Comparative proteomic analysis of saline tolerant, phosphate solubilizing endophytic Pantoea sp., and Pseudomonas sp. isolated from Eichhornia rhizosphere

Effect of microbial inoculation on nitrogen transformation, nitrogen functional genes, and bacterial community during cotton straw composting

The effects of microbial agents on nitrogen (N) conversion during cotton straw composting remains unclear. In this study, inoculation increased the germination index and total nitrogen (TN) by 24-29 % and 7-10 g/kg, respectively. Inoculation enhanced the abundance of nifH, glnA, and amoA and reduced that of major denitrification genes (nirK, narG, and nirS). Inoculation not only produced high differences in the assembly process and strong community replacement but also weakened environmental constraints. Partial least squares path modelling demonstrated that enzyme activity and bacterial community were the main driving factors influencing TN. In addition, network analysis and the random forest model showed distinct changing patterns of bacterial communities after inoculation and identified keystone microorganisms in maintaining network complexity and synergy, as well as system function to promote nitrogen preservation. Findings provide a novel perspective on high-quality resource recovery of agricultural waste.

Soilization utilization of solid waste: Ecological regulation of phosphorus tailings-based soil with physicochemical improvement and Bacillus_cereus-addition

Extraction and utilization of effective phosphorus from solid waste have been an important approach for alleviating phosphorus resource shortage. The extraction of available phosphorus by microbial method with low cost, mild conditions and simple process has been drawing attention from the majority of research scholars. However, relevant studies on special microbial communities for effective phosphorus extraction from solid waste are less. In this work，a functional Bacillus_cereus strain screened from phosphate tailings, phosphate ore and forest rhizosphere soil was inoculated into phosphate tailings (PT), modified phosphate tailings (IS) and highland red soil (SS). Compared with SS, the water-holding properties, fertility, leaching toxicity and microbial community diversity of PT and IS with and without bacteria were analyzed. PT+, SS+ and IS+ (after adding bacteria to PT, SS and IS) showed moderately alkaline pH, and the available phosphorus content enhanced by 31.73%, 20.05% and 39.41% respectively. The leaching toxicity phosphate of PT+ and IS + decreased by 4.89 mg/kg and 2.61 mg/kg respectively, while that of SS + increased by 5.45 mg/kg, indicating differences in the phosphorus solubilization mechanism of Bacillus_cereus for different soils. Furthermore, the modification and bacteria treatment improved the relative abundance of Pedobacter, Alcaligenaceae and Pseudomonas, thus enhancing the phosphorus solubility of the PT bacterial community. This work may achieve efficient utilization and ecological restoration of phosphorus tailings-based soil and contribute to long-term sustainable agricultural development.

An overview of plasmid transfer in the plant microbiome

Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.

Microbe-Responsive Proteomes During Plant-Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20

BACKGROUND

Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant-microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association.

RESULTS

In this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis-trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine-tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice.

CONCLUSIONS

Interaction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.

Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting

Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg^-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L^-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.