Project description:Intermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogen mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that both mcrA gene copies and mcrA transcripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance of mcrA genes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription of mcrA genes was reduced to a greater extent than the abundance of mcrA genes, resulting in very low mcrA transcript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance of mcrA transcripts than of mcrA genes in rice field soil.
Project description:In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.
Project description:A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum Ascomycota corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla Proteobacteria, Acidobacteriota and Bacteroidota integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3-4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus Cylindrocarpon was more abundant under CM, and Fusarium under OM.
Project description:Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.
Project description:In many terrestrial habitats, plants experience temporal heterogeneity in water availability both at the intra and inter annual scales, creating dry-wet pulse scenarios. This variability imposes two concomitant challenges for plants: surviving droughts and efficiently utilizing water when it becomes available, whose responses are closely interconnected. To date, most studies have focused on the response to drought following static designs that do not consider consequences of repeated transitions from one state to the other. In principle, different dry-wet pulse scenarios among years may differentially affect species performance, plant strategies, and promote coexistence through temporal niche separation. We predicted that short frequent droughts would disfavor drought-avoidant species, as rapid leaf loss and production could disrupt their carbon balance, whereas tolerant species, which maintain carbon gain during droughts, should thrive in such conditions. Prolonged droughts might harm tolerant species by causing severe cavitation. We assessed the survival and growth responses of seedlings from 19 tropical dry forest tree species to simulated natural dry-wet pulse scenarios, examining their relationships with the continuum of species' functional strategies under field conditions, and used greenhouse experiments to accompany the field experiment. As expected, different dry-wet pulse scenarios favored different plant functional strategies. Contrary to predictions, the most tolerant outperformed the most avoiders under all drought scenarios, while rapid water-exploiters thrived under non-drought conditions. The superiority of tolerant over avoider species was reverted in the greenhouse, suggesting that in addition to physiology, the fate of species may depend on extrinsic factors as natural enemies. The interplay between the marked variability of dry-wet pulse scenarios across the years and the diversity of water use strategies may contribute to species coexistence in the tropical dry forests. This research is relevant in predicting changes in dominant tree species under future climate scenarios characterized by increased temporal variation in water availability.
Project description:The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.
Project description:In order to study the deterioration and mechanism of dry-wet cycles and sulfate attack on the performance of concrete in seaside and saline areas, the deterioration of compressive strength of concrete with different water cement ratios under different erosion environments (sodium sulfate soaking at room temperature and coupling of dry-wet cycling and sodium sulfate) was studied here. At the same time, ICT (industrial computed tomography) and NMR (nuclear magnetic resonance) techniques were used to analyze the internal pore structure of concrete under different erosion environments. The results show that the compressive strength under different erosion environments increases first and then decreases, and the dry-wet cycle accelerates the sulfate erosion. With the increase of dry and wet cycles, larger pores are filled with erosion products and developed into small pores in the early stage of erosion; in the later stage of erosion, the proportion of larger pores increases, and cracks occur inside the sample. In the process of sulfate soaking and erosion, the smaller pores in the concrete account for the majority. As the sulfate erosion continues, the T2 spectrum distribution curve gradually moves right, and the signal intensity of the larger pores increases.
Project description:Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.
Project description:The Dry-Hot Valley is a unique geographical region in southwestern China, where steep-slope cultivation and accelerating changes in land-use have resulted in land degradation and have aggravated soil erosion, with profound impacts on soil fertility. Soil microbes play a key role in soil fertility, but the impact of land-use changes on soil microbes in the Dry-Hot Valley is not well known. Here, we compared characteristics and drivers of soil microbial community composition and soil fertility in typical Dry-Hot Valley land uses of sugarcane land (SL), forest land (FL), barren land (BL) converted from former maize land (ML), and ML control. Our results showed that BL and SL had reduced soil organic carbon (SOC), total nitrogen (TN), and total potassium (TK) compared to ML and FL. This indicated that conversion of ML to SL and abandonment of ML had the potential to decrease soil fertility. We also found that fungal phyla Zoopagomycota and Blastocladiomycota were absent in SL and BL, respectively, indicating that land-use change from ML to SL decreased the diversity of the bacterial community. Redundancy analysis indicated that the relative abundance of bacterial phyla was positively correlated with TN, SOC, and available potassium (AK) content, and that fungal phyla were positively correlated with AK. Land-use indirectly affected the relative abundance of bacterial phyla through effects on soil moisture, clay, and AK contents, and that of fungal phyla through effects on clay and AK contents. In addition, land-use effects on bacteria were greater than those on fungi, indicating that bacterial communities were more sensitive to land-use changes. Management regimes that incorporate soil carbon conservation, potassium addition, and judicious irrigation are expected to benefit the stability of the plant-soil system in the Dry-Hot Valley.
Project description:In recent decades, chromium contamination in soil has emerged as a serious environmental issue, demanding an exploration of chromium's behavioral patterns in different soil conditions. This study aims to simulate the release, migration, and environmental impact of chromium (Cr) in contaminated soils under natural rainfall conditions (wet-dry cycles). Clean soils sourced from Panzhihua were used to cultivate chromium-containing soils. Simulated rainfall, prepared in the laboratory, was applied to the cultivated chromium-containing soils in indoor simulated leaching experiments. The experiments simulated three years of rainfall in Panzhihua. The results indicate that soils with higher initial Cr contents result in higher Cr concentrations in the leachate, but all soils exhibit a low cumulative Cr release. The leachate shows similar patterns in total organic carbon (TOC), pH, electrical conductivity, and Cr content changes. An analysis of the speciation of Cr in the soil after leaching reveals a significant decrease in the exchangeable fraction for each Cr species, while the residual and oxidizable Cr fractions exhibit notable increases. The wet-dry cycle has the following effects on the soil: it induces internal reduction reactions in the soil, leading to the reduction of Cr(VI) to Cr(III); it alters the binding of Cr ions to the soil, affecting the migration of chromium; and it involves microorganisms in chemical processes that consume organic matter in the soil. After three years of rainwater leaching, chromium-containing soils released a relatively low cumulative amount of total chromium, resulting in a reduced potential risk of groundwater system contamination. Most of the chromium in the chromium-containing soil is fixed within the soil, leading to less biotoxicity.