Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced ...Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Drought is a major threat to crop productivity and causes decreased plant growth, poor yields, and crop failure. Nevertheless, the frequency of droughts is expected to increase in the coming decades. ...The microbial communities associated with crop plants can influence how plants respond to various stresses; hence, microbiome manipulation is fast becoming an effective strategy for improving the stress tolerance of plants. The effect of drought stress on the root microbiome of perennial woody plants is currently poorly understood. Using
Populus
trees as a model ecosystem, we found that the diversity of the root microbial community decreased during drought treatment and that compositional shifts in microbes during drought stress were driven by the relative abundances of a large number of dominant phyla, including Actinobacteria, Firmicutes, and Proteobacteria. A subset of microbes, including
Streptomyces rochei
,
Bacillus arbutinivorans
,
B. endophyticus
,
B. megaterium
,
Aspergillus terreus
,
Penicillium raperi
,
Trichoderma ghanense
,
Gongronella butleri
, and
Rhizopus stolonifer
, was isolated from the drought-treated poplar rhizosphere soils, which have potentially beneficial to plant fitness. Further controlled inoculation experiments showed that the isolated bacterial and fungal isolates positively impacted plant growth and drought tolerance. Collectively, our results demonstrate the impact of drought on root microbiome structure and provide a novel example of manipulating root microbiomes to improve plant tolerance.
Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and ...potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication.
RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs.
MiRNAs that originated in 5′ untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes.
Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Most biological nitrogen fixation is catalyzed by molybdenum-dependent nitrogenase, an enzyme complex comprising two component proteins that contains three different metalloclusters. Diazotrophs ...contain a common core of nitrogen fixation nif genes that encode the structural subunits of the enzyme and components required to synthesize the metalloclusters. However, the complement of nif genes required to enable diazotrophic growth varies significantly amongst nitrogen fixing bacteria and archaea. In this study, we identified a minimal nif gene cluster consisting of nine nif genes in the genome of Paenibacillus sp. WLY78, a gram-positive, facultative anaerobe isolated from the rhizosphere of bamboo. We demonstrate that the nif genes in this organism are organized as an operon comprising nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV and that the nif cluster is under the control of a σ(70) (σ(A))-dependent promoter located upstream of nifB. To investigate genetic requirements for diazotrophy, we transferred the Paenibacillus nif cluster to Escherichia coli. The minimal nif gene cluster enables synthesis of catalytically active nitrogenase in this host, when expressed either from the native nifB promoter or from the T7 promoter. Deletion analysis indicates that in addition to the core nif genes, hesA plays an important role in nitrogen fixation and is responsive to the availability of molybdenum. Whereas nif transcription in Paenibacillus is regulated in response to nitrogen availability and by the external oxygen concentration, transcription from the nifB promoter is constitutive in E. coli, indicating that negative regulation of nif transcription is bypassed in the heterologous host. This study demonstrates the potential for engineering nitrogen fixation in a non-nitrogen fixing organism with a minimum set of nine nif genes.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial ...community composition in
rhizosphere is not well understood.
This study measured soil physiochemistry properties and root exudates in a representative forest consists of four
species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing.
Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four
species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities.
,
,
,
, and
were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable
microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes.
This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of
plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in
rhizosphere.
Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating ...abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (
). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes.
transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of
(
) gene. To examine the potential biological functions of
, we generated a transgenic
plant that constitutively overexpresses the
gene. Compared to wild-type (WT) plants, overexpressing transgenic
plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that
mitigates abiotic stresses through the modulation of ROS scavenging.
Bacillus
has been extensively studied for agricultural application as a biocontrol agent.
B. altitudinis
GLB197, an endophytic bacterium isolated from grape leaves, exhibits distinctive inhibition to ...grape downy mildew based on unknown mechanisms. To determine the genetic traits involved in the mechanism of biocontrol and host-interaction traits, the genome sequence of GLB197 was obtained and further analyzed. The genome of
B. altitudinis
GLB197 consisted of one plasmid and a 3,733,835-bp circular chromosome with 41.56% G + C content, containing 3,770 protein-coding genes. Phylogenetic analysis of 17
Bacillus
strains using the concatenated 1,226 single-copy core genes divided into different clusters was conducted. In addition, average nucleotide identity (ANI) values indicate that the current taxonomy of some
B. pumilus
group strains is incorrect. Comparative analysis of
B. altitudinis
GLB197 proteins with other
B. altitudinis
strains identified 3,157 core genes. Furthermore, we found that the pan-genome of
B. altitudinis
is open. The genome of
B. altitudinis
GLB197 contains one nonribosomal peptide synthetase (NRPS) gene cluster which was annotated as lichenysin. Interestingly, the cluster in
B. altitudinis
has two more genes than other
Bacillus
strains (
lgrD
and
lgrB
). The two genes were probably obtained
via
horizontal gene transfer (HGT) during the evolutionary process from
Brevibacillus
. Taken together, these observations enable the future application of
B. altitudinis
GLB197 as a biocontrol agent for control of grape downy mildew and promote our understanding of the beneficial interactions between
B. altitudinis
GLB197 and plants.
Pantoea beijingensis
, a gram-negative pathogenic bacterium, causes soft rot disease in the fungus
Pleurotus eryngii
in China. However, the taxonomic classification of this pathogen is controversial ...due to close relationships between bacteria of the genera
Pantoea
and
Erwinia
. This study aimed to resolve the identity of
P. beijingensis
using phylogenomic and systematic analyses of
Pantoea
and
Erwinia
by whole-genome sequencing. Single-copy orthologs identified from the
Erwinia/Pantoea
core genomes were used to delineate
Erwinia/Pantoea
phylogeny.
P. beijingensis
LMG27579
T
clustered within a single
Erwinia
clade. A whole-genome-based phylogenetic tree and average nucleotide and amino-acid identity values indicate that
P. beijingensis
LMG27579
T
should be renamed
Erwinia beijingensis
. The
hrp/hrc
genes encoding type III secretion system (T3SS) proteins in
Erwinia
and
Pantoea
were divided into five groups according to gene contents and organization. Neighbor-joining-inferred phylogenetic trees based on concatenated HrcU, HrcN, and HrcR in the main
hrp/hrc
cluster showed that
E
.
beijingensis
T3SS proteins are closely related to those in
Ewingella americana
, implying that
E
.
beijingensis
and
E. americana
have a recent common
hrp
/
hrc
gene ancestor. Furthermore, T3SS proteins of
Erwinia
and
Pantoea
were clustered in different clades separated by other bacterial T3SS proteins. Thus, T3SS genes in
Pantoea
and
Erwinia
strains might have been acquired by horizontal gene transfer. Overall, our findings clarify the taxonomy of the bacterium causing soft rot in
P. eryngii,
as well as the genetic structure and classification of the
hrp
/
hrc
T3SS virulence factor. We propose that T3SS acquisition is important for
E
.
beijingensis
emergence and pathogenesis.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to ...fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of
gene family in 20 plant species (from green algae to angiosperms) and their functional roles in
. We identified 125 putative
genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that
genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of
genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In
, segmental duplication appears to be the main mechanism for the expansion of
genes. Specially, most
genes duplicated in salicoids are regulated by
-specific microRNAs. Furthermore, compared with common
-specific
s have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these
may have undergone functional divergence. Our study explores the specific roles of
in the
genome and provides new insights for functional investigation of this gene family.
Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating ...xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation. Here, we emphasize the necessity of using in situ transcriptomes and anatomical information to construct the most plausible xylem development model.
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