Addition of organic matter such as livestock manures and plant residues is a feasible practice to mitigate soil degradation caused by long-term application of chemical fertilizers, and the mitigation ...is largely mediated though activities of the soil-dwelling microorganisms. However, the roles of different kinds of organic matter in maintaining bacterial community structure have not been assessed in a comparative manner. In this study, 454 pyrosequencing of 16S rRNA gene was employed to compare the bacterial community structure among soils that had been subjected to 30 years of NPK fertilization under six treatment regimes: non-fertilization control, fertilization only, and fertilization combined with the use of pig manure, cow manure or low- and high-level of wheat straws. Consistent with expectation, long-term application of NPK chemical fertilizers caused a significant decrease of bacterial diversity in terms of species richness (i.e. number of unique operational taxonomic units (OTU)), Faith's index of phylogenetic diversity and Chao 1 index. Incorporation of wheat straw into soil produced little effects on bacterial community, whereas addition of either pig manure or cow manure restored bacterial diversity to levels that are comparable to that of the non-fertilization control. Moreover, bacterial abundance determined by quantitative PCR was positively correlated with the nutritional status of the soil (e.g., nitrate, total nitrogen, total carbon, available phosphorus); however, bacterial diversity was predominantly determined by soil pH. Together, our data implicate the role of livestock manures in preventing the loss of bacterial diversity during long-term chemical fertilization, and highlight pH as the major deterministic factor for soil bacterial community structure.
•Long-term chemical fertilization caused a decrease of bacterial diversity in soil.•Bacterial diversity was stabilized with the addition of livestock manures.•Addition of wheat straws increased bacterial abundance but not diversity levels.•Influence on bacterial community structure was mediated via alteration of soil pH.•Livestock manure can mitigate the deleterious effects of chemical fertilizers on soil.
Summary
Pseudomonas aeruginosa rugose small‐colony variants (RSCVs) are frequently isolated from chronic infections, yet, they are rarely reported in environmental isolates. Here, during the ...comparative genomic analysis of two P. aeruginosa strains isolated from crude oil, we discovered a spontaneous in‐frame deletion, wspAΔ280–307, which led to hyper‐biofilm and RSCV phenotypes. WspA is a homologue of methyl‐accepting chemotaxis proteins (MCPs) that senses surfaces to regulate biofilm formation by stimulating cyclic‐di‐guanosine monophosphate (c‐di‐GMP) synthesis through the Wsp system. However, the methylation sites of WspA have never been identified. In this study, we identified E280 and E294 of WspA as methylation sites. The wspAΔ280–307 mutation enabled the Wsp system to lock into a constitutively active state that is independent of regulation by methylation. The result is an enhanced production of c‐di‐GMP. Sequence alignment revealed three conserved repeat sequences within the amino acid residues 280–313 (aa280–313) region of WspA homologues, suggesting that a spontaneous deletion within this DNA encoding region was likely a result of intragenic recombination and that similar mutations might occur in several related bacterial genera. Our results provide a plausible explanation for the selection of RSCVs and a mechanism to confer a competitive advantage for P. aeruginosa in a crude‐oil environment.
Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment ...settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.
The idea that bacteria are social is a popular concept with implications for understanding the ecology and evolution of microbes. The view arises predominately from reasoning regarding extracellular ...products, which, it has been argued, can be considered "public goods." Among the best studied is pyoverdin—a diffusible iron-chelating agent produced by bacteria of the genus Pseudomonas. Here we report the de novo evolution of pyoverdin nonproducing mutants, genetically characterize these types and then test the appropriateness of the sociobiology framework by performing growth and fitness assays in the same environment in which the nonproducing mutants evolved. Our data draw attention to discordance in the fit between social evolution theory and biological reality. We show that pyoverdin-defective genotypes can gain advantage by avoiding the cost of production under conditions where the molecule is not required; in some environments pyoverdin is personalized. By exploring the fitness consequences of nonproducing types under a range of conditions, we show complex genotype-by-environment interactions with outcomes that range from social to asocial. Together these findings give reason to question the generality of the conclusion that pyoverdin is a social trait.
Abstract
Autoactivation of two-component systems (TCSs) can increase the sensitivity to signals but inherently cause a delayed response. Here, we describe a unique negative feedback mechanism ...enabling the global NtrB/NtrC regulator to rapidly respond to nitrogen starvation over the course of histidine utilization (hut) in Pseudomonas fluorescens. NtrBC directly activates transcription of hut genes, but overexpression will produce excess ammonium leading to NtrBC inactivation. To prevent this from occurring, the histidine-responsive repressor HutC fine-tunes ntrBC autoactivation: HutC and NtrC bind to the same operator site in the ntrBC promoter. This newly discovered low-affinity binding site shows little sequence similarity with the consensus sequence that HutC recognizes for substrate-specific induction of hut operons. A combination of genetic and transcriptomic analysis indicated that both ntrBC and hut promoter activities cannot be stably maintained in the ΔhutC background when histidine fluctuates at high concentrations. Moreover, the global carbon regulator CbrA/CbrB is involved in directly activating hut transcription while de-repressing hut translation via the CbrAB-CrcYZ-Crc/Hfq regulatory cascade. Together, our data reveal that the local transcription factor HutC plays a crucial role in governing NtrBC to maintain carbon/nitrogen homeostasis through the complex interactions between two TCSs (NtrBC and CbrAB) at the hut promoter.
The development of new metal‐organic frameworks (MOFs) thin films is important for expanding their functions and applications. Herein, we first report a new kind of MOF thin film by using ...aggregation‐induced emission (AIE) dicarboxyl ligand through a liquid‐phase epitaxial (LPE) layer‐by‐layer (LBL) spraying method (named AIE surface‐coordinated metal‐organic frameworks thin film, AIE‐SURMOF). The obtained AIE‐SURMOF Zn4O(TPE)3 (ZnTPE) has highly growth orientation and homogeneous thin film, showing strong fluorescent property. Furthermore, by loading chiral guest in the MOF pore, the formed chiral encapsulated AIE‐SURMOF can clearly indicate obvious circularly polarized luminescence performance with glum of 0.01. This study provides new MOF thin film and new strategy for expanding function and application of MOF materials.
A new kind of metal‐organic framework (MOF) thin film were prepared by using aggregation‐induced emission (AIE) based ligand through a liquid‐phase epitaxial (LPE) layer‐by‐layer (LBL) spraying method, which is named AIE surface‐coordinated metal‐organic frameworks thin film (AIE‐SURMOF). The obtained AIE‐SURMOF has highly growth orientation and homogeneous thin film, showing strong fluorescent property. Furthermore, by loading chiral guest in the MOF pore, the formed chiral encapsulated AIE‐SURMOF can clearly indicate obvious circularly polarized luminescence performance.
Plant diversity in experimental systems often enhances ecosystem productivity, but the mechanisms causing this overyielding are only partly understood. Intercropping faba beans (Vicia faba L.) and ...maize (Zea mays L.) result in overyielding and also, enhanced nodulation by faba beans. By using permeable and impermeable root barriers in a 2-y field experiment, we show that root–root interactions between faba bean and maize significantly increase both nodulation and symbiotic N₂ fixation in intercropped faba bean. Furthermore, root exudates from maize promote faba bean nodulation, whereas root exudates from wheat and barley do not. Thus, a decline of soil nitrate concentrations caused by intercropped cereals is not the sole mechanism for maize promoting faba bean nodulation. Intercropped maize also caused a twofold increase in exudation of flavonoids (signaling compounds for rhizobia) in the systems. Roots of faba bean treated with maize root exudates exhibited an immediate 11-fold increase in the expression of chalcone–flavanone isomerase (involved in flavonoid synthesis) gene together with a significantly increased expression of genes mediating nodulation and auxin response. After 35 d, faba beans treated with maize root exudate continued to show up-regulation of key nodulation genes, such as early nodulin 93 (ENOD93), and promoted nitrogen fixation. Our results reveal a mechanism for how intercropped maize promotes nitrogen fixation of faba bean, where maize root exudates promote flavonoid synthesis in faba bean, increase nodulation, and stimulate nitrogen fixation after enhanced gene expression. These results indicate facilitative root–root interactions and provide a mechanism for a positive relationship between species diversity and ecosystem productivity.
HutC is known as a transcriptional repressor specific for histidine utilization (
) genes in Gram-negative bacteria, including
SBW25. However, its precise mode of protein-DNA interactions hasn't been ...examined with purified HutC proteins. Here, we performed electrophoretic mobility shift assay (EMSA) and DNase I footprinting using His
-tagged HutC and biotin-labeled probe of the
promoter (P
). Results revealed a complex pattern of HutC oligomerization, and the specific protein-DNA interaction is disrupted by urocanate, a histidine derivative, in a concentration-dependent manner. Next, we searched for putative HutC-binding sites in the SBW25 genome. This led to the identification of 143 candidate targets with a
value less than 10
HutC interaction with eight selected candidate sites was subsequently confirmed by EMSA analysis, including the type IV pilus assembly protein PilZ, phospholipase C (PlcC) for phosphatidylcholine hydrolyzation, and key regulators of cellular nitrogen metabolism (NtrBC and GlnE). Finally, an isogenic
deletion mutant was subjected to transcriptome sequencing (RNA-seq) analysis and phenotypic characterization. When bacteria were grown on succinate and histidine,
deletion caused upregulation of 794 genes and downregulation of 525 genes at a
value of <0.05 with a fold change cutoff of 2.0. The
mutant displayed an enhanced spreading motility and pyoverdine production in laboratory media, in addition to the previously reported growth defect on the surfaces of plants. Together, our data indicate that HutC plays global regulatory roles beyond histidine catabolism through low-affinity binding with operator sites located outside the
locus.
HutC in
is a representative member of the GntR/HutC family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate-binding domain. HutC is generally known to repress expression of histidine utilization (
) genes through binding to the P
promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here, we first describe the detailed molecular interactions between HutC and its P
target site in a plant growth-promoting bacterium,
SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in the SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization
.
Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely ...been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness.
Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants.
Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.
Chiral capillary gas chromatography has been widely applied to separate volatile and thermally stable enantiomers due to its advantages of simplicity, high efficiency, fast analysis, good ...sensitivity, and absence of liquid mobile phases. In the first part of this article, recent research progress (from 2010 to the present) concerning newly developed chiral stationary phases based on cyclofructan derivatives and chiral porous materials, including metal-organic frameworks, covalent organic frameworks, inorganic mesoporous silicas, and molecular cages for use in gas chromatography, and the synthetic strategies for obtaining chiral porous materials, was reviewed. Finally, we discussed in detail the separation performances and chiral recognition mechanisms of novel chiral recognition materials coated on capillary columns towards various types of enantiomers, namely (1) amino acid derivatives; (2) alcohols, amines, and amino alcohols; (3) organic acids; (4) aldehydes and ketones; (5) ethers and epoxides, and (6) esters and other enantiomers.
•Advances on various novel CSPs for GC enantioseparation were reviewed during 2010–2019.•The synthesis strategies to construct chiral porous materials were covered.•The resolution of different types of enantiomers on the novel CSPs was discussed.•The chiral recognition mechanisms between novel CSPs and chiral analytes were explained.•We summarize the advantages and disadvantages of novel CSPs used in GC.
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