. is proposed. The type strain is NA20
(=KACC 22218
=LMG 32198
).
Two novel strains (N1Y82
and N1F302
) were isolated from a marine sediment sample taken from the coastal zone of Weihai, PR China. Cells of the two strains were Gram-strain-negative, ...catalase-positive, oxidase-positive, non-motile and ovoid- to rod-shaped. Strain N1Y82
grew optimally at 16 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. Strain N1F302
grew optimally at 28 °C, pH 7.0-7.5 and in the presence of 2.0-2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strains N1Y82
and N1F302
belonged to the genus
, and were mostly related to
KCTC 23959
with sequence similarity of 96.5 and 97.1 %, respectively. For these two novel strains, C
ω7
was the major fatty acid, ubiquinone 10 was the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and one unidentified phospholipid were the major polar lipids. The DNA G+C contents of strain N1Y82
and N1F302
were 61.3 and 59.0 %, respectively. Consequently, strains N1Y82
and N1F302
are considered to represent two novel species of the genus
, for which the names
sp. nov. and
sp. nov. are proposed. The type strains are N1Y82
(=KCTC 82768
=MCCC 1H00524
) and N1F302
(=KCTC 82412
=MCCC 1H00525
), respectively.
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