Biolog EcoPlates Research Articles

Effects of plastic film mulching on soil microbial carbon metabolic activity and functional diversity at different maize growth stages in cool, semi-arid regions

IntroductionPlastic film mulching has been widely used to enhance soil hydrothermal conditions and increase crop yields in cool, semi-arid areas. However, its impact on soil microbial carbon metabolic activity and functional diversity during plant growth remains unclear despite their important roles in nutrient cycling and soil quality evaluation.MethodsThis study used the Biolog EcoPlate technique to investigate the dynamics and driving factors of soil microbial carbon metabolic activity and functional diversity at different maize growth stages following plastic film mulching.Results and discussionThe results revealed that film mulching significantly increased microbial carbon metabolic activities [represented by average well color development (AWCD)] by 300% at the seedling stage and by 26.8% at maturity but decreased it by 47.4% at the flowering stage compared to the control (without mulching). A similar trend was observed for the microbial functional diversity index. Redundancy analysis identified soil moisture (SM), soil temperature (ST), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacteria amounts as the primary factors influencing changes in soil microbial carbon source utilization. The mulch treatment significantly increased SM at all growth stages, while its warming effect disappeared at the flowering stage. Soil DOC, MBC, and bacterial populations were notably higher under mulching at the seedling and maturity stages but lower at the flowering stage. Pearson correlation analysis showed that changes in SM, ST, DOC, MBC, and bacterial populations positively correlated with the utilization of all carbon source classes, AWCD, and functional diversity indexes after film mulching. Furthermore, maize grain yield and water use efficiency increased by 142 and 129%, respectively, following film mulching. In conclusion, plastic film mulching enhanced soil microbial carbon metabolic activity and functional diversity at the seedling and maturity stages, improving crop yields in cool, semi-arid areas. Furthermore, the decrease in soil carbon metabolic capacity at flowering stage highlights that supplementing soil carbon sources should be considered after continuous film mulching to sustain or enhance farmland productivity and soil quality.

A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed.

The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity. The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h. Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as α-cyclodextrin, D-cellobiose, glycogen, α-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.

Laundry Isolate Delftia sp. UBM14 Capable of Biodegrading Industrially Relevant Aminophosphonates.

Phosphonates such as ethylenediaminetetra (methylenephosphonic acid) (EDTMP) and aminotris (methylenephosphonic acid) (ATMP) are used every day in water treatment processes or in household products. Their consumption is still increasing, regardless of the debates on their environmental impact. Here, the microbial characterisation and determination of the biodegradation potential of selected industrially relevant phosphonates for the isolate Delftia sp. UMB14 is reported. The opportunistic strain was isolated from a biofilm that was derived from a conventional washing machine using conventional detergents containing phosphonates. In antimicrobial susceptibility testing, the strain was only susceptible to sulfonamide, tetracycline, and chloramphenicol. Physiological and biochemical characteristics were determined using the BIOLOG EcoPlate assay. Most importantly, the strain was shown to convert D-malic acid and D-mannitol, as confirmed for strains of Delftia lacustris, and thus the new isolate could be closely related. Biodegradation tests with different phosphonates showed that the strain preferentially degrades ATMP and EDTMP but does not degrade glyphosate (GS) and amino (methylphosphonic acid) (AMPA). A specific gene amplification confirmed the presence of phnX (phosphonoacetaldehyde hydrolase) and the absence of PhnJ (the gene for the core component of C-P lyase). The presence of PhnCDE is strongly suggested for the strain, as it is common in Delftia lacustris species.

Effects of exogenous copper on microbial metabolic function and carbon use efficiency of Panax notoginseng planting soil.

Soil copper (Cu) pollution is a serious environmental risk in the Panax notoginseng planting area. However, the effect of Cu on soil microbial metabolism and nutrient cycling in this area remains unknown. Therefore, Biolog ECO-plate and enzyme stoichiometry methods were utilized in this study to investigate the impact of exogenous Cu (control: 0 mg·kg-1; Cu100: 100 mg·kg-1; Cu400: 400 mg·kg-1; and Cu600: 600 mg·kg-1) on the metabolic function of soil microbial and nutrient limitation in the P. notoginseng soil. The results indicated that Cu100 significantly increased soil organic carbon (SOC), total phosphorus (TP), soil C:N, microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) 9.89%, 15.65%, 17.91%, 61.87%, and 90.56% higher than the control, respectively. Moreover, the carbon source utilization ratio of carbohydrates, amino acids, and amphiphilic compounds of Cu100 also increased by 7.16%, 25.47%, and 84.68%, respectively, compared with the control. The activities of β-1,4-glucosidase, cellobiohyrolase, leucine amino peptidase, β-1,4-N-acetylglucosaminidase, and phosphatase significantly decreased with increasing Cu concentration. Soil enzyme stoichiometry showed that all treatments were limited by nitrogen (vector angle < 45°; 19.045-22.081). Cu600 led to the lowest carbon limitation (1.798) and highest carbon use efficiency (CUE:0.267). The PLS-SEM model also showed that MBC, MBN, MBP, and microbial diversity positively affected carbon and nitrogen limitation (0.654 and 0.424). Soil carbon, nitrogen, phosphorus, stoichiometric ratio, MBC, MBN, and MBP positively affected CUE (0.527 and 0.589). The microbial diversity index significantly negatively affected CUE (-1.490). Multiple linear stepwise regression analyses showed that CUE was mainly influenced by MBC, AP, C:P, and LAP. Thus, P. notoginseng soil can benefit soil microbial carbon and nitrogen limitations at low Cu concentrations. Clarifying the metabolic activity and nutritional status of microorganisms under Cu stress can provide some theoretical basis for realizing China's comprehensive and effective management and control policies for environmental risks from metals by 2035.

Centimetre scale functional dispersal limitation of freshwater copiotrophs.

The freshwater microbiome harbours numerous copiotrophic bacteria that rapidly respond to elevated substrate concentrations. We hypothesized that their high centimetre-scale beta diversity in lake water translates into pronounced metabolic variability, and that a large fraction of microbial 'metabolic potential' originates from point sources such as fragile organic aggregates. Three experiments were conducted in pre-alpine Lake Zurich over the course of a harmful cyanobacterial bloom: Spatially explicit 9 ml 'syringe' samples were collected in situ at centimetre distances along with equally sized 'mixed' samples drawn from pre-homogenized lake water and incubated in BIOLOG EcoPlate substrate arrays. Fewer compounds promoted bacterial growth in the syringe than in the mixed samples, in particular during the pre- and late bloom periods. Community analysis of enrichments on three frequently utilized substrates revealed both pronounced heterogeneity and functional redundancy. Bacterial consortia had higher richness in mixed than in syringe samples and differed in composition. Members of the Enterobacter cloacae complex dominated the EcoPlate assemblages during the mid-bloom period irrespective of treatment or substrate. We conclude that small-scale functional dispersal limitation among free-living copiotrophs in lake water reduces local biotransformation potential, and that lacustrine blooms of harmful cyanobacteria can be environmental reservoirs for metabolically versatile potential pathogens.

Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate.

Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types (p < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities (p < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Effect of EDDS on the rhizosphere ecology and microbial regulation of the Cd-Cr contaminated soil remediation using king grass combined with Piriformospora indica

The negative impacts of soil heavy metals composite pollution on agricultural production and human health are becoming increasingly prevalent. The applications of green chelating agents and microorganisms have emerged as promising alternate methods for enhancing phytoremediation. The regulatory effects of root secretion composition, microbial carbon source utilization, key gene expression, and soil microbial community structure were comprehensively analyzed through a combination of HPLC, Biolog EcoPlates, qPCR, and high-throughput screening techniques. The application of EDDS resulted in a favorable rhizosphere ecological environment for the king grass Piriformospora indica, characterized by a decrease in soil pH by 0.41 units, stimulation of succinic acid and fumaric acid secretion, and an increase in carbon source metabolic activity of amino acids and carbohydrates. Consequently, this improvement enhanced the bioavailability of Cd/Cr and increased the biomass of king grass by 25.7%. The expression of dissimilatory iron-reducing bacteria was significantly upregulated by 99.2%, while there was no significant difference in Clostridium abundance. Furthermore, the richness of the soil rhizosphere fungal community (Ascomycota: 45.8%, Rozellomycota: 16.7%) significantly increased to regulate the proportion of tolerant microbial dominant groups, promoting the improvement of Cd/Cr removal efficiency (Cd: 23.4%, Cr: 18.7%). These findings provide a theoretical basis for the sustainable development of chelating agent-assisted plants-microorganisms combined remediation of heavy metals in soil.

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity

Recently, there has been considerable interest in the functions of gut microbiota in broiler chickens in relation to their use as feed additives. However, the gut-microbiota of chickens reared at different altitudes are not well documented for their potential role in adapting to prevailing conditions and functional changes. In this context, the present study investigates the functional diversity of gut-microbes in high-altitude (HACh) and low-altitude adapted chickens (LACh), assessing their substrate utilization profile through Biolog Ecoplates technology. This will help in the identification of potential microbes or their synthesized metabolites, which could be beneficial for the host or industrial applications. Results revealed that among the 31 different types of studied substrates, only polymers, carbohydrates, carboxylic acids, and amine-based substrates utilization varied significantly (p < 0.05) among the chickens reared at two different altitudes where gut-microbes of LACh utilized a broad range of substrates than the HACh. Further, diversity indices (Shannon and MacIntosh) analysis in LACh samples showed significant (p < 0.05) higher richness and evenness of microbes as compared to the HACh samples. However, no significant difference was observed in the Simpson diversity index in gut microbes of lowversus high-altitude chickens. In addition, the Principal Component Analysis elucidated variation in substrate preferences of gut-microbes, where 13 and 8 carbon substrates were found to constitute PC1 and PC2, respectively, where γ-aminobutyric acid, d-glucosaminic acid, i-erythritol and tween 40 were the most relevant substrates that had a major effect on PC1, however, alpha-ketobutyric acid and glycyl-l-glutamic acid affected PC2. Hence, this study concludes that the gut-microbes of high and low-altitudes adapted chickens use different carbon substrates so that they could play a vital role in the health and immunity of an animal host based on their geographical location. Consequently, this study substantiates the difference in the substrate utilization and functional diversity of the microbial flora in chickens reared at high and low altitudes due to altitudinal changes.

Effect of carbon nanomaterials on functional diversity and structure of soil microbial community under single and repeated exposures.

The extensive application of carbon nanomaterials (CNMs) has attracted increasing studies concerned about its environmental impact. These studies focus on single exposure to CNMs, but repeated exposures with relatively low concentration are more likely to occur under actual exposure scenario. In this study, we studied the metabolic functional and structure of soil microorganism community under single and repeated exposures to multiwalled carbon nanotubes (MW), graphene (GR), and fullerene (C60) by Biolog EcoPlates and high-throughput sequencing. Our findings revealed that repeated exposures to CNMs significantly increase the metabolic activity and diversity of the soil microbial community as compared with single exposure. Principal component and similarity analysis not only indicated that GR exerted a stronger effect on soil microbial diversity among three exposures compared to C60 and MW, but also revealed that the metabolic activity of the soil microbial community was more affected by the exposure scenarios of CNMs than the type of CNMs. These findings elucidated the effect of CNMs under different exposure scenarios on soil microorganism community, providing a new perspective on the risk assessment of nanomaterials.

Bacterial communities in residential wastewater treatment plants are physiologically adapted to high concentrations of quaternary ammonium compounds

AbstractBenzalkonium chloride (BAC) is a quaternary ammonium compound (QAC) widely used as the active ingredient of disinfectants. Its excessive discharge into wastewater is constant and in high concentrations, likely affecting the physiology of microbial communities. We compared the physiological community profile of activated sludge (AS) bacteria with and without prior in vitro exposure to a high concentration of BAC (10 mg L−1). We measured the community functional diversity, carbon substrate multifunctionality, and the median effective concentration that inhibits carbon respiration (EC50) using Biolog EcoPlates supplemented with a gradient of 0–50 mg L−1 of BAC. Surprisingly, we did not find significant differences in the physiological parameters among treatments. Certain abundant bacteria, including Pseudomonas, could explain the community's tolerance to high concentrations of BAC. We suggest that bacterial communities in wastewater treatment plants’ AS are “naturally” adapted to BAC due to frequent and high‐dose exposure. We highlight the need to understand better the effects of QACs in wastewater, their impact on the selection of tolerant groups, and the alteration in community metabolic profiles.

Microbially modified effect of exogenous organic matter on soil chemical and biological indices and plant responses

PurposeExogenous Organic Matter (EOM) enriches and regenerates the soil, while solving the problem of landfilling waste such as sewage sludge and bottom sediments. The main purpose of the presented study was to estimate the influence of type and dosage of applied EOM on soil biological characteristics and supporting plant growth, with consideration of inoculation with PGPR (plant growth-promoting rhizobacteria).Materials and methodsThe soil samples were characterized by measuring key enzyme activities, determining the community-level physiological profiling (CLPP) using Biolog EcoPlates, abundance of microorganisms and evaluation physical and chemical properties.Results and discussionApplication of EOM mostly increased enzyme activity as well as overall metabolic activity compared to control sample. Increasing the dose of poultry manure and sewage sludge from 20 to 40 t ha−1 increased dehydrogenase, acid and alkaline phosphatase activity. Moreover, the addition of EOM affected the metabolic activity and the number of selected groups of bacteria and fungi.ConclusionsIn the research it was proven that application of EOM leads to relatively rapid and positive changes in soil biological activity. The research also confirmed that the supporting factor for plant growth was the inoculation with PGPR bacteria. This approach, together with the reuse of organic wastes may become an attractive approach in sustainable cropping systems in a circular economy system.Graphical

Response of bacterial community characteristics in the rhizosphere soil of Stellera chamaejasme L. to its expansion on the Qinghai‐Tibet Plateau

AbstractQinghai‐Tibet Plateau is facing a serious environmental and ecological problem of Meadow degradation. Toxic weed invasion is a typical characteristic of grassland degradation. Soil microbial community composition is sensitive to environmental changes; however, the effects of poisonous weed expansion on soil bacterial communities are unclear. Here, we investigated the effects of Stellera chamaejasme L. expansion on the rhizosphere soil bacterial community structure and function using high‐throughput sequencing. The results showed that expansion of Stellera chamaejasme L. changed soil nitrogen(e.g., total nitrogen [TN, −39.02%], available nitrogen [AN, −32.95%]) and other soil nutrients. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that soil nutrients changed, leading to significant changes in the bacterial community structure. The expansion of Stellera chamaejasme L significantly reduced its rhizosphere bacterial alpha diversity, and the beta diversity had significant differences (p &lt; 0.05). Principal coordinates analysis (PCoA) and analysis of similarity (ANOSIM) indicated that the expansion caused significant variations in the rhizosphere bacterial community (R = 0.7037, p &lt; 0.01). The linear discriminant analysis (LDA) effect size (LEfSe) analysis identified 23 biomarkers, most of which were Proteobacteria, indicating that bacteria involved in soil nutrient cycling were better able to survive in the alpine grassland. The Biolog EcoPlate method was used to determine the soil microbial metabolic capacity in different S. chamaejasme expansions. The result showed that heavy expansion had higher carbon source usage ability and microbial diversity index values. Furthermore, it was also found that heavy expansion improved the usage rate of amino acid carbon sources. Tax4Fun prediction analysis further indicated that carbohydrate metabolism, amino acid metabolism, and membrane transport were central metabolic pathways of rhizosphere soil bacteria. Our study found that Stellera chamaejasme L. changed rhizosphere soil nutrient and bacterial community structure during expansion and helped it tolerate harsh conditions by enriching bacterial communities actively involved in carbon and nitrogen metabolism and promoting plant growth. These findings provided evidence to propose effective restoration measures for poisonous grassland degradation.

Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil

Soil microbes and enzymes mediate soil carbon–climate feedback, and their responses to increasing temperature partly affect soil carbon stability subjected to the effects of climate change. We performed a 50-month incubation experiment to determine the effect of long-term warming on soil microbes and enzymes involved in carbon cycling along permafrost peatland profile (0–150 cm) and investigated their response to water flooding in the active soil layer. Soil bacteria, fungi, and most enzymes were observed to be sensitive to changes in temperature and water in the permafrost peatland. Bacterial and fungal abundance decreased in the active layer soil but increased in the deepest permafrost layer under warming. The highest decrease in the ratio of soil bacteria to fungi was observed in the deepest permafrost layer under warming. These results indicated that long-term warming promotes recalcitrant carbon loss in permafrost because fungi are more efficient in decomposing high-molecular-weight compounds. Soil microbial catabolic activity measured using Biolog Ecoplates indicated a greater degree of average well color development at 15 °C than at 5 °C. The highest levels of microbial catabolic activity, functional diversity, and carbon substrate utilization were found in the permafrost boundary layer (60–80 cm). Soil polyphenol oxidase that degrades recalcitrant carbon was more sensitive to increases in temperature than β-glucosidase, N-acetyl-β-glucosaminidase, and acid phosphatase, which degrade labile carbon. Increasing temperature and water flooding exerted a synergistic effect on the bacterial and fungal abundance and β-glucosidase, acid phosphatase, and RubisCO activity in the topsoil. Structural equation modeling analysis indicated that soil enzyme activity significantly correlated with ratio of soil bacteria to fungi and microbial catabolic activity. Our results provide valuable insights into the linkage response of soil microorganisms, enzymes to climate change and their feedback to permafrost carbon loss.

Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives.

Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.

Microbial Biofilm Colonizing Plastic Substrates in the Ross Sea (Antarctica): First Overview of Community-Level Physiological Profiles

The microbial colonization of plastic substrates made of polyvinylchloride (PVC) and polyethylene (PE) was studied in Tethys and Road Bays (Ross Sea, Antarctica) in order to evaluate the metabolic profiles of the plastisphere community in comparison with those of the surrounding waters. PVC and PE panels, mounted on stainless steel structures, were deployed in the austral summer 2017 at 5 and 20 m and recovered one year later at four different stations (Amorphous Glacier-AG was potentially impacted by the ice-melting process, and its control site was within Tethys Bay-TB; Road Bay-RB, close to the wastewater plant of the Italian research station Mario Zucchelli and its control site Punta Stocchino-PTS). Additional panels were settled in Road Bay at 5 m and recovered after three months to follow time variability in the microbial colonization process. At the same times and depths as plastic substrates, water samples were also collected. Carbon substrates’ utilization rates were determined on scraped microbial biofilm and water samples, with a fluorimetric assay based on 96-well Biolog Ecoplates. Complex carbon sources, carbohydrate and amines were the organic substrates that mostly fuelled the community metabolism in the RB area, while in the TB area, in addition to carbohydrates, phosphate carbon compounds and amino acids were also actively utilized. Within Road Bay, small differences in the physiological profiles were found, with higher metabolic rates in the biofilm community after 3 months’ deployment (late austral summer period) compared to 12 months, suggesting that autumn to spring period conditions negatively affected foulers’ metabolism. Moreover, different metabolic profiles between the plastisphere and the pelagic microbial community were observed; this last utilized a higher number of carbon sources, while plastic substrates were colonized by a more specialized community. Higher carbon substrate utilization rates were recorded at RB and AG stations, receiving organic supply from anthropic activity or ice melting sources, respectively, compared to their control sites. These results highlighted the functional plasticity of the microbial community, with the adaptive ability to utilize a diversified range of organic substrates.

The Compound Forest–Medicinal Plant System Enhances Soil Carbon Utilization

The sensible use of forest resources and the sound management of forests have become increasingly important throughout the years. In keeping with the trend, a composite forestry operation model has emerged. Traditional Chinese culture and forest management are particularly intertwined in China. Thus, use of the forest–medicine compound management model is recommended. The majority of research on the management of forest–medicine compounds has focused on how to grow more effective medicinal plants, ignoring the effects of the chemicals used on the soil environment, particularly the soil micro-environment. A forest–medicine system was established in South China to investigate the impacts of planting Aspidistra elatior on the variety of rhizospheric microorganisms and their ability to use carbon sources. In the plots with or without A. elatior, three dominant plants (Castanopsis hystrix, Psychotria rubra, and Ficus hirta) grew soil rhizosphere microbes, which were analyzed using Biolog EcoPlates. The study found that planting medicinal plants in the understory improved the soil’s nutritional content, increased the inter-root microbial communities of other medicinal plants, and enhanced the microbes’ ability to use soil carbon sources. The forest–medicine complex model, which rationalizes the use of forest clearings and generates economic and ecological benefits, can significantly increase the quantity of dominant microorganisms and enhance the enrichment of other species, resulting in a positive impact on the soil environment. These findings suggest that the forest–medicine compound management model can improve the use of soil carbon sources throughout the forest system.

Differential Responses of Bacterial and Fungal Communities to Siderophore Supplementation in Soil Affected by Tobacco Bacterial Wilt (Ralstonia solanacearum).

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.

Assessment of the Impact of Ceftriaxone on the Functional Profile of Soil Microbiota Using Biolog EcoPlateTM

Background: Antibiotics are essential to the treatment of diseases, but they have also brought about concerns in terms of their environmental, economic, and health impacts. Antibiotics can be excreted in unchanged form or as metabolites, which can cause toxicity by contaminating different environmental compartments, including soil. Soil is a critical compartment due to the numerous functions it performs and its direct impact on the communities of microorganisms, plants, and animals that make up the soil ecosystem. The functional profile of soil microbiota has emerged as a promising tool to assess soil quality. This study aimed to evaluate the functional profile of soil microbiota and the gut microbiota of earthworms in ceftriaxone-contaminated soil using Biolog EcoPlate. Methods: Soil samples contaminated with varying concentrations of ceftriaxone (0, 1, and 10 mg/kg) were incubated for 14 days in the presence or absence of the earthworm Eisenia andrei. After exposure, the physiological profile of the soil microbiota and the gut microbiota of the earthworms were evaluated using Biolog EcoPlate. Results: No significant differences were observed in the parameters evaluated using different concentrations of the antibiotic. The functional profile of the microbiota in the soil with and without earthworms was found to be similar, but interestingly, it differed from the profile of the intestinal microbiota of the earthworms. Conclusions: The findings of this study indicate that the presence of earthworms did not significantly alter the functional profile of the soil microbiota in ceftriaxone-contaminated soil. Further studies are necessary to investigate the potential impact of ceftriaxone and other antibiotics on soil microbiota and the role of earthworms in this regard.

Effects of Plant-Growth-Promoting Rhizobacteria on Soil Bacterial Community, Soil Physicochemical Properties, and Soil Enzyme Activities in the Rhizosphere of Alfalfa under Field Conditions

Background: Inoculation with plant-growth-promoting rhizobacteria (PGPR) effectively increases plant growth in agriculture. However, the role of the rhizobiome in plant growth remains unclear. Methods: Biolog Ecoplate and 16S rRNA gene high-throughput sequencing techniques were used to analyze the changes in microbial community diversity, composition, and function after PGPR inoculation. Soil physicochemical and enzyme activities were also measured. Results: PGPR inoculation significantly promoted the growth of alfalfa. Using a Biolog Ecoplate, inoculation improved the metabolic activity and carbon source utilization of soil microorganisms. PGPR inoculation significantly increased the diversity and richness of the soil bacterial community in the rhizosphere of alfalfa and increased the relative abundance of key bacterial taxa such as Arthrobacter, Sphingomonas, and Bacillus, which are conducive to plant growth. Conclusions: Inoculation with PGPR enriched bacterial taxa and improved the utilization of carbon sources beneficial for plant growth. PGPR inoculation induced changes in microbial community diversity, and relevant functions in the rhizosphere contributed to alfalfa growth under field conditions.