Substrate Richness Research Articles

Unveiling the Diversity and Ecological Roles of Macrofungi in Ayer Hitam Forest Reserve, Selangor, Malaysia

The biodiversity of macrofungi in remaining lowland dipterocarp forest in highly urbanization pressures is infrequently studied, even though their significant impact on the ecosystem of forested and non-forested habitats. Therefore, this research endeavours to unravel the diversity of macrofungi from different substrates in the Ayer Hitam Forest Reserve located in Selangor, Malaysia. Through a combination of field surveys, the study seeks to contribute valuable insights into the complex relationships between macrofungi and the surrounding habitats where macrofungal community structure was mainly influenced by substrate richness and microclimates. Sporocarps of macrofungi were collected from selected sites using opportunistic sampling methods. A total of 333 sporocarps were obtained and identified based on morphological and molecular analysis. Basidiomycota prevailed in the Ayer Hitam Forest Reserve where 27 species belonging to 14 families were successfully identified. Saprophytic fungi (22 species, 81.5%) dominated the areas, and a small number of mycorrhizal (1 species, 3.7%) and parasitic (4 species, 14.8%) fungi were found. Based on species diversity, order Polyporales is the highest occurrence species in the sampling areas with a Shannon-Weiner Index value of 2.103 and Simpson Index value of 0.954, Evenness Index value of 0.601, making it the most abundant order containing Microporus species, The findings are expected to enhance our knowledge of the biodiversity of macrofungi from different substrates in Ayer Hitam Forest Reserve, which can lead to conservation efforts and promote the ecological significance of macrofungi in tropical forest ecosystems.

High-throughput screening carbon and nitrogen sources to promote growth and sporulation in Rhizopus arrhizus

Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-d-galactosamine and l-phenylalanine ranking at the top of the list. Eight substrates, especially l-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.

Soil microbial functional diversity is primarily affected by soil nitrogen, salinity and alkalinity in wetland ecosystem

Wetland ecosystems, recognized as important carbon sinks, face challenges due to climate change. Although wetland soil microorganisms play a major role in the wetland carbon cycle, the mechanisms influencing their spatial distribution remain elusive. Here, we investigate the impact of soil properties on the spatial distribution of soil microorganisms across five saline-alkali wetlands (Xianghai [XH], Niuxintaobao [NX], Momoge [MMG], Zhalong [ZL], and Halahai [HLH]) within the Songnen Plain, China. We utilized the Biolog-ECO method to assess the carbon metabolic activity, microbial diversity, and carbon source utilization preference of soil microorganisms. Using the structural equation model, we analyzed factors influencing microbial carbon metabolic activity and microbial diversity. Results indicate that southern wetlands harbor soil microbial communities exhibiting higher carbon metabolic activity, Shannon index, and substrate richness, compared to their northern counterparts. Specifically, soil microorganisms in NX and XH wetlands demonstrate a preference for labile organic carbon, whereas those in HLH and ZL wetlands preferred to use recalcitrant carbon. Furthermore, soil microbial carbon metabolic activity is primarily regulated by soil total nitrogen content, whereas soil microbial diversity is primarily regulated by soil salinity and alkalinity. Our findings revealed the distribution characteristics and influencing factors of soil microorganisms in the Songnen Plain wetland, contributing to understanding the maintenance mechanism of wetland carbon sink function.

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years.Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H′), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H′ and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity.The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

Functional diversity and behavioral changes of microbial communities under salt affected soils

Salt-affected soils (SASs) are globally distributed especially in the arid and semi-arid regions of the world which highly affect the crop growth and productivity. The soil physico-chemical and biological properties largely vary with different types of SASs which trigger the crop yield, nutrient imbalance and soil quality. Therefore, to understand the changes in soil microbiology in relation to soil characteristics, a micro plot study was conducted to evaluate the impact of soil salinity/sodicity on physical, chemical properties at surface (0–15 cm) and subsurface (15–30 cm) soils in relation to soil microbial population, activities and functional diversity with focusing on community-level physiological profiling (CLPP) study. Five types of soils based on pH, electric conductivity (EC) and salt concentration maintained for last 25 years - highly saline, moderately saline, highly sodic, moderately sodic and normal were evaluated in micro plots to understand the changes in soil biological properties in relation to salt concentration. The results revealed that the highest value of pHs, ECe (EC of soil saturated paste extract), cation exchange capacity (CEC), exchangeable sodium percentage (ESP), sodium adsorption ratio (SAR), anions and cations concentrations, bulk density (BD), infiltration rate (IR), penetration resistance (PR) were observed in highly saline and highly sodic soils at surface and subsurface soil layer. In surface and subsurface layers, organic carbon (0.67 and 0.52 %) and available N (110 and 195 kg ha−1) were found higher under normal soils than SASs (% OC: 0.20–0.34 and 0.17–0.38; available N: 75–80 and 47–77 kg ha−1), respectively. In relation to changes in soil physicochemical properties, average well color development (AWCD) was found highest with normal soils followed by moderately saline and moderately sodic soils and lowest was found in highly sodic soils at surface soils which indicates interference of salts in metabolic activities of microbes. The utilization of amino acids, amines, carboxylic acids, phenolic compounds and polymers was highest for normal soils followed by moderately saline and lowest was recorded for highly sodic soils. But AWCD for carbohydrates was highest in highly saline soils, followed by highly sodic soils in contrast to normal soil and lowest was found under moderately sodic soils. Shannon diversity index (H) and substrate richness (SR) were found higher (3.19 and 24.07) in normal soils than SASs. Similarly, effect of salt load was also reflected on less soil enzymatic activities such as dehydrogenase, aryl sulfatase, invertase, etc. under varying types of SASs. Thus, with the increasing salt load, chemical and physical properties of soils were found to deteriorate and directly affected the microbial population, activities and their diversity in soil. This study indicated that soil physico-chemical properties, functional diversity, population and community of microbes were highly influenced by nature of salts and their concentration that may affect the soil quality and crop yield.

Global meta-analysis reveals positive effects of biochar on soil microbial diversity

Biochar has gained global attention due to its potential for climate change mitigation and soil quality improvement. Yet, the consequences of biochar additions for soil microbes -the major biotic drivers of soil function- remain unknown across global environmental gradients. We aimed to explore the responses of soil bacterial communities to biochar addition, and further investigate how biochar and soil properties impact these responses. We conducted a global meta-analysis and found that, in general, biochar has a limited impact on the proportion of major bacterial phyla, with only Acidobacteria and Gemmatimonadetes being largely impacted: the relative abundance of Acidobacteria decreased by 14.6%, while that of Gemmatimonadetes increased by 19.8%. Also, the experimental type played a role in shaping the response of microbial community to biochar application. In addition, biochar significantly promoted the diversity of soil bacteria, i.e., genetic richness and diversity. These changes were significantly associated with biochar load, C/N ratio, pyrolysis temperature, biochar pH, as well as soil C/N ratio and pH. We further found that the impacts of biochar on functional diversity, i.e., C substrate richness consumed by soil microbes increased with the biochar load, which might relate to increased genetic richness. Our work suggests that selecting key biochar properties can improve soil quality, microbial function, and climate change mitigation while maintaining the positive impacts of biochar on soil microbial diversity. Further research is needed to link the response of soil microbial composition at the genus level to biochar addition, with microbial functions.

Metabolic activity on Biolog FF MicroPlate suggests organic substrate decomposition by Aspergillus terreus NTOU4989 isolated from Kueishan Island Hydrothermal Vent Field, Taiwan

Aspergillus terreus NTOU4989 was isolated from sulfur sediment collected at Kueishan Island Hydrothermal Vent Field, Taiwan, and was shown to be able to grow at 45 °C and pH 3 in seawater, characteristics of hydrothermal vent sites. Fungi are one of the major decomposers in the marine environment, and to find out whether A. terreus NTOU4989 can fulfill such a role at the site, this study investigated its metabolic activity using the Biolog FF MicroPlate™ under different growth conditions (45 °C/pH 3, 45 °C/pH 7, 25 °C/pH 3, 25 °C/pH 7) with/without addition of Al 3+ , Fe 2+ and Mn 2+ , major metal ions in the vent effluent. The greatest metabolic activity was observed at 25 °C/pH 3 with/without the metal ions based on substrate richness (R S , metabolic richness), average well colour development (AWCD, metabolic capacity) and average well turbidity development (AWTD, mycelial production). Significant low R S , AWCD and AWTD were observed at 45 °C, suggesting that A. terreus NTOU4989 is a thermotolerant fungus. The presence of the metal ions did not have a significant effect on its metabolic activity. Monomers of lignin, cellulose and hemicellulose, and common sugars and amino acids of algae were utilized in selected conditions, providing evidence of wood and algal decomposition by the fungus at the hydrothermal vent site.

Impact of vineyard management on grape fungal community and Montepulciano d’Abruzzo wine quality

In this study the effect of farming practices on the diversity of grape fungal community of Vitis vinifera L. cultivar Montepulciano and the microbial metabolic activity was investigated. Small-scale vinifications were performed and wines were characterized. Agronomic management system affected the fungal community composition. Hanseniaspora, Areobasidium and Botrytis genera represented 30%, 20% and 10% of the total reads in all samples. A. pullulans, and Cladosprium cladosporioides mainly occurred on organic and biodynamic grapes. Saccharomyces and Pseudopithomyces genera were present only on organic or biodynamic grapes, respectively. The agronomic managements also influenced the potential functionality of microbial community. In fact, the metabolic function was increased in organic and biodynamic grapes. Polymers were used only by organic and biodynamic microbial communities, which also showed the highest values of Shannon’s diversity index, and substrate richness. However, no significative differences were observed for the oenological parameters analyzed, with the only exception of the content of sugars which were higher on conventional grapes. The fermentation profiles showed that conventional wines had a lower residual sugars content, and a higher amount of alcohol. The differences observed in the volatile composition of the wines were both quantitative and qualitative. Conventional wines showed a lower content of esters, and a higher concentration of alcohols than organic and biodynamic ones. Biodynamic wines were characterized by the highest content of organic acids. The obtained results revealed that farming practices shape the fungal community influencing wine traits linking the wine with the viti-vinicultural area of origin.

Metabolic Capacity Differentiates Plenodomus lingam from P. biglobosus Subclade 'brassicae', the Causal Agents of Phoma Leaf Spotting and Stem Canker of Oilseed Rape (Brassica napus) in Agricultural Ecosystems.

In contrast to the long-lasting taxonomic classification of Plenodomus lingam and P. biglobosus as one species, formerly termed Leptosphaeria maculans, both species form separate monophyletic groups, comprising sub-classes, differing considerably with epidemiology towards Brassicaceae plants. Considering the great differences between P. lingam and P. biglobosus, we hypothesized their metabolic capacities vary to a great extent. The experiment was done using the FF microplates (Biolog Inc., Hayward, CA, USA) containing 95 carbon sources and tetrazolium dye. The fungi P. lingam and P. biglobosus subclade ‘brassicae’ (3 isolates per group) were cultured on PDA medium for 6 weeks at 20 °C and then fungal spores were used as inoculum of microplates. The test was carried out in triplicate. We have demonstrated that substrate richness, calculated as the number of utilized substrates (measured at λ490 nm), and the number of substrates allowing effective growth of the isolates (λ750 nm), showed significant differences among tested species. The most efficient isolate of P. lingam utilized 36 carbon sources, whereas P. biglobosus utilized 60 substrates. Among them, 25–29 carbon sources for P. lingam and 34–48 substrates for P. biglobosus were efficiently used, allowing their growth. Cluster analysis based on Senath criteria divided P. biglobosus into two groups and P. lingam isolates formed one group (33% similarity). We deduce the similarities between the tested species help them coexist on the same host plant and the differences greatly contribute to their different lifestyles, with P. biglobosus being less specialized and P. lingam coevolving more strictly with the host plant.

The Biolog EcoPlate™ Technique for Assessing the Effect of Metal Oxide Nanoparticles on Freshwater Microbial Communities.

The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8–100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

Hydrocarbon substrate richness impacts microbial abundance, microbiome composition, and hydrocarbon loss

Manipulating the taxonomic richness of communities can impact numerous community functions. One proposed explanation is that certain taxa can exploit resources or habitat space that others cannot, leading to additive contributions to process rates. It is of interest to learn whether the reverse could also be true. That is, can increasing the richness of resources in an environment impact community size, composition, and function? We mimicked hydrocarbon spills in an uncontaminated soil by introducing individual substrates and all possible combinations of hexadecane, fluorene, and pyrene at four total concentrations, along with a crude oil treatment. We hypothesized that increasing substrate richness would increase microbial abundance, diversity, and function. When a single hydrocarbon substrate was added, we observed lower bacterial and fungal abundance (qPCR) relative to controls receiving no hydrocarbons. Interestingly, however, regardless of total hydrocarbon concentration, microbial abundance increased as the number of added substrates increased. We observed large changes in microbial composition, diversity, and hydrocarbon loss based on specific hydrocarbon substrate combinations, but this was not clearly linked to hydrocarbon substrate richness. These results show that introduced hydrocarbon richness has a strong influence on microbial abundance, but that changes to other soil processes may depend more on other properties of the added compounds.

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach.

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon–Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed.

Emerging environmental contaminants (silver nanoparticles) altered the catabolic capability and metabolic fingerprinting of microbial communities

Microbial community functional diversity enhances the degradation of organic matter and pollutants in the environment, but there is a growing concern that these ecosystem services may be altered by the introduction of emerging environmental contaminants including silver nanoparticles (AgNPs) into aquatic systems. We added 0, 25, 50, 75, 100, and 125 mg L−1 (nominal concentrations) of citrate-AgNP and polyvinylpyrrolidone-AgNP (PVP-AgNP) each to freshwater sediment and examined their antimicrobial effects on microbial communities using community-level physiological profiling. The results showed that citrate-AgNP decreased the overall microbial catabolic activity by 80% from 1.16 ± 0.02 to 0.23 ± 08 while PVP-AgNP decreased the catabolic activity by 51% from 1.25 ± 0.07 to 0.61 ± 0.19 at 125 mg L−1. Citrate-AgNP and PVP-AgNP caused a statistically significant reduction in substrate richness and substrate diversity that decreased microbial functional diversity. AgNPs decreased microbial catabolic capability and functional diversity at concentrations ranging from 0.12 ± 0.04 to 0.43 ± 0.07 mg Ag kg-1 which are lower than the predicted concentrations in freshwater sediment. To our knowledge, this is the first study to demonstrate inhibition of microbial functional diversity by citrate-AgNP and PVP-AgNP in a pathogen impaired stream. Citrate-AgNP caused greater inhibition of carbon substrate utilization but amino acids, carbohydrates, and carboxylic acids were the most affected carbon groups which led to a shift in the metabolic fingerprint pattern of the microbial community. AgNPs decreased the catabolic capability and the ability of the microbial community to degrade organic matter and a variety of pollutants in the environment.

Continuous Monoculture of Alfalfa and Annual Crops Influence Soil Organic Matter and Microbial Communities in the Rainfed Loess Plateau of China

Cropping systems are structured to maximize crop yields and increase sustainability in agricultural production. A field study was conducted to investigate different long-term cropping systems on soil organic matter and microbial communities. The cropping systems studied were: (i) a 14-year continuous alfalfa (Medicago sativa L.) (CA), (ii) a 9-year alfalfa removed and rotated with 4–5 years continuous annual crops (spring wheat (Triticum aestivum L.), maize (Zea mays L.), potato (Solanum tuberosum L.), and millet (Panicum miliaceum L.)), and (iii) a 5-year field fallow after alfalfa. Results showed that continued annual crops decreased total organic C and labile organic C by 10 to 20% and 17 to 34% in the topsoil (0–30 cm), and by 15 to 35% and 20 to 46% in the subsoil (30–60 cm), respectively, compared with CA. Similar trends were found in soil total N concentration, which decreased by 7 to 20% in the topsoil. Highest microbial biomass C was found in CA. Shannon-Wiener diversity and substrate richness of soil microbes measured by Biolog EcoPlates was significantly affected by cropping system with CA exhibiting a higher degree of soil microbial functional diversity in the topsoil, while the lowest values were found in the alfalfa-potato system. The higher soil organic matter content and functional diversity of soil microbe in CA indicates that soil nutrition and microbial activity did not limit alfalfa development and growth in the dryland area. The lower microbial activity and functional diversity observed in the potato field indicates the importance of crop selection in cropping systems.

Conversion of peat swamp forest to oil palm cultivation reduces the diversity and abundance of macrofungi

Deforestation of tropical peat swamp forests is rapidly taking place across Southeast Asia to make way for agricultural expansion. Within forest ecosystems, macrofungi play a vital role, including wood decomposition and nutrient cycles. To reveal the effects of deforestation and land cover conversion on macrofungi in Southeast Asian tropical forests we assessed the relationship between environmental variables such as air temperature, relative air humidity, soil pH, soil moisture, canopy cover, canopy closure, habitat type (i.e., peat swamp forest, large-scale plantation, monoculture smallholding, and polyculture smallholding) and available substrata with macrofungal species richness and abundance. We sample macrofungi across four habitats on Peninsula Malaysia including peat swamp forest, large-scale plantations, monoculture smallholding and polyculture smallholding. We found that substrate richness had a positive effect on macrofungal morphospecies richness, while soil pH and air temperature had a negative effect. For macrofungal abundance, canopy closure and soil moisture had negative effects, whereas substrate richness and relative air humidity had positive effects. Our data showed considerable variation in functional group responses to environmental variables. The abundance of wood-inhabiting fungi was driven primarily by substrate richness, while relative air humidity, soil moisture, and habitat type play minor roles. The abundance of terricolous saprotrophic fungi was determined principally by habitat type, substrate richness, and relative air humidity. Macrofungal community structure was mainly influenced by substrate richness, followed by microclimates and soil characteristics. Our results can provides critical ecological data to support conservation stakeholders conserve macrofungi in natural and agricultural peatlands. Our study suggests that the expansion of oil palm monocultures, to the detriment of peat swamp forests, is likely to have negative effects on macrofungal biodiversity and further agricultural expansion should be prevented.

Sprouting process affects the lactic acid bacteria and yeasts of cereal, pseudocereal and legume flours

The aim of this work was to investigate how sprouting process may affect the indigenous lactic acid bacteria (LAB) and yeasts of wheat, barley, quinoa, lentil and chickpea flours. LAB and yeasts inhabiting the raw and sprouted flours were described by culture-dependent and -independent approach. Based on community-level catabolic profiles, the sprouting process led to a strong increase of the Shannon's diversity and substrate richness indices. Compared to raw flours, the highest ability to consume carbohydrates, polymers, amines, carboxylic acid and amino acids sources was found for the microbial communities of wheat, chickpea and lentil sprouted flours. Except for LAB detected in quinoa, sprouting process caused significant (P < 0.05) changes in the cell density of LAB and yeasts. Compared to raw flours, all sprouted flours harboured a different microbiome and a higher number of LAB strains. Positive correlations (r > 0.70; FDR < 0.05) were found between cell density of LAB and yeasts with the time of sprouting process and the concentrations of free sugars content in flours.This study demonstrated that the sprouting process of wheat, barley, quinoa, lentil and chickpea grains modifies the microbial metabolic activities and composition of the lactic acid bacteria and yeasts of the resulting flours.

Impacts of elevated CO2 on nitrogen uptake of cucumber plants and nitrogen cycling in a greenhouse soil

It remains unclear whether elevated CO2 would increase N uptake of vegetable and alleviate soil degradation via reducing N residual in greenhouse soils. This study investigated the effect of three CO2 concentrations 400 (ambient CO2), 800 (elevated CO2) and 1200 μmol mol−1 (super-elevated CO2) and two N application rates 0.06 (low N) and 0.24 g N kg−1 (high N) on N uptake of cucumber plants and N cycling in a greenhouse soil in open top chambers. Elevated CO2 increased the biomass and N concentration of fine roots in high N by 24% and 4%, respectively, indicating a greater improvement in N uptake efficiency. The improvement was greater under low N but to a lesser extent under super-elevated CO2. Elevated CO2 altered microbial community as indicated by decreased Shannon diversity, substrate richness and Shannon evenness when averaged N treatments possibly associated with the increased plant N uptake efficiency. Elevated CO2 and super-elevated CO2 tended to decrease gene abundances of soil bacterial amoA, nirS and nosZ in high N with increased plant N uptake and decreased concentrations of NH4+, NO2− and NO3− in soils resulting in less soil N loss. To conclude, moderate CO2 enrichment enhances N uptake efficiency in fine roots of cucumber plants and decreases soil N loss associated with decreased nitrification and denitrification under high N application in a greenhouse soil.

Effects of agronomic treatments on functional diversity of soil microbial community and microbial activity in a revegetated coal mine spoil

Successful restoration of coal mine spoil requires functional microbial community for soil development and biogeochemical cycling to ensure long term sustainability of established plants. The current study investigated functional diversity of the soil microbial community, microbial activities, and physico-chemical properties of a revegetated coal mine spoil that was exposed to different agronomic practices. Treatments included Control (conventional revegetation practice), selective herbicide (SH), mulching (M), succession planting (SP), and green manure (GM) crops. Fluorescein diacetate (FDA) hydrolysis revealed significantly (P < 0.05) higher microbial activity in the GM treatment compared to the Control and all other treatments. Patterns of microbial biomass C (MBC), determined by the chloroform fumigation extraction method, also showed significant (P < 0.05) differences between treatments, with the SH treatment showing the lowest MBC. Basal respiration (BR) and substrate induced respiration (SIR) did not differ amongst the treatments. Principal component analysis of community level physiological profiles data based on Biolog® Ecoplate data revealed differing bacterial functional (metabolic) diversity amongst the treatments. Overall, the study demonstrated significantly (P < 0.05) higher average well color development (AWCD), indicating high metabolic activity, and substrate richness (R) and Shannon's index (H) showed greater functional diversity of the bacterial community in the SP treatment, as compared to other treatments. These results demonstrate that the agronomic treatments such as SP will not only boost microbial activity, but they also play a constructive role in increasing functional diversity of soil microbial communities. Based on these results, we recommend that agronomic practices such as SP should be used as an important component in mine site revegetation programs.

Functional Diversity of Soil Microbial Communities in Response to the Application of Cefuroxime and/or Antibiotic-Resistant Pseudomonas putida Strain MC1

Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on this topic, the scope of this study was to assess the functional diversity and catabolic activity of the microbial community in soil treated with XM (1 mg/kg and 10 mg/kg soil) using the community-level physiological profile (CLPP) approach during a 90-day experiment. In addition, the effect of antibiotic-resistant Pseudomonas putida strain MC1 (Ps) was also evaluated. The resistance/resilience concept and multifactorial analysis were used to interpret the data. The results showed that the introduction of XM and/or Ps into the soil caused changes in the catabolic activity and functional diversity of the microbial community. A decrease in the values of the CLPP indices (i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six carbon substrate groups) for the XM-treated soil was generally detected up to 30 days. In turn, at the same time, the activity measured in the Ps-inoculated soil was higher compared to the control soil. A stimulatory effect of XM at 10 mg/kg (XM10) and XM10+Ps on the utilization pattern of each substrate group was found at the following sampling times (days 60 and 90). The AWCD values for the utilization of amines, amino acids, carbohydrates, carboxylic acids, miscellaneous compounds and polymers for these treatments were found to be up to 2.3-, 3.1-, 2.3-, 13-, 3.4- and 3.3-fold higher compared to the values for the nontreated control, respectively. The resistance of the CLPP indices and the AWCD values for the carbon substrate groups were categorized as follows: E &gt; H &gt; R &gt; AWCD and amino acids = carbohydrates &gt; polymers &gt; amines &gt; miscellaneous &gt; carboxylic acids, respectively. The results suggest a low initial resistance of the soil microbial community to XM and/or Ps, and despite the short-term negative effect, the balance of the soil ecosystem may be disturbed.

Invasion of the alien shrub Prunus laurocerasus in suburban deciduous forests: Effects on native vegetation and soil properties

Most invading alien plants affect native biodiversity and ecosystem functioning. In a field survey, we assessed the impact of the invasive shrub Prunus laurocerasus on the native vegetation and soil properties in suburban deciduous forests in the region of Basel, Switzerland. We installed four pairs of plots in patches of P. laurocerasus and in adjacent not invaded areas in each of twelve forest areas. Native species richness, Shannon-diversity and species composition of the ground vegetation and shrub layer were assessed in each plot. Furthermore, in each plot we measured physical and soil chemical characteristics, enzyme activities and the carbon source utilization pattern of the soil microbial community using Ecoplates™. The maximum age of P. laurocerasus in each plot was determined using tree ring analysis, indicating the time elapsed since the invasive plant has established. A lower native plant species richness in both the ground vegetation and shrub layer was observed in plots with presence of P. laurocerasus. A different species composition of the ground vegetation was also found among plots with and without the invasive shrub. Plots invaded by P. laurocerasus had a lower soil moisture content than control plots. The intensity, diversity and substrate richness of the carbon sources were increased in soil from invaded plots compared to soil in control plots. However, the chemical soil characteristics examined and the activities of enzymes were not influenced by the invasive plant. The effects of P. laurocerasus became more pronounced with the time elapsed since the invasive plant has established. Thus, the removal of young P. laurocerasus individuals would be an appropriate management practice for this invasive shrub species.