Dawei Guan

Complete Genome Sequence of Paenibacillus polymyxa SC2, a Strain of Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity

Paenibacillus polymyxa SC2 is an important plant growth-promoting rhizobacterium (PGPR). Here, we report the complete genome sequence of P. polymyxa SC2. Multiple sets of functional genes have been found in the genome. As far as we know, this is the first complete genome sequence of Paenibacillus polymyxa.

Complete genome sequence of Paenibacillus mucilaginosus 3016, a bacterium functional as microbial fertilizer.

Paenibacillus mucilaginosus is a ubiquitous functional bacterium in microbial fertilizer. Here we report the complete sequence of P. mucilaginosus 3016. Multiple sets of functional genes have been found in the genome. To the best of our knowledge, this is the first announcement about the complete genome sequence of a P. mucilaginosus strain.

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Proteomic Study on Two Bradyrhizobium japonicum Strains with Different Competitivenesses for Nodulation

Competitiveness for nodulation of Bradyrhizobium japonicum strains plays a key role in symbiotic nitrogen fixation. In order to reveal the difference in competitiveness, B. japonicum 4534 with high competitiveness and B. japonicum 4222 with low competitiveness for nodulation were analyzed by proteomic technique. The results showed that differential proteins were fewer when two strains were treated with just daidzein. Only 24 and 10 differential proteins were detected with an up-regulated rate of 58 and 40% in B. japonicum 4534 and B. japonicum 4222, respectively. However, more differential proteins were detected upon treatment with daidzein and mutual extracellular materials simultaneously. There were 78 differential proteins detected in B. japonicum 4534 with 43 being up-regulated and 35 being down-regulated. These differential proteins, such as metabolism-related proteins, transporters, transcription-related proteins, translation-related proteins, and flagellin, were found to be associated with nodulation process. 25 up-regulated and 22 down-regulated proteins were detected in B. japonicum 4222. Some of these proteins were not related to nodulation. More differential proteins associated with nodulation in B. japonicum 4534 may be the reason for its high competitiveness. The results can provide a guide to the selection and inoculation of effective strains and are significant to biological nitrogen fixation.

Proteins involved in nodulation competitiveness of two Bradyrhizobium diazoefficiens strains induced by soybean root exudates

Competitiveness for nodulation is one of the major restrictive factors in symbiotic nitrogen fixation between rhizobia and their host legumes. Soybean root exudates that include a variety of compounds are thought to act as signals to trigger the early symbiotic events between Bradyrhizobium diazoefficiens and soybeans, and thus they act as a key determinant of the competitiveness for nodulation. To gain a better understanding of the molecular mechanism of competitiveness at the level of protein expression, we compared the proteomic responses of two B. diazoefficiens strains that demonstrated completely different nodulation abilities, strain 4534 being the most competitive and strain 4222 being the least competitive in nodulation. In the proteomic analysis, 40 of the 65 and 22 of the 29 differential proteins were identified in response to soybean root exudates in strain 4534 and strain 4222, respectively. Compared to strain 4222, a higher amount and a number of differential proteins were detected in strain 4534, including S-adenosylmethionine synthetase (SAMS), PhyR-σEcfG regulon, ABC-type transporters, flagellar proteins, molecular chaperones, and proteins involved in redox state maintenance as well as several unknown proteins. Noteworthy was the induction of the PhyR-σEcfG regulon and flagellar proteins, recently demonstrated to be involved in the competitiveness for nodulation in Bradyrhizobium japonicum. Our results indicate that the role of root exudates can go far beyond inducing the expression of nodulation genes in B. diazoefficiens. Many other proteins/enzymes involved in the metabolism and environmental fitness were also upregulated when exposed to root exudates. More proteins were upregulated by the high nodulation competitive strain than that by the low, and the reasons for this need further investigation. The outcome of such study may contribute to our understanding of molecular mechanisms of different competitiveness in B. diazoefficiens as well as specific adaptation in the legume host.

Transcriptional analysis of genes involved in competitive nodulation in Bradyrhizobium diazoefficiens at the presence of soybean root exudates

Nodulation competition is a key factor that limits symbiotic nitrogen fixation between rhizobia and their host legumes. Soybean root exudates (SREs) are thought to act as signals that influence Bradyrhizobium ability to colonize roots and to survive in the rhizosphere, and thus they act as a key determinant of nodulation competitiveness. In order to find the competitiveness-related genes in B. diazoefficiens, the transcriptome of two SREs treated B. diazoefficiens with completely different nodulation abilities (B. diazoefficiens 4534 and B. diazoefficiens 4222) were sequenced and compared. In SREs treated strain 4534 (SREs-4534), 253 unigenes were up-regulated and 204 unigenes were down-regulated. In SREs treated strain 4534 (SREs-4222), the numbers of up- and down-regulated unigenes were 108 and 185, respectively. There were considerable differences between the SREs-4534 and SREs-4222 gene expression profiles. Some differentially expressed genes are associated with a two-component system (i.g., nodW, phyR-σEcfG), bacterial chemotaxis (i.g., cheA, unigene04832), ABC transport proteins (i.g., unigene02212), IAA (indole-3-acetic acid) metabolism (i.g., nthA, nthB), and metabolic fitness (i.g., put.), which may explain the higher nodulation competitiveness of B. diazoefficiens in the rhizosphere. Our results provide a comprehensive transcriptomic resource for SREs treated B. diazoefficiens and will facilitate further studies on competitiveness-related genes in B. diazoefficiens.

Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols

How fungi respond to long‐term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high‐throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long‐term chemical and organic fertilization strategies. Soils were collected in a 35‐year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant–fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.

Isolation and Identification of PGPR Strain and its Effect on Soybean Growth and Soil Bacterial Community Composition

Plant growth-promoting rhizobacteria (PGPR) are considered environmentally sound option to reduce chemical fertilizer inputs, improve soil quality and increase crop yields. The objective of this study was to isolate an effective PGPR strain and investigate its effects on soybean growth and soil bacterial community composition. A total of 163 bacterial isolates were obtained from rhizospheres of plants in four provinces of China. According to capacities for mineral potassium and phosphate solubilization, the best strain (designated 3016) was selected and identified as Paenibacillus mucilaginosus based on biochemical characterization and phylogenetic analysis. Moreover, strain 3016 showed a higher capacity for nitrogen fixation and phytohormone production than commercial strains. In a field experiment, P. mucilaginosus 3016 was used as an inoculant for seed dressing survived in the soybean rhizosphere as revealed by a species-specific PCR method. Inoculation significantly improved symbiotic nodulation, soybean growth parameters, nutrient contents and yields. The number of nodules was increased by 31.8% for the inoculation treatment compared with CK. Soybean height, pods and seeds per plant and dry weight of nodules were also significantly higher for the inoculation, as well as nutrient contents. Regarding yields, the highest of 3191.4 kg hm -2 was obtained under inoculation regime. Moreover, numerous bacterial classes and genera, which were associated with symbiotic nitrogen-fixation, plant growth promotion, biological control and soil catalase activity improvement, were also overrepresented in the inoculation treatment. Some taxa with negative impacts on soil quality decreased. In conclusion, inoculation with P. mucilaginosus 3016 had beneficial effects on both soybean growth and soil quality, and is a potential candidate for developing commercial inoculants of PGPR to be used as a bio-fertilizer.

Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols

Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.

Analysis of Two Bradyrhizobium japonicum Strains with Different Symbiotic Matching for Nodulation by Primary Proteomic

Abstract The symbiotic matching for nodulation of Bradyrhizobium japonicum strains is a synergy of multi-proteins and plays a key role in symbiotic nitrogen fixation in nature. Studies on mechanism of symbiotic matching are significant in both theory and practice. In this paper, B. japonicum USDA110-A with high symbiotic matching with high-oil content soybean cultivar Suinong 20 and B. japonicum 2178 with low symbiotic matching were selected for proteomic to reveal mechanism of different symbiotic nodulation. The results showed that the amount and categories of proteins identified in this test were different when the two strains were treated by symbiotic nodulation. There were 10 up-regulated proteins and 5 down-regulated proteins with significant difference for B. japonicum USDA110-A. Proteins associated with nodulation and metabolism of energy and material, which were propitious to symbiotic nodulation, were all up-regulated, such as PHDPS synthase, metal-dependent phosphohydrolase, glycosyl transferase family. In contrast, only 5 up-regulated and 7 down-regulated differential proteins were detected in B. japonicum 2178. Molecular chaperones and defensive proteins, which influence the folding of nascent polypeptide chains and the active of azotase were down-regulated. To a certain extent, the different responses of B. japonicum to daidzein were one of the most important reasons that cause varieties in symbiotic matching ability.