Burning season and vegetation coverage influenced the community-level physiological profile of Mediterranean mixed-mesogean pine forest soils

Bacterial Community Structure in Soils With Fire-Deposited Charcoal Under Rotational Shifting Cultivation of Upland Rice in Northern Thailand

Rotational shifting cultivation (RSC) is a traditional agricultural practice in mountainous areas that uses fire to clear land after cutting vegetation for cultivation. However, few studies have assessed the effect of fire-deposited charcoal on the diversity and composition of soil microbial communities, and none have been conducted in Thailand. Therefore, this study was conducted 1 year after a fire in an abandoned 12-year RSC in Chiang Mai Province, northern Thailand. Charcoal samples were collected from the surface litter layer, while charcoal-soil mixtures were taken from the surface soil (0-2 cm). Soil samples from 2 to 7 cm captured the charcoal-soluble layer, and samples from 7 to 15 cm represented soil without charcoal incorporation. The results revealed that charcoal led to higher pH and electrical conductivity in the charcoal layer, with notable differences in soil texture across layers, including the highest sand and silt content in the charcoal-mixed soil layer (0-2 cm). Soil organic matter and total nitrogen were significantly higher in the charcoal-mixed layer compared to deeper layers, indicating improved nutrient retention due to charcoal presence. Enhanced microbial diversity was observed in the charcoal and charcoal-mixed soil layers, with Proteobacteria, Chloroflexi, and Planctomycetota dominating across all soil samples. The bacterial genus Ilumatobacter exhibited significant changes in abundance in the charcoal layer. Additionally, Pseudolabrys was more abundant in charcoal-leached soil, while JG30a-KF-32 showed greater abundance in soil without charcoal. Shifts in Proteobacteria and Planctomycetota abundance were evident in the charcoal leaching and non-charcoal layers. Network analysis indicated more complex bacterial interactions in the charcoal-mixed soil layer, with reduced network complexity observed in the charcoal leaching layer and the layer without charcoal. These findings imply that charcoal provides a favorable environment for diverse and interactive bacterial communities, potentially benefiting soil health and fertility recovery in RSC fields.

Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era

BACKGROUND

The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS

Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION

This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

Contrasting immediate impact of prescribed fires and experimental summer fires on soil organic matter quality and microbial properties in the forest floor and mineral soil in Mediterranean black pine forest

Prescribed fire (PB) is used to achieve ecological objectives and to reduce fuel hazard thus limiting detrimental impacts of wildfire and appropriate selection of prescription window is critical for these goals. Operational use of PB in the Mediterranean forest is scarce and information about its effects on soil remains incomplete. This study for the first time i) compared the immediate impact of spring and autumn PB and experimental summer fire on key properties of forest floor and mineral topsoil in Mediterranean black pine forest, and ii) assessed the capacity of PB to reduce fuel, with limited immediate impacts on soil. PB significantly reduced the 32.5 % of pre-fire forest floor depth, while summer fire consumed 88.5 % and exposed about 30 % of the mineral soil surface. Mean maximum temperature during fire at the mineral soil surface was 23 °C in PB, in contrast to 128 °C in summer fire, while soil heating at 2 cm depth was negligible in both cases. PB did not cause immediate changes in OM quality parameters, and chemical (C and N concentrations, C/N and pH) and microbiological properties (Cmic, Cmic/C, and β-glucosidase, acid phosphatase and alkaline phosphatase activities) in forest floor or mineral topsoil (0-2 cm). By contrast, summer fire greatly increased OM recalcitrance and reduced Cmic, Cmic/C and enzyme activities in forest floor immediately after fire. In the mineral topsoil, only microbial properties were significantly reduced. The maximum temperature reached during fire in forest floor and topsoil was associated with most of the overall changes in properties in both layers. The findings suggest that prescribed fire can significantly reduce fuel with limited initial impacts on soil. Although these findings are encouraging for operational use of prescribed burning in the ecosystem under study, long-term monitoring of repeated application of the technique on soil properties and other ecosystem components is necessary.

Promoting aerobic denitrification in reservoir water with iron-activated carbon: Enhanced nitrogen and organics removal efficiency, and biological mechanisms

Carbon scarcity limits denitrification in micropolluted water, especially in drinking water reservoirs. Therefore, a Fe-activated carbon (AC) carrier was used in this study to enhance the nitrogen removal capacity of aboriginal denitrification in drinking water reservoirs under aerobic conditions. Following carrier addition, total nitrogen (TN) and permanganate index (CODMn) removal efficiencies reached 81.89% and 72.66%, respectively, and were enhanced by 40.45% and 39.65%. Nitrogen balance analysis indicated that 77.86% of the initial TN was converted into gaseous nitrogen. Biolog analysis suggested that the metabolic activity of denitrifying bacteria was substantially enhanced. 16S rRNA gene sequencing indicated that organic degradation bacteria, hydrogen-consuming, Fe-oxidizing, and Fe-reducing denitrifying bacteria (e.g., Arenimonas, Hydrogenophaga, Zoogloea, Methylibium, and Piscinibacter) evolved into the dominant species. Additionally, napA, nirS, nirK, and nosZ genes were enriched by 3.17, 6.68, 0.40, and 6.70 folds, respectively, which is conducive to complete denitrification. These results provide a novel pathway for the use of Fe-AC to promote aerobic denitrification in micropolluted drinking water reservoirs.

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.

Fire Damage to the Soil Bacterial Structure and Function Depends on Burn Severity: Experimental Burnings at a Lysimetric Facility (MedForECOtron)

The soil microbiota is vulnerable to burning; however, it shows some resilience. No indices have yet been developed to assess fire damage related to soil biota. We evaluated the biological soil indices recorded by a Biolog EcoPlate System in a Mediterranean ecosystem. The experiment was carried out in an outdoor forest lysimeter facility (MedForECOtron), where we simulated burns with different burn severities. Burning increased the metabolic diversity of bacteria and most C-substrate utilization groups. Soil organic matter, phosphorus, electric conductivity, and calcium increased with increasing burn severity. Microbial richness and activity, as well as the integrated capacity of soil microbes to use a C source, lowered by burning, but recovered 6 months later. The functional diversity and amount of the C source used by microbes immediately increased after fire, and values remained higher than for unburned soils. We evaluated the changes in the vulnerability and resilience of fire-adapted ecosystems to improve their adaptive forest management. We found that the high burn severity reduced microbial richness, functional diversity, and the C source utilization of soil microbes (marked vulnerability to high temperatures), which recovered in the short term (high resilience). These results help to understand the main mechanisms of the effects of wildfire on semi-arid Mediterranean ecosystems, whose field validation will be helpful for fire prevention planning and restoration of burned areas.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO₃^– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.

Monitoring post-fire neighborhood competition effects on pine saplings under different environmental conditions by means of UAV multispectral data and structure-from-motion photogrammetry

In burned landscapes, the recruitment success of the tree dominant species mainly depends on plant competition mechanisms operating at fine spatial scale, that may hinder resource availability during the former years after the disturbance. Data acquisition at very high spatial resolution from unmanned aerial vehicles (UAV) have promoted new opportunities for understanding context-dependent competition processes in post-fire environments. Here, we explored the potentiality of UAV-borne data for assessing inter-specific competition effects of understory woody vegetation on pine saplings, as well as intra-specific interactions of neighboring saplings, across three burned landscapes located along a climatic/productivity gradient in the Iberian Peninsula. Geographic object-based image analysis (GEOBIA), including multiresolution segmentation and support vector machine (SVM) classification, was used to map pine saplings and understory shrubs at species level. Input data were, on the one hand, multispectral (11.31 cm·pixel^-1) and Structure-from-Motion (SfM) canopy height model (CHM) data fusion, hereafter MS-CHM, and, on the other, RGB (3.29 cm·pixel^-1) and CHM data fusion, hereafter RGB-CHM. A Random Forest (RF) regression algorithm was used to evaluate the effects of neighborhood competition on the relative growth in height of 50 pine saplings randomly sampled across the MS-CHM classified map. Circular plots of 3 m radius were set from the centroid of each target pine sapling to measure percentage cover, mean height of all individuals in the plot and mean height of individuals contacting the target sapling. Competing shrub species were differentiated according to their fire-adaptive traits (i.e. seeders vs resprouters). Object-based image classification applied on MS-CHM yielded higher overall accuracy for the three sites (83.67% ± 3.06%) than RGB-CHM (74.33% ± 3.21%). Intra-specific competitive effects were not detected, whereas increasing cover and height of shrub neighbors had a significant non-linear impact on the growth on pine saplings across the study sites. The strongest competitive effects of seeder shrubs occurred in open areas with low vegetation cover and fuel continuity, following a gap-dependent model. The non-linear relationships evidenced in this study between the structure of neighboring shrubs and the growth of pine seedlings/saplings have profound implications for considering possible competing thresholds in post-fire decision-making processes. These results endorse the use of UAV multispectral and SfM photogrammetry as a valuable post-fire management tool for measuring accurately the effect of competition in heterogeneous burned landscapes.

Mix-cultured aerobic denitrifying bacterial communities reduce nitrate: Novel insights in micro-polluted water treatment at lower temperature

Three mix-cultured aerobic denitrifiers were screened from a source water reservoir and named HE1, HE3 and SU4. Approximately 72.9%, 68.6% and 66.2% of nitrate were effectively removed from basal medium, respectively, after 120 h of cultivation at 8 °C. The nitrogen balance analysis revealed about one-fifth of the initial nitrogen was converted into gaseous denitrification products. According to the results of Biolog, the three microfloras had high metabolic capacity to carbon sources. The dominant genera were Pseudomonas and Paracoccus in these bacterial communities based on nirS gene sequencing. Response surface methodology elucidated that the denitrification rates of identified bacteria reached the maximum under the following optimal parameters: C/N ratio of 7.51-8.34, pH of 8.03-8.09, temperature of 18.03-20.19 °C, and shaking speed of 67.04-120 rpm. All results suggested that screened aerobic denitrifiers could potentially be applied to improve the source water quality at low temperature.

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

Although the importance of microbiota in the natural environment and in industrial production has been widely recognized, little is known about the formation and succession patterns of the microbial community, particularly secondary succession after disturbance. Here, we choose the Xiaoqu liquor brewing process as an experimental model in which sorghum grains were first aerobically saccharified and then anaerobically fermented after being stirred and acidified to explore multistage community succession patterns. We analyzed microbial composition, physicochemical factors, and metabolites of brewing grains inoculated with two different starters, pure starter and traditional starter, respectively. Two groups showed similar succession patterns where the saccharification microbiota was mainly derived from starters, while environmental microorganisms, mainly Lactobacillaceae and Saccharomyces, dominated the fermentation microbiota regardless of the original saccharification community composition. Species replacement shaped the bacterial community, while species replacement and loss both contributed to fungal community succession in both groups. Grain acidification and hypoxia led to the succession of bacterial and fungal communities during fermentation, respectively. Despite inoculation with starters containing different microorganisms, similar microbial communities during the fermentation stage of the two groups exhibited similar metabolite composition. However, higher abundance of Rhizopus in the saccharification of the pure starter group led to more alcohols, while higher abundance of Monascus and Saccharomycopsis in the traditional starter group promoted acid and ester metabolism. These results revealed the microbial succession patterns of two-stage liquor brewing and its influence on flavor metabolism, which could be used to regulate the microbial community in food fermentation to further promote the modernization of the fermented food industry.

IMPORTANCE Revealing formation and assembly mechanisms of microbiota can help us to understand and further regulate its roles in the ecosystems. The Xiaoqu liquor brewing system is a tractable microbial ecosystem with low complexity. This two-stage microbial ecosystem can be used as an experimental model to analyze the multistage temporal succession pattern of microbial communities. Our results demonstrated the dynamic composition and succession pattern of a microbial community in the two-stage liquor brewing system. The results also revealed the microbial origins determining community composition, the ecological processes dominating microbial community succession patterns, the determinants affecting microbial community successions, and the effect of microbial community changes on metabolite synthesis. Overall, our study not only provides an insight into multistage succession patterns of microbial communities in liquor brewing systems but also provides reference for optimizing the quality of fermented products, which will be helpful to understand the succession patterns of microbial communities in other natural ecosystems.