Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil

Manfredini, Andrea; Malusà, Eligio; Pinzari, Flavia; Canfora, Loredana

doi:10.1093/jambio/lxad169

Cited by 4 publications

(3 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several studies have shown that soil bacterial composition can be modified via agronomic practices or external drivers [63,64], but in our case, it is difficult to mechanistically explain the observed correlation between diversity and function. Nevertheless, it has also been shown that simple NGS analysis can bias the analyses of the function [65] as it also includes sequences from dead or dormant state cells or extracellular DNA [66], making it feasible to hypothesize that the discrepancy observed in the evaluation of the bacterial biodiversity could be accounted to these biases.…”

Section: Living Mulches Effect On Soil Biodiversitymentioning

confidence: 99%

Insights into the Belowground Biodiversity and Soil Nutrient Status of an Organic Apple Orchard as Affected by Living Mulches

Furmanczyk,

Malusà,

Kozacki

et al. 2024

Agriculture

Self Cite

View full text Add to dashboard Cite

The impact of living mulches established with three officinal plants (Alchemilla vulgaris, Fragaria vesca and Mentha x piperita) on the soil bacterial microbiome and activity, the nematodes population, and the nutrient status of an organic apple orchard was assessed. The composition and diversity of the bacterial communities were differentially modified by living mulches. The activity of the bacterial microbiome associated with F. vesca was higher and utilized more C sources in comparison to other treatments. The combined analysis of the core bacterial microbiome and metabolic activity pointed to a potential effect of F. vesca on different levels of the soil’s trophic network. The living mulches did not affect the overall number of nematodes, but in some cases, they modified the structure of the population: F. vesca induced the highest share of bacteria feeders and the lowest number of herbivores and fungal feeders. The living mulches modified the availability of some nutrients and the pH. Multivariate analysis of the whole dataset showed several potential inter-dependencies between the assessed parameters that are worthy of further study. In conclusion, the introduction of multifunctional living mulches based on officinal plants induced changes to the soil’s genetic and functional biodiversity and chemical properties. These modifications could deliver ecosystem services particularly relevant to organic apple orchards.

show abstract

Section: Living Mulches Effect On Soil Biodiversitymentioning

confidence: 99%

Insights into the Belowground Biodiversity and Soil Nutrient Status of an Organic Apple Orchard as Affected by Living Mulches

Furmanczyk,

Malusà,

Kozacki

et al. 2024

Agriculture

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, upon treatment with PMAxx concentrations >10 µM, the Ct values of dead S. Typhimurium significantly increased (p < 0.001) (Figure 1A). As Ct values are on a log2 scale, dCt of primer sets 1, 2, 3, 4, and 5 indicates approximately 75.000%, 87.500%, 93.750%, and 96.875% removal of bacterial DNA, respectively [28]. The dCt values for dead S. Typhimurium observed at PMAxx concentrations of 10, 25, 50, 75, and 100 µM of PMAxx were 10.74 ± 0.72, 12.67 ± 0.21, 13.18 ± 0.05, 13.30 ± 0.14, and 13.31 ± 0.23, respectively (Figure 1B).…”

Section: Effect Of Pmaxx Treatment On Viable and Dead S Typhimurium I...mentioning

confidence: 99%

Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow

Lee,

2024

Diagnostics

View full text Add to dashboard Cite

Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30–43 °C), time (1–25 min), and endonuclease IV concentration (0.025–0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.

show abstract

“…In the past decade, there has been increasing interest from civil engineering researchers in a soil consolidation technology that is based on the principle of microbial mineralization [6,7]. This technology, which combines microbiology and engineering, is not only an innovation in theory and technology, but also contributes to long-term environmental protection [8,9]. Microbial mineralization refers to the ability of certain microorganisms to produce inorganic compounds during their metabolism, which can fill and bond soil materials, thereby improving the engineering properties of the soil.…”

Section: Introductionmentioning

confidence: 99%

Effect of Calcium Carbonate Deposition Induced by Microorganisms and Plant Urease on Sand Reinforcement

Xie,

Yang,

Yang

et al. 2024

Pol. J. Environ. Stud.

View full text Add to dashboard Cite

Soil solidification based on microbial mineralization is an environmentally friendly and sustainable technology. This study utilized microbial induced calcium carbonate precipitation (MICP) and urease-induced calcium carbonate precipitation (EICP) to solidify standard sand and silty sand. The physical and mechanical properties of the soil samples before and after solidification were tested, and the mechanisms of Sporosarcina pasteurii and urease-induced calcium carbonate solidification were analyzed. The results showed that the compressive strength of standard sand after MICP and EICP treatment was higher than that of silty sand. MICP treatment resulted in significantly higher compressive strength compared to EICP treatment. MICP formed a "skeleton" with calcium carbonate, enhancing shear strength and compressive strength but reducing permeability. EICP sealed the pores with calcium carbonate crystals, improving impermeability. The mechanical properties of solidified silty sand were worse due to particle shape and size, but it had better impermeability. During solidification, Sporosarcina pasteurii mainly stayed at the contact points between sand particles, with extracellular polymeric substances (EPS) containing negative ion groups. This enabled stronger adsorption capacity for calcium ions and facilitated the formation of "nucleation sites". Larger-sized, higher-strength calcium carbonate crystals were produced by MICP, aggregating at particle contact points. MICP treatment resulted in a sand microstructure resembling a "skeleton", enhancing shear strength, compressive strength, and permeability. In contrast, EICP directly used smaller-sized urease enzymes, which were more likely to be free in the pores. This caused the catalytically precipitated calcium carbonate to deposit between the pores, closing some of them and improving permeability. However, EICP often produced calcium carbonate in a disordered aggregate form with smaller size and brittle texture. The solidified samples were more brittle and prone to brittle failure. The research findings have certain guiding significance for sand soil solidification engineering.

show abstract

Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil

Cited by 4 publications

References 49 publications

Insights into the Belowground Biodiversity and Soil Nutrient Status of an Organic Apple Orchard as Affected by Living Mulches

Insights into the Belowground Biodiversity and Soil Nutrient Status of an Organic Apple Orchard as Affected by Living Mulches

Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow

Effect of Calcium Carbonate Deposition Induced by Microorganisms and Plant Urease on Sand Reinforcement

Contact Info

Product

Resources

About