Search Results (19)

The Sanjiang Plain hosts the largest freshwater wetland in Northeastern China and plays a critical role in regional climate stability. However, climate change and human activities have degraded the wetland, forming a successional gradient from the original flooded wetland to dry shrub and forest vegetation with a lower ground water level. This degradation has altered soil microbial structure and functions, reducing ecological and socio-economic benefits. Along this successional gradient, we used Biolog-ECO plates combined with soil enzyme assays (catalase, urease, sucrase, and acid phosphatase) to assess the dynamics of microbial carbon metabolic activity, measured by average well color development (AWCD). The results showed a systematic decline in AWCD values with advancing succession, revealing a pronounced reduction in overall microbial metabolic activity during wetland degradation. This trend correlated with loss of soil moisture, organic carbon, and nitrogen nutrients. Microbial communities in early successional wetland stages (i.e., original natural wetland and wetland edge) preferred labile carbon sources (e.g., carbohydrates, amino acids), while forested stages favored relatively more structural (e.g., polymers, phenolic compounds). These findings indicate that vegetation succession regulates microbial carbon metabolism by modifying soil physicochemical properties, providing insights for wetland restoration. Full article

There are discrepancies that exist in the effects of different land uses on soil organic carbon (SOC) and soil microbial carbon metabolism functions. However, the impact of land-use type changes on soil microbial carbon metabolism in alpine grassland arid areas is not well understood, hindering our understanding of the carbon cycling processes in these ecosystems. Therefore, we chose three types of land use (continuous reclamation of grassland (RG), abandoned grassland (AG), and natural grazing grassland (GG)) to study the microbial carbon metabolism and its driving factors by the Biolog-ECO method. The results showed that the soil organic carbon content decreased by 16.02% in the RG and by 32.1% in the AG compared to the GG in the 0–20 cm soil layer (p < 0.05). Additionally, microorganisms have the highest utilization efficiency of carbohydrate carbon sources, the average values of average well color development (AWCD) were RG (0.26), AG (0.35), and GG (0.26). In the 0–20 cm soil layer, the Shannon–Wiener and the Simpson indices were 3% and 1% higher in the AG compared to the GG, respectively. The soil TOC/TN and soil available phosphorus (AP) were key factors that affected the diversity of soil microbial and carbon metabolism. They were closely related to land-use types. This study holds that abandoning grasslands accelerates the carbon metabolism of microorganisms, leading to the loss of SOC content. Full article

Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat microbiomes metabolism. Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ Ecoplates. The results of average well color development (AWCD) showed that the degree of mycotrophy of preceding crop and soil disturbance affected the soil microbiome, although no impact on Shannon Evenness Index was observed during the experiment. The Shannon–Wiener Diversity Index showed variations among the different preceding plants, but not in wheat analysis. The pattern of the C sources metabolism also changed differentially regarding plant type and soil disturbance during the experiment, being also different within the highly mycotrophic plants (legume and grass). In the legume, an increase in the metabolism of amine/amides and phenolic acids was observed, whilst in the grass, an increase in the metabolism of phosphate-carbons (P carbon) and carbohydrates was more evident. Principal component analysis showed that a grouping in the distinct phases of the experiment correlated with the widening of the metabolism of amino acids, carboxylic acids, and carbohydrates. The results indicate that soil functional community structure reflects soil agricultural practice conditions. Previous plant types and soil disturbance impacted the soil microbiome metabolic response (AWCD) in wheat, generating different patterns of carbon metabolism related to previous plant mycotrophy. Full article

Siderophores secreted by microorganisms can promote ecological efficiency and could be used to regulate the unbalanced microbial community structure. The influence of the siderophore activity of Trichoderma yunnanense strain 2-14F2 and Beauveria pseudobassiana strain (2-8F2) on the physiological/biochemical functions and community structure of soil microbes affected by tobacco bacterial wilt (TBW) was studied. DNS Colorimetry and Biolog-eco plates were used to quantify the impacts of strain siderophores on soil enzyme activities and microbial metabolism. Based on Illumina MiSeq high-throughput sequencing, the soil 16S rDNA and ITS sequences were amplified to dissect the response characteristics of alpha/beta diversity and the structure/composition of a soil microbial community toward siderophores. The KEGG database was used to perform the PICRUSt functional prediction of the microbial community. We found that siderophores of 2-14F2 and 2-8F2, at certain concentrations, significantly increased the activities of sucrase (S-SC) and urease (S-UE) in the TBW soil and enhanced the average well color development (AWCD, carbon source utilization capacity) of the microbial community. The metabolic capacity of the diseased soil to amino acids, carbohydrates, polymers, aromatics, and carboxylic acids also increased significantly. The response of the bacterial community to siderophore active metabolites was more significant in alpha diversity, while the beta diversity of the fungal community responded more positively to siderophores. The relative abundance of Actinobacteria, Chloroflexi, and Acidobacteria increased and was accompanied by reductions in Proteobacteria and Firmicutes. LEfSe analysis showed that Pseudonocardiaceae, Gemmatimonas, Castellaniella, Chloridiumand and Acrophialophora altered the most under different concentrations of siderophore active metabolites. The PICRUSt functional prediction results showed that siderophore increased the abundance of the redox-related enzymes of the microbial community in TBW soil. The BugBase phenotypic prediction results showed that the siderophore activity could decrease the abundance of pathogenic bacteria. The study concludes that siderophore activity could decrease the abundance of pathogenic bacteria and regulate the composition of the microbial community in TBW soil. The activities of sucrase (S-SC) and urease (S-UE) in TBW soil were significantly increased. Overall, the siderophore regulation of community structures is a sustainable management strategy for soil ecosystems. Full article

Studying the quality of freshwater systems and drinking water in highly urbanized megalopolises around the world remains a challenge. This article reports data on the quality of select freshwater systems in Mega Manila, Philippines. Water samples collected between 2020 and 2021 were analyzed for physico-chemical parameters and microbial community metabolic fingerprints, i.e., carbon substrate utilization patterns (CSUPs). The detection of arsenic, lead, cadmium, mercury, polyaromatic hydrocarbons (PAHs), and organochlorine pesticides (OCPs) was carried out using standard chromatography- and spectroscopy-based protocols. Physiological profiles were determined using the Biolog EcoPlate™ system. Eight samples were free of heavy metals, and none contained PAHs or OCPs. Fourteen samples had high microbial activity, as indicated by average well color development (AWCD) and community metabolic diversity (CMD) values. Community-level physiological profiling (CLPP) revealed that (1) samples clustered as groups according to shared CSUPs, and (2) microbial communities in non-drinking samples actively utilized all six substrate classes compared to drinking samples. The data reported here can provide a baseline or a comparator for prospective quality assessments of drinking water and freshwater sources in the region. Metabolic fingerprinting using CSUPs is a simple and cheap phenotypic analysis of microbial communities and their physiological activity in aquatic environments. Full article

As a key part of the forest ecosystem, soil microorganisms play extremely important roles in maintaining the ecological environment and the security of water quality in reservoir areas. However, it is not clear whether there are differences in the functional diversity of soil microorganisms in different types of water-conservation forests in reservoir areas, and which factors affect the functional diversity of soil microorganisms. In our study, the Biolog-Eco microplate technique was used to analyze the carbon source metabolic characteristics of soil microbial communities in three typical water-conservation forests and a non-forest land: Pinus massoniana-Quercus variabilis mixed forest (MF), Pinus massoniana forest (PF), Quercus variabilis forest (QF) and non-forest land (CK). The results showed that the average well color development (AWCD), the Shannon diversity index (SDI) and the richness index (S) of the three forest lands was significantly greater than that of the non-forest land (p < 0.05). The mean values of AWCD, SDI and S of the three forests had the same order (QF > PF > MF), but there was no significant difference among different types of forests. The microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) of QF and PF were higher than those of MF and CK, but the microbial biomass C/N ratio (MBC/MBN) was lower. The variance partitioning analysis (VPA) showed that 86.4% of the variation was explained by plant (community) diversity, soil physical and chemical properties and soil microbial biomass, which independently explained 10.0%, 28.9%, and 14.9% of the variation, respectively. The redundancy analysis (RDA) showed that total phosphorus (TP), microbial biomass carbon (MBC), total nitrogen (TN), number of plant species (N_um) and alkali-hydro nitrogen (W_n) were the key factors affecting the functional diversity of soil microorganisms. This study confirmed that forest ecosystem is better than non-forest land in maintaining soil microbial function diversity. Moreover, Quercus variabilis forest may be a better stand type in maintaining the diversity of soil microbial functions in the study area. Full article

Sthenoteuthis oualaniensis is an important biological resource in the South China Sea. However, the microbiological characteristics of this squid, especially those of the dwarf-form, are poorly understood. This study was conducted to analyze the microbial community structure and metabolic characteristics of the intestinal and gill tissues of dwarf-form populations of S. oualaniensis. The dwarf-form squids of different sexes and gonadal maturities were collected from South China Sea in spring 2020. Results showed that Mycoplasma was the most dominant group of bacteria in the intestinal samples of the females with immature gonads (FN), females at sexual maturity (FY), and males at sexual maturity (MY) and the second-highest relative abundance group in males with immature gonads (MN). The microbial community structure in squid gills differed from that of intestinal flora. The BD1-7 clade was the dominant genus in gill samples of all groups. Furthermore, the microbial community activities in gills were higher than in intestinal groups, especially FYG. The larger dwarf-form populations had microbial communities with more robust utilization of carbon sources, assessed via average well color development (AWCD). Correlation and redundancy analysis determined that AWCD significantly positively correlated with the relative abundance of BD1-7 clade (p < 0.05). The results indicated that the dominant group of bacteria and microbial community structure were different between the intestinal and gill microbial communities in the dwarf-form S. oualaniensis populations of different sexes and maturities. Moreover, the metabolic potential of the gill microbial community was higher than that of the intestinal microbial community in the dwarf-form populations. Full article

Phytoremediation is an important solution to heavy metal pollution in soil. However, the impact of plants on microbial communities in contaminated soil also requires attention. Community-level physiological profiling (CLPP) based on the Biolog™ EcoPlate and high-throughput sequencing were used to study the soil microbial community in this article. The rhizosphere and bulk soil samples of six native species were collected from the iron mine tailings on Jiulong Mountain, Jiangxi Province. According to the average well color development (AWCD), all plants improved the activity and diversity of the contaminated soil microbial community to varying degrees. Cunninghamia lanceolate is considered to have good effects and led to the appearance of Cunninghamia lanceolata > Zelkova schneideriana > Toona ciliata > Alnus cremastogyne > Cyclobalanopsis myrsinifolia > Pinus elliottii. The Shannon–Wiener diversity index and principal component analysis (PCA) show that the evenness and dominance of soil microbial communities of several plants are structurally similar to those of uncontaminated soil (UNS). The results of high-throughput sequencing indicated that the bacterial community diversity of C. lanceolata, A. cremastogyne, and P. elliottii is similar to UNS, while fungal community diversity is different from UNS. C. lanceolata has a better effect on soil nutrients, C. myrsinifolia and P. elliottii may have a better effect on decreasing the Cu content. The objective of this study was to assess the influence of native plants on microbial communities in soils and the soil remediation capacity. Mortierellomycota was the key species for native plants to regulate Cu and microbial community functions. Native plants have decisive influence on microbial community diversity. Full article

Microorganisms in sediments are an important part of the aquatic ecosystem, and their functional activities are sensitive to external environmental pressure. Shallow lakes are characterized by frequent sediment resuspension events, leading to large amounts of nutrients being released. However, information about the potential impacts of sediment resuspension events on the functional activities of microbial communities is limited. In this study, the responses of microbial carbon metabolism in sediments under different wind–wave disturbance were analyzed by BIOLOG ECO microplates. The results showed that under four disturbance conditions (wind speeds of 0, 1.60, 3.62, and 14.10 m/s), the total carbon metabolism function of the sediment microbial community (represented as average well-color development, AWCD) remained unchanged (p > 0.05), and the final total AWCD value stabilized at about 1.70. However, compared with the control group, some specific carbon sources (e.g., amines and carboxylic acids) showed significant changes (p < 0.05). We found that short-term (8 h) resuspension events did not affect the total carbon metabolism of sediment microbial communities, while it affected the microbial utilization ability of some specific types of carbon sources. For example, we found that the microbial utilization capacity of polymers in the 14.10 m/s group was the best. This study provides a new insight into the carbon cycle process of shallow lake sediments that resuspension events will affect the carbon cycle process of sediments. Full article

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. Full article

The toxicity of nanomaterials to microorganisms is related to their dose and environmental factors. The aim of this study was to investigate the shifts in the microbial community structure and metabolic profiles and to evaluate the environmental factors in a laboratory scale intertidal wetland system exposed to zinc oxide nanoparticles (ZnO NPs). Microbial assemblages were determined using 16S rRNA high-throughput sequencing. Community-level physiological profiles were determined using Biolog-ECO technology. Results showed Proteobacteria was the predominant (42.6%–55.8%) phylum across all the sediments, followed by Bacteroidetes (18.9%–29.0%). The genera Azoarcus, Maribacter, and Thauera were most frequently detected. At the studied concentrations (40 mg·L⁻¹, 80 mg·L⁻¹, 120 mg·L⁻¹), ZnO NPs had obvious impacts on the activity of Proteobacteria. Adverse effects were particularly evident in sulfur and nitrogen cycling bacteria such as Sulfitobacter, unidentified_Nitrospiraceae, Thauera, and Azoarcus. The alpha diversity index of microbial community did not reflect stronger biological toxicity in the groups with high NP concentrations (80 mg·L⁻¹, 120 mg·L⁻¹) than the group with low NP concentration (40 mg·L⁻¹). The average well color development (AWCD) values of periodically submersed groups were higher than those of long-term submersed groups. The group with NP concentration (40 mg·L⁻¹) had the lowest AWCD value; those of the groups with high NP concentrations (80 mg·L⁻¹, 120 mg·L⁻¹) were slightly lower than that of the control group. The beta diversity showed that tidal activity shaped the similar microbial community among the periodically submerged groups, as well as the long-term submerged groups. The groups with high DO concentrations had higher diversity of the microbial community, better metabolic ability, and stronger resistance to ZnO NPs than the groups with a low DO concentration. Full article

In the drinking water reservoir ecosystem, phytoplankton and bacteria play important roles in shaping freshwater health and function. In this work, the associated bacterial community functional diversity during degradation of phytoplankton was determined using the substrate utilization profiling (BIOLOG) technique, meanwhile, the composition and concentration of phytoplankton were examined using a microscope. The results indicated that Euglena decreased 58.33% from 0 to 38 d, while the smallest degradation of Bacillariophyta was 20.19%. Average well color development (AWCD_590nm) increased during the static periods from 0 to 38 d; however, the AWCD_590nm of 18 and 38 d had no significant difference (p < 0.05). The Simpson’s index (D) was in accordance with Shannon’s diversity (H) and species richness(S); it was measured to be18 > 38 > 5 > 0 d. There were significant differences in the pattern and level of carbon sources used by the phytoplankton-associated bacteria. In addition, the principle component analyses (PCA) suggested that the first principle component (PC1) and the second principle component (PC2) explained 46.76% and 21.49% of the total variation for bacterial community, respectively. Redundancy analysis (RDA) revealed that cell abundance of phytoplankton was negatively correlated with the AWCD_590nm, amino acids and other functional indexes. Therefore, the data suggest that there are differences in the phytoplankton-associated bacterial community functional diversity during different static stages of water samples collected from the drinking water reservoir. Full article

Nanoplastic (NP) contamination is becoming a pervasive issue as NPs, originating from microplastic particles, pose potentially harmful environmental impacts on aquatic ecosystems. The environmental hazards of NPs on microorganisms have been well documented in recent studies; however, little is known about their ecotoxicity effects on freshwater biofilms, which serve as important primary producers and decomposers and are highly connected with other ecosystem components. We investigated the effects of NPs on the microbial metabolic functions of freshwater biofilms in terms of carbon source utilization ability. Biofilm samples were collected, cultivated in a hydrodynamic flume for six weeks, and then exposed in polystyrene (PS) beads (100 nm in size) with different NP concentrations (1, 5, and 10 mg/L). BIOLOG ECO microplates were used to quantify carbon source utilization characteristics. The data were analyzed using average well-color development (AWCD), functional diversity indices, and principle component analysis (PCA). Results showed that the total carbon metabolic functions (represented by AWCD) remained constant (p > 0.05) with elevated NP concentrations, but some specific carbon sources (e.g., esters) changed in their utilization ability (p < 0.05). The microbial functional diversity (Shannon–Wiener diversity index, Simpson diversity index, and Shannon evenness index) was significantly reduced under 10 mg/L NPs (p < 0.05), indicating an inhibiting effect of NPs on biofilm metabolic diversity. This study examined NP ecotoxicity effects on microbial metabolic activities at the community level, but further studies are required to fully understand the mechanisms driving this change. Full article

Soil formation in post-mining sites is crucial for restoring ecosystem function, and soil formation depend on the accumulation of soil organic matter and the development of an active microbial community. In this study, we used substrate-induced respiration (SIR) and Biolog plates to characterize microbial catabolic profiles in a chronosequence of soil samples from 15 unreclaimed post-mining sites in Sokolov, Czech Republic. The sites had been undergoing spontaneous succession for 3 to 45 years. Biolog ECO plates included 31 substrates. Of substrates used for SIR (glucose, chitin, cellulose, Tween 80, phenylethylamine, N-acetyl-D-glucosamine, L-asparagine, D-mannitol, D-galacturonic acid, α-cyclodextrin, and 4-hydroxy benzoic acid), eight were also used for the Biolog plates. Soil respiration, total bacteria number, and culturable bacteria number were also measured. The total and culturable number of bacteria increased with site age (p < 0.01 and p < 0.05, respectively). The percentage of culturable bacteria decreased with site age (p < 0.01). Biolog analysis indicated that average well-color development (AWCD), evenness, and richness increased with site age. SIR data indicated that only average activities tended to increase with site age (p = 0.06). According to redundancy analysis (RDA), the eight substrates, which were commonly used in both methods (SIR and BIOLOG) explained 74.4% of the variation of data from all Biolog substrates. Among the eight substrates common to both methods, only data for N-acetyl-D-glucosamine were positively correlated (p < 0.01) between Biolog and SIR. Both methods revealed microbial catabolic profile changed along the chronosequence. PCA indicated that site age, soil carbon, and pH were the most important drivers of microbial catabolic profiles. Full article

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 > H > R > AWCD and amino acids = carbohydrates > polymers > amines > miscellaneous > 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. Full article