Profiling the changes of nitrogen-relative soil microbiomes under the excessive fertilization input

摘要：

Excessive fertilizer application in agriculture, while enhancing crop yield, can lead to detrimental consequences such as soil salinization, degradation, and increased greenhouse gas emissions. Soil microbial communities, crucial for nutrient cycling, organic matter degradation, and plant-microbe interactions, are significantly influenced by these environmental perturbations. However, our understanding of how excessive fertilization impacts the functional dynamics of soil microbiomes remains limited. This study investigates the effects of varying nitrogen (N) fertilizer inputs on soil microbiomes in three flint corn fields. Three treatment levels were established: (i) rational fertilization (control, CT): 165 kgN/ha; (ii) low fertilization (LF): 124 kgN/ha; (iii) high fertilization (HF): 247 kgN/ha. Soil samples were collected at four time points: before planting, and 30, 75, and 150 days after planting. Concurrent measurements of N₂O and CO₂ emission were conducted 2–6 days following each fertilization event. Preliminary results indicate delayed N₂O emissions and elevated CO₂ emissions under high fertilization conditions. Shotgun metagenomic sequencing is employed to characterize the soil microbiomes and identify functional genes, primarily those involved in nitrogen cycling, including genes related to nitrogen fixation, nitrification and denitrification. By analyzing these functional shifts within the soil microbiome, this research aims to provide valuable insights into soil health assessment under different fertilization regimes.

中興大學賴廷瑋

Exploration of the Evolution and Distribution of Carbon-Fixing Microorganisms Using the Wood-Ljungdahl Pathway in Natural Environments 

摘要:

Microorganisms can fix CO2 through multiple enzymes and then convert it into soil organic matter (SOC). The stable SOC is soil carbon sink, and it is one of the indispensable projects for our country and the world to achieve net-zero carbon emissions in 2050. However, many parts of environments (including soil) are anaerobic, so these environments do not use the familiar rubisco enzyme to fix CO2. The Wood-Ljungdahl Pathway (WLP) is an anaerobic CO2 fixation reaction. Before the emergence of rubisco, it was the main CO2 fixation reaction on the earth. Nowadays, relevant microorganisms have been found in various anaerobic environments (including agricultural soil). However, few studies have carefully explored its distribution and contribution in the natural environments. Therefore, this study not only identified 5157 bacterial and archaeal species with WLP from >80,000 genomes database, but also analyzed their evolution (constructing phylogeny) and distribution in natural environments. We found that species carrying WLP not only can be found in extreme environments, such as high-salinity or high-temperature conditions, but also can be found in various natural environments, including soils, oceans, animal intestines. In total, we collected 3892 natural environments data, and 424 of which were soil samples from 29 different countries. Combining genome evolution analysis with environmental data, this study provide new insights into the evolution and environmental status of Earth's WLPs. Combining huge genomes analysis and environmental data, this study provide new insights into the evolution and environmental status of WLPs on Earth, and also provide potential for WLP microorganisms applied in different environments in the future. 

中央研究院賴宜豊

Gut in the Game: Multi-Omics Mapping of Gut Microbiota's Role in Progesterone Metabolism

摘要:

Background

The female reproductive hormone, progesterone, is crucial in regulating the menstrual cycle and maintaining pregnancy. Despite known correlations between gut microbiota, sex hormones, and host phenotypes, the metabolic fates of progesterone in the human gut remain unclear.

Results

Here, an integrated multi-omics approach was employed to investigate gut microbiota-mediated progesterone metabolism. Fresh fecal samples were collected from infertile women with progesterone treatment (n = 14). Progesterone (1 mM) was amended into fecal cultures to enrich progesterone-metabolizing gut microbes, and the key players were identified through culturomics-based metagenomics analysis. Microbial functions were predicted by tracking temporal changes in metabolite profiles and microbial abundances. The prevalence of progesterone metabolism genes among gut microbiota was explored through functional genomics analysis. Pregnanolone was identified as the primary microbial metabolite of gut progesterone. Members of Enterobacteriaceae and Veillonellaceae were identified as crucial pregnanolone producers; progesterone metabolism genes were abundant in these bacterial families. Moreover, these bacterial families showed significant abundance differences among healthy women (n = 19) and women with miscarriages (n = 41).

Conclusions

This study provides potent therapeutic targets for improving progesterone bioavailability and demonstrates stereoselective production of neurosteroids using characterized bacterial strains and their corresponding metabolic pathways. 

Develop a novel natural-extract toothpaste to control Lactococcus garvieae on the surface of enamel

摘要：

Lactococcus garvieae is a Gram-positive cariogenic bacterium. The cause of cavities is the acid produced by L. garvieae bacteria, which dissolves the hard tissues of the teeth. Botanical natural extracts (BNE) are bioactive compounds derived from plants, equipped with antioxidant, anti-inflammatory, and antiviral properties. This study develops a novel BNE toothpaste to control Lactococcus garvieae growth on enamel. The results show the minimum inhibitory concentrations (MIC) of xylitol (X), quercetin (Q), xylitol/quercetin (X/Q) against L. garvieae are 250 mM, 400 µM, and 250 mM/400 µM, respectively. These BNE (X, Q, and X/Q) were added to an abrasive (100% sodium bicarbonate) to create the BNE toothpaste. The antibacterial effects of the BNE toothpastes on the growth of L. garvieae were evaluated. The relative antimicrobial inhibition rates of different toothpastes were compared as follows: Q (91.63%), X/Q (91.19%), X (60.09%), and no BNE-containing toothpaste (69.03%). Q toothpaste presented the best control of L. garvieae growth for 1 to 3 days. Additionally, the relative enamel demineralization of tooth bridges made of hydroxyapatite (HAP) was compared for 1-7 days: X/Q (5.29%), Q (5.60%), X (6.20%), and no BNE toothpaste (8.50%). These results present significant evidence that Q can be selected as an additive in toothpaste for controlling cariogenic microorganisms. Further evaluation of the compatibility of BNE toothpastes with human cells is required.