The impact of climate change in the European Alps has been roughly twice the global average, dramatically reducing permafrost extent and thickening of its active layer. Therefore, the study of the ...abiotic factors (i.e. chemical/physical parameters) affecting the microbial diversity inhabiting Alpine permafrost appears to be of dramatic relevance. Within the European Alps, the Stelvio area exhibits these effects in a particularly evident way, with important consequences on microbial ecosystems. Therefore, microbial communities inhabiting a permafrost core collected in the Scorluzzo active rock glacier (Stelvio Pass, Italian Central Alps) were investigated along a depth gradient (410 to 524 cm from the surface). The taxonomic structures of bacterial and fungal communities were investigated via a next-generation sequencing (NGS) approach (Illumina MiSeq), targeting the bacterial V3-V4 regions of 16S rDNA and the fungal ITS2 region. Abiotic soil factors (grain size, electrical conductivity, ice/water content, pH, Loss-on-Ignition - LOI, total and organic carbon, nitrogen and phosphorous) were analysed. Richness and Shannon-H diversity indices were correlated to abiotic factors. Bacterial diversity was significantly (p < 0.05) correlated with LOI, while fungal diversity was significantly (p < 0.05) correlated with the depth gradient. The Constrained Analysis of Principal (CAP) coordinates were used to study the correlation between abiotic parameters and the taxonomic structure of bacterial and fungal communities. Among all tested variables, the depth gradient, water content, pH and LOI affected the taxonomic structure of bacterial communities (in particular, the abundance of bacterial amplicon sequence variants - ASVs - assigned to Afipia sp., Chloroflexi, Gaiella sp., Oryzihumus sp. and Serratia, sp.), while fungal communities (ASVs assigned to Naganishia sp., Rhodotorula sp., Sordariomycetes and Taphrinales) were affected by the depth gradient. Co-occurrences (calculated by Pearson correlation coefficient) among microbial taxa (i.e. bacteria vs bacteria, bacteria vs fungi, fungi vs fungi) were investigated: the prevalence of significant (p < 0.05) positive co-occurrences was found, suggesting that the coexistence of different microbial taxa could play a crucial role in maintaining the ecological and taxonomic balance of both bacterial and fungal communities inhabiting the Alpine permafrost ecosystem. These findings suggest that the bacterial and fungal diversity of Alpine permafrost are affected in different ways by some abiotic factors.
•The structure of bacterial communities is affected by depth, % of water, pH and LOI.•The structure of fungal communities is affected by depth.•Bacterial communities are dominated by Actinobacteria and Proteobacteria.•Meyerozyma is the prevalent fungal genera found in Alpine permafrost.•The prevalence of positive co-occurrences between bacteria and fungi was found.
•Effects of herbaceous plant species on beech and riparian forest soils were studied.•Plant growth had a positive effect on microbiological performance in both soil types.•Species combinations had a ...stronger effect than single-species treatments.•Plant treatments had different effects on the soil physicochemical properties.•Species identity significantly affected soil parameters.
Although herbaceous plant species have the potential to affect soil abiotic and biotic properties, and thus ecosystem processes, they still remain an underappreciated component of forest ecosystems. We performed an outdoor pot experiment to assess the influence of four herbaceous plant species and their combinations on beech and riparian forest soils. The following plant cover treatments were used in the experiment: (1) bare (unplanted) soil, (2) Aegopodium podagraria, (3) Allium ursinum, (4) Anemone nemorosa, (5) Ficaria verna, (6) two-species combination (A. podagraria + A. ursinum), and (7) four-species combination. After 15 months of the experiment, the soils were collected from the pots and analyzed for microbiological properties, i.e., basal respiration, substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) concentrations, enzymatic activity, and physicochemical properties, including moisture, pH, total and available nutrient contents. Herbaceous plants strongly influenced beech and riparian forest soils. Plant growth, either in monocultures or in combinations, resulted in high microbial performance. On the contrary, bare soils were characterized by the lowest values of many microbial indices. Overall, species combinations and A. podagraria had the strongest positive effects on microbes and processes, though the latter mainly in riparian soil; they increased PLFA-biomass (total, bacteria, G+ and G- bacteria, saprotrophic fungi), SIR-biomass, soil respiration, acid phosphatase, alkaline phosphatase, arylsulfatase, and/or urease activity. Plant species combinations and A. podagraria (in riparian soil) also stood out from other treatments in their effects on soil physicochemical properties, decreasing soil water content and the availability of some nutrients (N-NO3, P-PO4). Moreover, A. podagraria increased organic C and total N in riparian soil. Concluding, our experiment showed that the presence of herbaceous plant species positively influences microbes in beech and riparian forest soils, and this effect becomes stronger as plant species diversity increases. Herbaceous plant species are an important component of temperate forests because they play a significant role in supporting soil microorganisms and processes, maintaining soil health in these ecosystems. As such, they should be included in forest management practices.
Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, ...dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.
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•The efficacy of zeolite was tested on water quality, C/N ratio, and microbiota in the sediment and crayfish gut.•Suspended zeolite showed higher C/N retention ability over time.•Suspended zeolite improved gut microbial diversity, metabolic functions, and immune response.•Rhodoferax spp., was found positively correlated to nitrogen waste removal.•Zeolite in suspended form can be used for crayfish aquaculture.
Abstract
Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental ...factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.
This study demonstrated that bacterial community composition but not functions shifted in long-term N-, P-, K- and NPK-fertilized grassland.
This study demonstrated that bacterial community composition but not functions shifted in long-term N-, P-, K- and NPK-fertilized grassland.
A novel integrated bio-electrochemical system with sulfur autotrophic denitrification (SAD) and electrocoagulation (BESAD-EC) system was established to remove nitrate (NO3−-N) and phosphorus from ...contaminated groundwater. The impacts of a current intensity gradient on the system’s performance and microbial community were investigated. The results showed that NO3−-N and total phosphorus (TP) could be effectively removed with maximum NO3−-N reduction and TP removal efficiencies of 94.2% and 75.8% at current intensities of 200 and 400 mA, respectively. Lower current intensities could improve the removal efficiencies of NO3−-N (≤200 mA) and phosphorus (≤400 mA), while higher current intensity (600 mA) caused the inhibition of nutrients removal in the system. MiSeq sequencing analysis revealed that low electrical stimulation improved the diversity and richness of microbial community, while high electrical stimulation reduced their diversity and richness. The relative abundance of some genus involved in denitrification and phosphorus removal processes such as Rhizobium, Hydrogenophaga, Denitratisoma and Gemmobacter, significantly (P < 0.05) reduced under high current conditions. This could be one of the main reasons for the deterioration of denitrification and phosphorus removal performance. The results of this study could be helpful to enhance the nutrient removal performance of bio-electrochemical systems in groundwater treatment processes.
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•Suitable currents could improve the nutrient removal efficiencies.•Higher current intensity (600 mA) inhibited wastewater nutrient removal.•Currents changed the microbial diversity in a bio-electrochemical system.•Some genus involved in nitrate and phosphorus removal reduced under high currents.•Key genus Thiobacillus contributed to better denitrification performances.
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•The physicochemistry of leaves is unique and is a major driver of leaf colonisation.•Competition and cooperation may be major drivers of bacterial colonisation.•Leaves respond to ...bacterial colonisation locally and systemically.•How leaf responses shape bacterial colonisation patterns is unclear.•Plant-microbe interaction should be studied at the micrometer resolution.
Bacteria establish complex, compositionally consistent communities on healthy leaves. Ecological processes such as dispersal, diversification, ecological drift, and selection as well as leaf surface physicochemistry and topology impact community assembly. Since the leaf surface is an oligotrophic environment, species interactions such as competition and cooperation may be major contributors to shape community structure. Furthermore, the plant immune system impacts on microbial community composition, as plant cells respond to bacterial molecules and shape their responses according to the mixture of molecules present. Such tunability of the plant immune network likely enables the plant host to differentiate between pathogenic and non-pathogenic colonisers, avoiding costly immune responses to non-pathogenic colonisers. Plant immune responses are either systemically distributed or locally confined, which in turn affects the colonisation pattern of the associated microbiota. However, how each of these factors impacts the bacterial community is unclear. To better understand this impact, bacterial communities need to be studied at a micrometre resolution, which is the scale that is relevant to the members of the community. Here, current insights into the driving factors influencing the assembly of leaf surface-colonising bacterial communities are discussed, with a special focus on plant host immunity as an emerging factor contributing to bacterial leaf colonisation.
Increased nitrogen (N) deposition has been found controversial affecting soil CO₂ emission in terrestrial ecosystems, which leads to serious debate on the efficiency of estimated C sequestration ...induced by N enrichment. The forms of input N might be responsible for this controversy. This study aims to explore the effects of NH₄ ⁺ (reduced N) and NO₃ ⁻ (oxidized N) on soil CO₂ flux and the underlying microbial mechanisms. An N addition experiment, two N fertilizers (NH₄Cl and NaNO₃) and two rates (40 and 120 kg N ha⁻¹ year⁻¹), was carried out in a slash pine plantation of southern China. Soil-atmospheric CO₂ exchange, soil microbial biomass, and community composition were measured using static chamber-gas chromatography and phospholipid fatty acid (PLFA) analyses in the active growing and nonactive growing seasons, respectively. Low level of NaNO₃ addition significantly increased soil CO₂ flux in the active growing season, whereas other N treatments did not change soil CO₂ flux. High level of NH₄Cl addition significantly reduced soil fungal biomass (fungal PLFA) and changed microbial community composition (ratio of fungal to bacterial (F/B) PLFAs). The positive relationships between the change in soil CO₂ flux and the change in fungal biomass, as well as between the change in soil CO₂ flux and the change in community composition, were observed in the nonactive growing season. The N forms as NO₃ ⁻ or NH₄ ⁺ are important factors affecting C cycles in the subtropical coniferous plantation. These results suggested that the variations of soil CO₂ emission and microbial biomass and community composition in the subtropical plantation depended on the seasons and the levels and forms of N addition.
Climate change is triggering rapid shifts in plant communities and alterations in soil abiotic conditions in peatlands, with cascading effects on belowground decomposers and ecosystem C turnover. ...However, elucidating the dominant causal relationships between plant communities, soil biota and C fluxes in these vulnerable ecosystems requires a better understanding of the spatio-temporal variability of abiotic and biotic drivers. In this study we investigated the effects of biotic (plant functional types, PFTs) and abiotic factors (soil temperature and soil moisture) in determining dynamic patterns of soil microbial community structure and C cycling. Four representative temperate peatland habitats were selected based on their peat forming vegetation – an Atlantic wet heathland, two active blanket bogs with herbaceous plants (Molinia caerulea and Eriophorum angustifolium), and a transition mire dominated by Sphagnum mosses located along an altitudinal gradient to include the natural variations in soil temperature and water content regimes. We found that peat microbial communities were more strongly linked to local abiotic conditions than to the dominant above-ground vegetation. Aerobic conditions and warmer temperatures accelerated fungal driven decomposition and CO2 emissions under shrubs, whereas decreases in Gram−negative bacteria promoted increased C losses under Molinia. These findings suggest that small spatial differences in abiotic conditions can create local “hotspots” of organic matter decomposition. We propose that temperate peatlands should be considered as ‘ecosystem sentinels’ for climate change, acting as early-warning indicators of climate-carbon feedbacks.
•Peat microbial communities were more strongly linked to microclimatic conditions than to vegetation.•More aerobic and warmer soils under shrubs accelerated fungal driven decomposition and CO2 emissions.•Decreases in Gram-negative bacteria under grasses promoted C losses as DOC.•In the absence of abiotic stress, more C was retained (i.e. under mosses and sedges).•We propose temperate peatlands as ‘ecosystem sentinels’ for climate-mediated impacts on the C cycle.
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