Synthetic consortia of four strains promote Schisandra chinensis growth by regulating soil microbial community and improving soil fertility.

MAIN CONCLUSION: Synthetic consortia performed better in promoting Schisandra chinensis growth than individual strains, and this result provides valuable information for the development of synthetic microbial fertilizers. Schisandra chinensis is an herbal medicine that can treat numerous diseases. However, the excessive reliance on chemical fertilizers during the plantation of S. chinensis has severely restricted the development of the S. chinensis planting industry. Plant growth-promoting rhizobacteria (PGPR) can promote the growth of a wide range of crops, and synthetic consortia of them are frequently superior to those of a single strain. In this study, we compared the effects of four PGPR and their synthetic consortia on S. chinensis growth. The pot experiment showed that compared with the control, synthetic consortia significantly increased the plant height, biomass, and total chlorophyll contents of S. chinensis, and their combined effects were better than those of individual strains. In addition, they improved the rhizosphere soil fertility (e.g., TC and TN contents) and enzyme activities (e.g., soil urease activity) and affected the composition and structure of soil microbial community significantly, including promoting the enrichment of beneficial microorganisms (e.g., Actinobacteria and Verrucomicrobiota) and increasing the relative abundance of Proteobacteria, a dominant bacterial phylum. They also enhanced the synergistic effect between the soil microorganisms. The correlation analysis between soil physicochemical properties and microbiome revealed that soil microorganisms participated in regulating soil fertility and promoting S. chinensis growth. This study may provide a theoretical basis for the development of synthetic microbial fertilizers for S. chinensis.

Detecting and quantifying Veillonella by real-time quantitative PCR and droplet digital PCR.

Veillonella spp. are Gram-negative opportunistic pathogens present in the respiratory, digestive, and reproductive tracts of mammals. An abnormal increase in Veillonella relative abundance in the body is closely associated with periodontitis, inflammatory bowel disease, urinary tract infections, and many other diseases. We designed a pair of primers and a probe based on the 16S rRNA gene sequences of Veillonella and conducted real-time quantitative PCR (qPCR) and droplet digital PCR (ddPCR) to quantify the abundance of Veillonella in fecal samples. These two methods were tested for specificity and sensitivity using simulated clinical samples. The sensitivity of qPCR was 100 copies/µL, allowing for the accurate detection of a wide range of Veillonella concentrations from 103 to 108 CFU/mL. The sensitivity of ddPCR was 11.3 copies/µL, only allowing for the accurate detection of Veillonella concentrations from 101 to 104 CFU/mL because of the limited number of droplets generated by ddPCR. ddPCR is therefore more suitable for the detection of low-abundance Veillonella samples. To characterize the validity of the assay system, clinical samples from children with inflammatory bowel disease were collected and analyzed, and the results were verified using isolation methods. We conclude that molecular assays targeting the 16S rRNA gene provides an important tool for the rapid diagnosis of chronic and infectious diseases caused by Veillonella and also supports the isolation and identification of Veillonella for research purposes. KEY POINTS: • With suitable primer sets, the qPCR has a wider detection range than ddPCR. • ddPCR is suitable for the detection of low-abundance samples. • Methods successfully guided the isolation of Veillonella in clinical sample.

Insulin-like growth factor-2 mRNA-binding protein 3 promotes cell migration, invasion, and epithelial-mesenchymal transition of esophageal squamous cell carcinoma cells by targeting zinc finger E-box-binding homeobox 1 mRNA.

The role and mechanism of insulin-like growth factor-2 mRNA-binding protein 3 (IGF2BP3) in the metastasis of esophageal squamous cell carcinoma (ESCC) remain unclear. In this study, IGF2BP3 mRNA and protein expression levels were evaluated in ESCC tissues. Small interfering RNAs (siRNAs), plasmid overexpression, and stable lentivirus transfection were used to manipulate intracellular IGF2BP3 expression levels. The role of IGF2BP3 in ESCC tumorigenesis was investigated in vitro and in vivo. IGF2BP3 target transcripts were detected, and the acetylation effect ratios of the IGF2BP3 promoter region by H3K27ac were determined. IGF2BP3 mRNA expression levels were significantly higher in ESCC tissues than in normal esophageal tissues. Increased IGF2BP3 expression levels were detected in node-negative ESCC tissues and correlated with greater lesion depth in ESCC. Overexpression of IGF2BP3 promoted ESCC development in vitro and in vivo, and IGF2BP3 knockdown caused an opposite effect. IGF2BP3 was found to directly bind to the zinc finger E-box-binding homeobox 1 (Zeb1) mRNA, and the downregulation of IGF2BP3 reduced the stability of Zeb1 mRNA. IGF2BP3 induced epithelial-mesenchymal transition in ESCC cells in a Zeb1-dependent manner. IGF2BP3 was transcriptionally activated in ESCC cell lines via H3K27 acetylation. Our results demonstrate that IGF2BP3 plays a vital role in ESCC cell proliferation, invasion, and metastasis and is a potential therapeutic target for treating ESCC.

Deciphering soil amendments and actinomycetes for remediation of cadmium (Cd) contaminated farmland.

Soil heavy metal pollution is one of the most serious environmental problems in China, especially cadmium (Cd), which has the most extensive contaminated soil coverage. Therefore, more economical and efficient remediation methods and measures are needed to control soil Cd contamination. In this study, different amendments (biochar (B), organic fertilizer (F), lime (L)) and actinomycetes (A) inoculants were applied to Cd contaminated farmland to explore their effects on wheat growth. Compared with Control, all treatments except A treatment were able to significantly increase the underground parts dry mass of wheat, with the highest increase of 57.19 %. The results showed that the B treatment significantly increased the plant height of wheat by 3.45 %. All treatments increased wheat SOD activity and chlorophyll content and reduced the MDA, which contributes to wheat stress resistance under Cd contamination. F, L and AF treatments can significantly reduce the Cd content in wheat above- and underground parts by up to 56.39 %. Soil amendments can modify the physical and chemical properties of the soil, which in turn affects the absorption of Cd by wheat. Moreover, the addition of soil amendments significantly affects the composition and structure of the rhizospheric soil bacterial community at the wheat jointing stage. The application of organic fertilizer increases the richness and diversity of the bacterial community, while lime makes it significantly decreases it. T-test and microbiome co-occurrence networks show that actinomycetes could not only effectively colonize in local soil, but also effectively enhance the complexity and stability of the rhizosphere microbial community. Considering the practical impact of different treatments on wheat, soil microorganisms, economic benefits and restoration of soil Cd contamination, the application of organic fertilizer and actinomycetes in Cd contaminated soil is a more ideal remediation strategy. This conclusion can be further verified by studying larger repair regions and longer consecutive repair cycles to gain insight into the repair mechanism.

Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation.

Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.

Mitsuaria noduli sp. nov., isolated from the root nodules of Robinia pseudoacacia in a lead-zinc mine.

A novel endophytic bacterium, designated strain HZ7T, was isolated from the root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County, Shaanxi Province, China. Cells were Gram-reaction-negative, aerobic, motile, rod-shaped, methyl-red-negative, catalase-positive, positive for chitosan-degrading activity and did not produce H2S. Strain HZ7T grew at 4-45 °C (optimum 25-30 °C), at pH 5-9 (optimum pH 7-8) and with 0-1 % (w/v) NaCl. The quinone type was ubiquinone 8 (UQ-8). The major fatty acids were identified as C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The G+C content of the genomic DNA was 68.5 mol% by whole genome sequencing. According to 16S rRNA gene sequence analysis, the closest phylogenetic relative was Mitsuaria chitosanitabida 3001T (99.05 % similarity). Genome relatedness was computed using average nucleotide identity and genome-to-genome distance analysis, both of which strongly supported strain HZ7Tas belonging to the genus Mitsuaria as a representative of a novel species. On the basis of phylogenetic analysis, chemotaxonomic data and physiological characteristics, strain HZ7T represents a novel species of the genus Mitsuaria, for which the name Mitsuaria noduli sp. nov. is proposed. The type strain is HZ7T (=JCM 31671T=CCTCC AB 2014353T).

Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead-zinc mine.

A novel endophytic bacterium, designated strain HZ10T, was isolated from root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County, Shaanxi Province, China. The bacterium was Gram-stain-negative, aerobic, motile, slightly curved- and rod-shaped, methyl red-negative, catalase-positive, and did not produce H2S. Strain HZ10T grew at 4-45 °C (optimum, 25-30 °C), pH 5-9 (optimum, pH 7-8) and 0-1 % (w/v) NaCl. The major fatty acids were identified as C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and the quinone type was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of the genomic DNA was 64.9 mol% based on the whole genome sequence. According to the 16S rRNA gene sequence analysis, the closest phylogenetic relative to strain HZ10T is Herbaspirillum chlorophenolicum CPW301T (98.72 % sequence identity). Genome relatedness of the type strains H. chlorophenolicum CPW301T, Herbaspirillum seropedicae Z67T and Herbaspirillum aquaticum IEH 4430T, was quantified by using the average nucleotide identity (86.9-88.0 %) and a genome-to-genome distance analysis (26.6 %-29.3 %), with both strongly supporting the notion that strain HZ10T belongs to the genus Herbaspirillum as a novel species. Based on the results from phylogenetic, chemotaxonomic and physiological analyses, strain HZ10T represents a novel Herbaspirillum species, for which the name Herbaspirillum robiniae sp. nov. is proposed. The type strain is HZ10T (=JCM 31754T=CCTCC AB 2014352T).

Temporal dynamics of microbial communities in microcosms in response to pollutants.

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments.

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.

Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling.

As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.

Soil microorganisms play an important role in the detrimental impact of biodegradable microplastics on plants.

Biodegradable plastics were developed to mitigate environmental pollution caused by conventional plastics. Research indicates that biodegradable microplastics still have effects on plants and microorganisms as their non-biodegradable counterparts, yet the effects on vegetable crops are not well-documented. Additionally, the function of soil microorganisms affected by biodegradable microplastics on the fate of microplastics remains unverified. In this study, Brassica chinensis was cultivated in soil previously incubated for one year with low-density polyethylene (LDPE-MPs) and poly (butylene adipate-co-terephthalate) microplastics (PBAT-MPs) at 0.05 % and 2 % concentrations. High concentrations of PBAT-MPs significantly reduced the biomass to 5.83 % of the control. The abundance of Methyloversatilis, IS-44, and UTCFX1 in the rhizosphere bacterial community increased significantly in the presence of PBAT-MPs. Moreover, these microplastics significantly enhanced soil enzyme activity. Incubation tests were performed with three PBAT plastic sheets to assess the function of the altered bacterial community in the soil of control (Control-soil) and soil treated with high concentrations of PBAT-MPs (PBAT-MPs-soil). Scanning Electron Microscopy and Atomic Transfer Microscopy (SEM/ATM) results confirmed enhanced PBAT degradation in the PBAT-MPs-soil. PICRUST2 analysis revealed that pathways related to substance degradation were upregulated in the PBAT-MPs-soil. Furthermore, a higher percentage of strains with PBAT-MPs-degrading ability was found in PBAT-MPs-soil. Our results confirm that PBAT-MPs significantly inhibit the growth of vegetable crops and that soil bacterial communities affected by PBAT-MPs are instrumental in degrading them.

The bifunctional impact of polylactic acid microplastics on composting processes and soil-plant systems: Dynamics of microbial communities and ecological niche competition.

Although extensive research has been conducted on the environmental impact of microplastics (MPs), their effects on microorganisms during the composting process and on the compost-soil system remain unclear. Our research investigates the microbial response to polylactic acid microplastics (PLAMPs) during aerobic composting and examines how compost enriched with PLAMPs affects plants. Our findings reveal that PLAMPs play a dual role in the composting process, influencing microorganisms differently depending on the composting phase. PLAMPs reduce the relative abundance of sensitive bacterial ASVs, specifically those belonging to Limnochordaceae and Enterobacteriaceae, during composting, while increasing the relative abundance of ASVs belonging to Steroidobacteriaceae and Bacillaceae. The impact of PLAMPs on microbial community assembly and niche width was found to be phase-dependent. In the stabilization phase (S5), the presence of PLAMPs caused a shift in the core microbial network from bacterial dominance to fungal dominance, accompanied by heightened microbial antagonism. Additionally, these intricate microbial interactions can be transferred to the soil ecosystem. Our study indicates that composting, as a method of managing PLAMPs, is also influenced by PLAMPs. This influence is transferred to the soil through the use of compost, resulting in severe oxidative stress in plants. Our research is pivotal for devising future strategies for PLAMPs management and predicting the subsequent changes in compost quality and environmental equilibrium.

Naturally Occurring Dehydrocostus Lactone Covalently Binds to KARRIKIN INSENSITIVE 2 by Dual Serine Modifications in Orobanche cumana and Arabidopsis.

Parasitic weeds, such as Orobanche and Striga, threaten crops globally. Contiguous efforts on the discovery and development of structurally novel seed germination stimulants targeting HYPOSENSITIVE TO LIGHT/KARRIKIN INSENSITIVE 2 (HTL/KAI2) have been made with the goal of weed control. Here, we demonstrate that a natural compound dehydrocostus lactone (DCL) exhibits effective "suicide germination" activity against Orobanche cumana and covalently binds to OcKAI2d2 on two catalytic serine sites with the second modification dependent on the first one. The same interactions and covalent modifications of DCL are also confirmed in AtKAI2. Further in-depth evolution analysis indicates that the proposed two catalytic sites are present throughout the streptophyte algae, hornworts, lycophytes, and seed plants. This discovery is particularly noteworthy as it signifies the first confirmation of a plant endogenous molecule directly binding to KAI2, which is valuable for unraveling the elusive identity of the KAI2 ligand and for targeting KAI2 paralogues for the development of novel germination stimulants.

Host genetics regulate the plant microbiome.

Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.

Polyethylene mulching film degrading bacteria within the plastisphere: Co-culture of plastic degrading strains screened by bacterial community succession.

As an ecological niche close to the polymer, microorganisms in the plastisphere possess the advantage of degrading plastics. This study aims to investigate the bacterial community succession and obtain degrading bacteria in the plastisphere, as well as identify the most efficient degradation combination by co-culture of multiple strains. The findings demonstrate the alpha-diversity indices of the plastisphere bacterial community are significantly lower, and the community structure is regularly and significantly altered. With the time of culture, the plastisphere community composition alters regularly, and the hydrocarbon-degrading genera become the core members. Functional prediction of community reveals the potential for Xenobiotics Biodegradation and Metabolism of plastisphere, and the apparent variations detections of polyethylene mulching film (PMF) indicating the PMF degrading ability of plastisphere. Besides, three PMF-degrading bacterial strains, Rhodopseudomonas sp. P1 (P), Rhodanobacter sp. Rs (R) and Microbacterium sp. M1 (M), are screened for co-culture with PMF degrading strain Bacillus aryabhattai 5-3 (B). By considering bacterial growth, biofilm adhesion, and apparent degradation of different samples, RB (R. sp. Rs + B. aryabhattai 5-3) is ultimately selected as the best PMF degradation combination. This study provides a new possibility for plastisphere-related research from the perspective of mitigating plastic pollution on agricultural land.

Genome sequence of the arsenite-oxidizing strain Agrobacterium tumefaciens 5A.

Microbial transformations of arsenic influence its mobility and toxicity. We report the draft genome sequence of the arsenite-oxidizing strain Agrobacterium tumefaciens 5A isolated from an As-contaminated soil in the Madison River Valley, MT. A large number of metal (or metalloid) resistance genes, especially contributing to arsenite oxidation, were identified.

Draft genome sequence of plant growth-promoting rhizobium Mesorhizobium amorphae, isolated from zinc-lead mine tailings.

Here, we describe the draft genome sequence of Mesorhizobium amorphae strain CCNWGS0123, isolated from nodules of Robinia pseudoacacia growing on zinc-lead mine tailings. A large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil.

Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8.

We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic arsenic island, an intact type III secretion system, and multiple metal(loid) transporters. The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and pathogenicity.

Draft genome sequence of Pseudomonas psychrotolerans L19, isolated from copper alloy coins.

We report the draft genome sequence of Pseudomonas psychrotolerans strain L19, isolated from a European 50-cent copper alloy coin. Multiple genes potentially involved in copper resistance were identified; however, it is unknown if these copper ion resistance determinants contribute to prolonged survival of this strain on dry metallic copper.

Draft genome sequence of Halomonas sp. strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil.

We report the draft genome sequence of arsenite-oxidizing Halomonas sp. strain HAL1, isolated from the soil of a gold mine. Genes encoding proteins involved in arsenic resistance and transformation, phosphate utilization and uptake, and betaine biosynthesis were identified. Their identification might help in understanding how arsenic and phosphate metabolism are intertwined.