Identification of Thiobacillus bacteria in agricultural soil in Iran using the 16S rRNA gene

Changes in selenium bioavailability in selenium-enriched paddy soils induced by different water management and organic amendments

Combined effects of water management and agricultural organic waste return on selenium (Se) bioavailability and mechanisms in Se-enriched paddy soils remain unclear. We investigated the effects of continuous flooding (CF) and alternating wet and dry (AWD), two types (cotton straw biochar [BC] and sheep manure [SM]) and concentrations (10 and 50 g·kg-1) of organic amendments on soil Se bioavailability, bacterial community structure in naturally Se-enriched soils (1.69 mg·kg-1). Results showed that 10 g·kg-1 SM treatment was the most effective in increasing Se bioavailability, especially under AWD treatment, whereas BC treatment reduced it. Compared with CF treatment, AWD treatment increased the Se content of root surface iron plaque and rhizosphere affinity for Se, and promoted the conversion of soil weakly organic matter bound Se to soluble-Se and exchangeable-Se. BC and SM addition significantly altered soil solution Fe(II), dissolved organic carbon, and soil bacterial community structure and function, including sulfur-oxidizing bacteria (Thiobacillus) and Se-reducing bacteria (Pseudarthrobacter), under different water management regimes. Notably, these bacteria showed a significant correlation with bioavailable Se. The present study provides theoretical guidance for agronomic practices in Se-enriched paddy soils.

Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach

Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.

Uranium bioavailability in soil pore water: A long-term investigation in a contaminated soil mesocosm

Uranium in soil can exist in both (IV) and (VI) oxidation states, distributed among different soil fractions (exchangeable, carbonate, oxidizable, reducible, and residual). Following its release from these fractions, uranium enters the soil pore water, becoming bioavailable and potentially posing risks due to its radio and chemical toxicity. Given the significant health and environmental risks associated with uranium, it is crucial to understand its behaviour in contaminated soil pore water and how it changes over time, especially in response to seasonal variations. To address this issue, study was designed to investigate the temporal changes in uranium availability in soil pore water, with a special focus on effect of seasonal variations and biogeochemical reactions that govern the bioavailability of uranium in a contaminated soil mesocosm. This field investigation was carried out for two consecutive years, and revealed that, seasonal variation has a significant effect on the bioavailability of the uranium in the upper soil layers (<30 cm). The biogenic NO3- induced oxidative dissolution of uranium was found to be the predominant reaction causing the dissolution of uranium into soil pore water, followed by ion-exchange in upper layer, whereas at higher depths (30 cm < d < 70 cm) bioavailability is predominantly controlled by ion-exchange reaction. Furthermore, the study shows that at upper layers bioavailability is high during the summer, which is attributed to higher rate of biogenic denitrification and ion exchange reactions. Fast vertical migration of uranium in the soil column is attributed to formation of stable mobile species such as hydroxo‑carbonato ((UO2)xCO3(OH)y-), hydroxo (UO2)x(OH)y and carbonato (UO2CO3) complexes, identified by speciation modelling. For the first time, this study reports the process controlling uranium behaviour in soil pore water and the effect of seasonal variation on it in a contaminated soil. The findings are essential for assessing its potential radiological impact and remediation planning.

Assessing the enhanced reduction effect with the addition of sulfate based P inactivating material during algal bloom sedimentation

The typical harm effect of algal bloom sedimentation is to increase sulfides level in surroundings, threatening aquatic organisms and human health; whereas, P inactivating materials containing sulfate are commonly attempted to be used to immobilize reactive P or to flocculate excessive algae in water columns for eutrophication control. In this study, variations in sulfate reduction during algal bloom sedimentation with the addition of sulfate based inactivating materials was comprehensively assessed based on using Al₂(SO₄)₃ with comparison to AlCl₃. The results showed that addition of Al₂(SO₄)₃ had more substantial effect on overlying water and sediment properties compared to those of ACl₃. Al₂(SO₄)₃ can enhance sulfate reduction, resulting in temporary increase of sulfides (p < 0.01) and quick decrease of various Fe (p < 0.01) in overlying water and then promoting the formation of FeS and FeS₂ (determined by EXAFS analysis) in sediments. Most importantly, the increased sulfides, as well as the physical barrier on sediment formed due to Al₂(SO₄)₃ addition, enhanced the transformation of sulfides to odorous contaminants, increasing odorous contaminants (especially methyl thiols) production by approximately one order of magnitude in overlying water. Furthermore, the increased sulfides facilitated to the enrichment of microorganisms related to S cycles (Thiobacillu with relative abundance of 23.8%) and even promoted to enrich bacterial genus potentially with pathogenicity (Treponema) in sediments. The impacts of sulfate tended to be regulated by algae concentration; however, careful management was recommended for sulfate based inactivating materials application to control eutrophication with algal blooms.

Isolation and thermo-acclimation of thermophilic bacteria in hyperthermophilic fermentation system

Hyperthermophilic microorganisms play a key role in the hyper-thermophilic composting (HTC) technique. However, little information is available about the hyperthermophilic microorganisms prevalent in HTC systems, except for the Calditerricola satsumensis, Calditerricola yamamurae, and Thermaerobacter. To obtain effective hyper-thermophilic microorganisms, a continuous thermo-acclimation of the suitable thermophilic microorganisms was demonstrated in this study. Bacillus thermoamylovorans with high-temperature endurance (70 °C) were newly isolated from sludge composting, and an adequate slow heating rate (2 °C per cycle) was applied to further improve its thermostability. Finally, a strain with a maximum growth temperature of 80 °C was obtained. Moreover, structural and hydrophobic changes in cell proteins, the special amino acid content ratio, and the membrane permeability of the thermophilic bacterium after thermo-acclimation were evaluated for improved thermostability. In addition, the acclimated hyperthermophilic bacterium was further inoculated into the HTC system, and an excellent performance with a maximum operating temperature of 82 °C was observed.

Genome-wide identification, expression, and interaction analysis for ovate family proteins in peach

Ovate family proteins (OFPs), which are involved in aspects of plant development and growth, is a class of plant-specific transcription factors. Although OFPs have been reported in some species, little is known about their evolution, structure, fruit developmental expression, and interactions among OFP members in peach (Prunus persica). In this study, 15 peach OFP (PpOFP) genes were identified. Phylogenetic analysis showed that 716 OFPs from 32 species were divided into 15 subgroups; 10 subgroups (Ia, Ib, Ic, Id, Ie, If, Ig, Ih, Ii, and Ij) were composed of dicotyledonous plants only and five (IIa, IIb, IIc, IId, and IIe) were composed of monocotyledonous plants only. Structure analysis showed that the OFP genes in monocotyledonous and dicotyledonous plants had no introns. Chromosomal localization analysis showed that 15 PpOFP genes were unevenly mapped on seven chromosomes. Furthermore, eight of the 15 PpOFP genes were cloned successfully by the RT-PCR method. To some extent, eight PpOFPs were expressed in all the detected peach tissues. In addition, analysis by Y2H and BiFC technologies indicated that both PpOFP4 and PpOFP5 formed homodimers with themselves, and PpOFP5 interacted with PpOFP7 or PpOFP8 to form heterodimers. These results serve as the theoretical basis for the analysis of the biological function and regulation of peach OFP transcription factors in the growth, development and other conditions, as well as evolution studies of OFP transcription factors in higher plants.