Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy

Distribution modelling and future prediction of a threatened species - Heracleum candicans Wall. ex DC.; Within the framework of biotic and abiotic interactions

Heracleum candicans Wall. ex DC. (Hogweed) is under huge anthropogenic pressure in terms of multipurpose collection coupled with climate-driven environmental changes in the region. It was hypothesized that establishment of H. candicans with plant associations was due to the complex biotic and abiotic interactions which play a crucial role in its present as well as future distribution. Therefore, we aimed to find out the impact of biotic and abiotic interactions as well as habitat suitability of hogweed, under the current and future climatic scenarios. The association pattern and biotic interactions were evaluated via Cluster Analysis (CA) and Two-Way Cluster Analysis (TWCA). Generalized Linear Model (GLM) and Canonical Correspondance Analysis (CCA) were carried out to assess H. candicans in relations to biotic and abiotic variables, simultaneously. Findings showed that abundance of the plant increased with increase in soil pH, EC, OM, N, P, K, sand and silt while decreased with increase in soil erosion and elevation from sea level. H. candicans exist in three different plant associations ranging from elevation of 1800-3000 m.a.s.l. For the distribution modelling of the H. candicans three machine algorithms such as RF, CART and SVM were used to predict potential habitats suitability, till the end this century. Future distribution of the considered species is primarily influenced by temperature and precipitation seasonality. Ensemble modelling-RF achieved high performance based on AUC-ROC values with training and test data of 1 and 0.979, respectively. The suitable habitat of the plant is expected to show contrasting range changes from 2040 to 2070 under both SSP126 and SSP370 scenarios. By the year 2100, the range of suitable habitat is expected to expand under optimistic, and to shrink in a pessimistic scenarios, SSP126 and SSP370, respectively. The predictive modelling approach could be beneficial for assessing the conservation importance and devising the future management strategies and policies for this and number of other endemic and threatened species, especially the medicinal plants.

Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas

Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Vegetation assessments under the influence of environmental variables from the Yakhtangay Hill of the Hindu-Himalayan range, North Western Pakistan

Vegetation structures and dynamics are the result of interactions between abiotic and biotic factors in an ecosystem. The present study was designed to investigate vegetation structure and species diversity along various environmental variables in the Yakhtangay Hills of the Hindu-Himalayan Mountain Pakistan, by using multivariate statistical analysis. Quadrat quantitative method was used for the sampling of vegetation. PC-ORD version 5 software was used to classify the vegetation into different plants communities using cluster analysis. The results of regression analysis among various edaphic variables shows that soil organic matter, total dissolved solids, electrical conductivity, CaCO₃ and moisture contents shows a significant positive correlation with species abundance, while the soil pH has inverse relationship with plant species abundance. Similarly, species richness increases with increase in soil organic matter, CaCO₃ and moisture contents, while decrease with increase in soil pH, total dissolved solids and electrical conductivity (p < 0.05). The vegetation was classified into four major plant communities and their respective indicators were identified using indicator species analysis. Indicator species analysis reflects the indicators of the study area are mostly the indicators to the Himalayan or moist temperate ecosystem. These indicators could be considered for micro-habitat conservation and respective ecosystem management plans not only in the study area but also in other region with similar sort of environmental conditions.

Microbial Community Composition and Activity in Saline Soils of Coastal Agro-Ecosystems

Soil salinity is a serious problem for agriculture in coastal regions. Nevertheless, the effects of soil salinity on microbial community composition and their metabolic activities are far from clear. To improve such understanding, we studied microbial diversity, community composition, and potential metabolic activity of agricultural soils covering non–, mild–, and severe–salinity. The results showed that salinity had no significant effect on bacterial richness; however, it was the major driver of a shift in bacterial community composition and it significantly reduced microbial activity. Abundant and diverse of microbial communities were detected in the severe–salinity soils with an enriched population of salt–tolerant species. Co–occurrence network analysis revealed stronger dependencies between species associated with severe salinity soils. Results of microcalorimetric technology indicated that, after glucose amendment, there was no significant difference in microbial potential activity among soils with the three salinity levels. Although the salt prolonged the lag time of microbial communities, the activated microorganisms had a higher growth rate. In conclusion, salinity shapes soil microbial community composition and reduces microbial activity. An addition of labile organic amendments can greatly alleviate salt restrictions on microbial activity, which provides new insight for enhancing microbial ecological functions in salt–affected soils.

Deposition Flux, Stocks of C, N, P, S, and Their Ecological Stoichiometry in Coastal Wetlands With Three Plant Covers

The depositional flux of coastal wetlands and the deposition rate of biogenic elements greatly affect the carbon sink storage. Ecological stoichiometry is an important ecological indicator, which can simply and intuitively indicate the biogeochemical cycle process of the region. This study investigated the soil deposition flux, stocks, and ecological stoichiometric ratios of C, N, P, and S under different water and salt conditions based on 137Cs dating technology in the Yellow River Delta (YRD) of China. The results showed that the deposition fluxes were 0.38 cm/year for PV wetlands, 1.08 cm/yr for PA wetlands, and 1.06 cm/yr for SS wetlands. Similarly, PA wetlands showed higher deposition fluxes of C, N, and S compared with SS and PV wetlands. PA wetlands had higher stocks of C (5.86 kg/m2), N (0.36 kg/m2) and S (0.36 kg/m2) in the top 1-m soil layer compared with PV and SS wetlands. However, the highest deposition rate of P (9.82 g/yr/m2) was observed in SS wetlands among the three wetlands. Three accumulative hotspots of C, N, and S in soil profiles of PA and SS wetlands were observed at soil depths of 0–10, 40–60, and 90–100 cm, whereas one accumulative hotspot of P was at the soil depth of 10–12 cm in SS wetlands and 80–82 cm in PA wetlands. PV wetlands showed higher accumulations of C, P, and S in the top 10 cm soil layer and N at the soil depth of 90–100 cm. The higher top concentration factors in these three wetlands indicated that the dominant input of plant residues was the main reason. The ratios of C/N and C/N/P of each sampling site were higher in the surface soils and decreased with depth. The ratios of C/P and N/P were larger in the surface layer (0–20 cm), the middle layer (40–60 cm), and the deep layer (90–100 cm). The ratios of N/P and C/N/P were relatively lower, indicating that these studied wetlands were N-limited ecosystems. The results implied that the coastal wetlands in the YRD have huge storage potential of biogenic elements as blue carbon ecosystems.

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

Influence of plants and environmental variables on the diversity of soil microbial communities in the Yellow River Delta Wetland, China

Microorganisms play an important role in the biogeochemical cycle and ecological function regulation of wetlands, have a major impact on global climate change and are critical for maintaining the health of the global ecosystem. In order to investigate the relationships among plants, environmental variables, and microbial communities in coastal wetlands in the Yellow River Delta, we selected soils growing plants such as Suaeda salsa, Tamarix chinensis, Phragmites australis, and cotton etc. The results show that there were differences in microbial diversity among areas with different vegetation cover and the microbial abundance in Phragmites australis and Tamarix chinensis areas was higher than that in mudflat, Suaeda glauca and cotton field, plants increased the diversity of soil microorganisms. The structure and diversity of soil microorganisms were significantly higher than that of endophytes. The Shannon index of soil bacteria was about 4-5.5, while that of endophytes was about 0-4. The soil bacteria were mainly Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria, accounting for more than 90.0% in all samples. The Mn⁴⁺, Fe³⁺ and hydrolytic nitrogen contents in the soil of vegetation covered areas was lower than that of the bare beach, the content of hydrolytic nitrogen in Phragmites australis area was generally higher, and the content of SO₄^2- and NO₂^- in the area was lowest near oil fields. Redundancy analysis shows that the explanatory rates of environmental factors at the phylum and genus levels were 89.70% and 86.80%, respectively, and K (23.40%), NO₂^- (11.80%), Mn⁴⁺ (9.80%) and Na (8.00%) were the main factors explaining the structural changes and composition of microbial flora at the phylum level. This study provides an ecological perspective for understanding the influence mechanism between wetland microbial diversity and wetland ecosystem function. It is helpful for us to understand the interactions among plants, environmental variables, and microbial communities in the coastal wetland of the Yellow River Delta, and has important guiding significance for the scientific research of soil environmental remediation in the degraded coastal wetland of the Yellow River Delta.

PCR-terminal restriction fragment length polymorphism for direct detection and identification of dermatophytes in veterinary mycology

The biological diagnosis of dermatophytosis in veterinary medicine usually relies on direct microscopic examination and inoculation of the samples on appropriate culture media. However, identification of dermatophytes needs expertise, and cultures which require from days to weeks to be conclusive, may lack of sensitivity because of the quite common overgrowth of contaminants. Here we developed a polymerase chain reaction (PCR) assay based on terminal restriction fragment length polymorphism (TRFLP), which may improve sensitivity of the biological diagnosis and reduce the delay for initiation of treatment. This study was first conducted on pure cultures of various dermatophytes (27 species), yeasts (14 species) and moulds (45 species). After DNA extraction, the internal transcribed spacer (ITS)-28S region of ribosomal DNA was amplified with primers targeting specifically pathogenic dermatophytes, and species of interest were identified by TRFLP with appropriate restriction enzymes. After validation, this assay was applied to veterinary samples and results were compared to those obtained by direct microscopic examination and cultures. All target species were correctly identified, and none of the yeast or mould species was amplified, demonstrating specificity of the assay. Regarding clinical samples, the causative agent was detected by PCR-TRFLP from 97.1% of the samples with both positive direct microscopic examination and cultures. No dermatophytes were detected when both conventional tests were negative. PCR-TRFLP developed here demonstrated to be highly sensitive and specific, allowing rapid detection and direct identification of dermatophytes in veterinary practice. Therefore, this assay is especially suitable for the biological diagnosis of dermatophytosis in different animal species.

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

Black alder (Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall). The dominant type of root microsymbionts of alder were ectomycorrhizal fungi, whose distribution depended on site (salinity): Tomentella, Lactarius, and Phialocephala were more abundant at the saline site. Mortierella and Naucoria (representatives of saprotrophs or endophytes) displayed the opposite tendency. Arbuscular mycorrhizal fungi belonged to Glomeromycota (orders Paraglomales and Glomales), however, they represented less than 1% of all identified fungi. Bacterial community structure depended on test site but not on season. Sequences affiliated with Rhodanobacter, Granulicella, and Sphingomonas dominated at the saline site, while Bradyrhizobium and Rhizobium were more abundant at the non-saline site. Moreover, genus Frankia was observed only at the saline site. In conclusion, bacterial and fungal community structure of alder root microsymbionts and endophytes depends on five soil chemical parameters: salinity, phosphorus, pH, saturation percentage (SP) as well as total organic carbon (TOC), and seasonality does not appear to be an important factor shaping microbial communities. Ectomycorrhizal fungi are the most abundant symbionts of mature alders growing in saline soils. However, specific distribution of nitrogen-fixing Frankia (forming root nodules) and association of arbuscular fungi at early stages of plant development should be taken into account in further studies.