Community-level Physiological Profiles Research Articles

Effects of Nitrogen Addition on Soil Microbial Functional Diversity and Extracellular Enzyme Activities in Greenhouse Cucumber Cultivation

Greenhouses, commonly used for vegetable production, are experiencing large nitrogen (N) inputs in North China, which leads to soil acidification, increases soil N availability, and affects microbial community structure and composition. However, it remains unclear how N enrichment influences soil microbial functional activities in this region. In this study, we conducted a two-year pot experiment in a greenhouse to evaluate the effects of four different rates of N addition (0, 334, 668, and 1002 kg N ha−1 year−1) on cucumber soil properties, extracellular enzyme activities, and community level physiological profiles (CLPP). We found that high-N addition (1002 kg N ha−1) caused a massive accumulation of inorganic nitrogen and soil acidification, which was not beneficial to soil microbial activities. The color development (AWCD) values for the metabolism of microbial carbon sources and the activities of soil extracellular enzymes also showed a significant decrease in high N(N3) treatment. Additionally, the activity of leucine aminopeptidase (LAP) and polyphenol oxidase (PPO) of N3 decreased by 36% and 50% compared to the N0 and could be a good predictor for microbial functional diversity and microbial biomass carbon (MBC). Structural equation modeling (SEM) confirmed that the reduction of microbial functional diversity is mainly coregulated by the decline of soil pH and the change of cucumber BGB (belowground biomass) resulting from soil C and N imbalance. Overall, excessive N-fertilizer amendment can be more dangerous to microbial community functional diversity, especially for carbohydrate utilization which adversely affects cucumber yield in current intensive management.

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei.

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

Effects of Different Native Plants on Soil Remediation and Microbial Diversity in Jiulong Iron Tailings Area, Jiangxi

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.

Impact of eight widely consumed antibiotics on the growth and physiological profile of natural soil microbial communities

Antibiotics’ (ATBs) occurrence in soil ecosystems has a relevant effect in the structure and functionality of edaphic microbial communities, mainly because of their amendment with manure and biosolids that alter their key ecological functions.In this study, the impact of eight widely consumed ATBs on a natural soil microbial community, characterized through 16 S rRNA gene sequencing, was evaluated. Changes induced by the ATBs in the growth of the soil microbiota and in the community-level physiological profiling (CLPP), using Biolog EcoPlates™, were measured as endpoint.The eight assayed ATBs lead to a significant decrease in the growth of soil microbial communities in a dose-dependent way, ordered by its effect as follows: chloramphenicol > gentamycin > erythromycin > ampicillin > penicillin > amoxicillin > tetracycline > streptomycin. Chloramphenicol, gentamycin, and erythromycin adversely affected the physiological profile of the soil community, especially its ability to metabolize amino acids, carboxylic and ketonic acids and polymers. The analysis of the relationship between the physico-chemical properties of ATBs, as well as their mechanism of action, revealed that, except for the aminoglycosides, each ATB is influenced by a different physico-chemical parameters, even for ATBs of the same family.Significant effects were detected from 100 μg mL to 1, concentrations that can be found in digested sludge, biosolids and even in fertilized soils after repeated application of manure, so cumulative and long-term effects of these antibiotics on soil environment cannot be ruled out.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming.

Simple SummaryBottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer.The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Differences in Microbial Communities Stimulated by Malic Acid Have the Potential to Improve Nutrient Absorption and Fruit Quality of Grapes.

Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson’s correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae. Furthermore, Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae were closely related to grape nutrient absorption and fruit quality. Bacillaceae and Woeseiaceae were positively correlated with total soluble sugar, while Planococcaceae and Rhodobacteraceae were positively correlated with titratable acid. Hence, Bacillaceae and Woeseiaceae were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.

Exploration of Soil Functional Microbiomes-A Concept Proposal for Long-Term Fertilized Grasslands.

Exploring grassland microbiomes is a challenge in the current context of linking soil microorganism activity with the balance of these ecosystems. Microbiologists are constantly attempting to develop faster and lower-cost methods, and propose new and best-fitted indicators that will provide a more complex data analysis. A different concept was proposed for assessing functional microbiomes by splitting the functional ecological niche into complementary segments. The comparison with the upper and lower limits of the ecological niche provides a clearer image of community alterations due to long-term applied treatments. The method allows the extraction of the most sensitive and stable functional guilds, with the extraction of the most critical dominant–codominant functional groups in every segment of the functional niche. The resulting microbial functional–sociological model is ready to use on community-level physiological profile databases and also can be applied backward for vegetation analysis.

Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.

Differences in bacterial functional profiles from loamy sand and clay loam textured soils under fungicide QuadrisR impact

The non-target effect of the fungicide QuadrisR on the bacterial community from grassland loamy sand (LS) and cropland clay loam (CL) soils with unknown history of fungicide usage was investigated. QuadrisR was applied to soil mesocosms at 0.0 mg kg-1 (Az0), 2.90 mg kg-1 (Az1), 14.65 mg kg-1 (Az2) and 35.0 mg kg-1 (Az3) calculated towards the active ingredient azoxystrobin (Az). Response of bacterial communities to QuadrisR was investigated during a 120-day incubation experiment, evaluating the shifts in bacterial catabolic profiles by the community-level physiological profiling (CLPP) technique and Biolog EcoPlatesTM method. QuadrisR decreased the overall catabolic activity (AWCD) of soil bacterial communities and the rate of decrease was independent of soil type and fungicide concentration. Fungicide affected negatively the utilisation of amines and positively that of amino acids in both soil types, whereas the effects on other carbon guilds (carbohydrates, carboxylic acids and polymers) corresponded closely to the respective soil type and fungicide concentration. Results indicated the presence of non-target effects of QuadrisR on bacterial functioning; hence, it is important to address the fungicide side-effects on soil health.

Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars.

Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20-34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon-Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.

Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea.

This study investigated the bacterial community structure and metabolic diversity and their relationship with Hg and other environmental variables in sediments collected from different locations (HSR-1-HSR-6) in the Hyeongsan River estuary in South Korea. The results showed that the highest total mercury (THg) and methylmercury (MeHg) concentrations were in HSR-2, with values of 4585.3µg/kg and 13.4µg/kg, respectively. The lowest THg (31.9µg/kg) and MeHg (0.1µg/kg) concentrations were found in HSR-1. Sulfate and organic matter (OM) were more influential environmental variables, revealing a positive association with THg and MeHg and negatively affecting bacterial and metabolic diversities. Bacterial and metabolic diversities were also negatively impacted by the THg and MeHg concentrations. Proteobacteria and Bacteroidetes were abundantly distributed in all the sediments. The dominance of Proteobacteria was upscaled in all the heavily Hg-contaminated sites (HSR-2-HSR-6), and it was the only phylum that showed a significant positive correlation with THg, MeHg, and OM. The genera Sulfurovum and Sulfurimonas were abundantly observed in sites with high Hg contamination, whereas Congregibacter, Gaetbulibacter, Ilumatobacter, Methylotenera, Nevskia, and Sediminibacter were only detected in low Hg-contaminated sites (HSR-1). The community-level physiological profile data showed the highest (1.0) average well color development (AWCD) value in HSR-1 and the lowest (0.45) AWCD value in HSR-2. Overall, these results demonstrated the inhibitory effects of THg, MeHg, and other environmental variables on microbial communities and metabolic diversity. These findings broaden the current knowledge on the dynamics of bacterial and metabolic diversities in Hg-contaminated sediments and might be useful in the management of Hg pollution.

Microbial responses are unreliable indicators of copper ecotoxicity in soils contaminated by mining activities

Metal contamination of soil has become a serious environmental problem worldwide. Many studies have attempted to infer metal ecotoxicity from soil microbial responses. However, much of the data from these studies tends to be inconsistent and difficult to interpret. We hypothesized that microbial response would be a useful indicator of metal toxicity in soils contaminated by copper mining in Chile. Eighty-four topsoils (0–20 cm) were collected from three areas historically contaminated by copper mining (total Cu: 46–1106 mg kg−1, soluble Cu: 0.05–2.3 mg kg−1, pCu2+: 6.3–10, pH: 5.1–7.8, organic matter: 1.1–10%, clay: 0–28%). Based on soil metal concentrations and ecotoxicity thresholds, Cu was expected to be toxic to microorganisms in the studied soils, while the effects of other metals (total Zn: 79-672, As: 1.9–60, Pb: 19-220, Cd: 0.4–5.1 mg kg−1) were expected to be minor. Soil microbial responses (microbial biomass and numbers, nitrogen mineralization and nitrification, and community-level physiological profiles) were also measured. The results showed that the different responses of soil microbes were not correlated with each other. Furthermore, the soil microbial responses were mainly influenced by the physicochemical properties of the soil, not by the metal concentrations in the soil. The effect of copper on the microbial response was either stimulating (positive) or toxic (negative). Of the soil microbial responses measured in this study, only the microbial biomass was useful for calculating dose-response curves. However, the microbial biomass response was not consistent among the different soil copper pools (total copper, soluble copper, and activity of free Cu2+ ions). It is important to emphasize that the thresholds obtained for copper toxicity cannot be adopted in a robust manner because of the different microbial responses in different sampling areas. Thus, in the copper-contaminated soils under study, microbial response was found to be an unreliable indicator of metal toxicity.

Organic amendment regulates soil microbial biomass and activity in wheat-maize and wheat-soybean rotation systems

Long-term heavy application of inorganic fertilizers is associated with a decrease in soil quality and biodiversity. Organic amendments have been reported to positively affect soil quality; however, relatively little is known regarding soil carbon (C) cycle enzyme kinetic parameters (Vmax and Km), community-level physiological profiles (CLPP), and the interactions between these factors and soil microbes and physicochemical properties under sustained organic amendment. Therefore, this study aimed to evaluate the effect of organic amendments on crop yield, soil chemical properties, microbial activity, enzyme kinetic parameters of five extracellular C cycle-related hydrolase enzymes, and soil microbial functional diversity in wheat-maize (WM) and wheat-soybean (WS) rotation crop systems. The results of the study showed that combined application of organic and inorganic fertilizers increased crop yield (6.81–17.47%), soil total organic C (TOC, 29.44–39.54%), total nitrogen (TN, 24.22–50.79%), available potassium (AK, 39.47–59.62%), total dissolved nitrogen (TDN, 19.68–33.75%), dissolved organic C (DOC, 14.54–55.10%), available phosphorus (AP, 34.81–243.90%), and microbial biomass C and nitrogen (MBC, 17.65–40.86% and MBN, 18.63–50.76%) concentration. The combined application also enhanced microbial growth when compared with an inorganic amendments regime. Additionally, the combined application of organic and inorganic fertilizers increased soil microbial activity and catabolic diversity and maintained a high substrate-induced respiration (SIR) value. Furthermore, the conversion from a WM rotation to a WS rotation increased both soil pH and microbial biomass, and the resultant soil exhibited lower potential activity and higher enzyme-substrate affinity. Overall, the findings of this study showed that an increase in soil microbial biomass is a key determinant of microbial catabolic activity and functional diversity.

Enzymatic activity and functional diversity of soil microorganisms along the soil profile – A matter of soil depth and soil-forming processes

Most studies concerning soil microorganisms and enzymes are focused on the upper horizons of the soil profile even though they transform soil organic matter at every depth of the soil profile. The aim of this study was to determine how the soil microbial functional diversity and enzymatic activity changed as a function of depth across the soil profiles which developed on the same parent material (glacial till) but differed in their soil-forming processes thereby resulting in the formation of different reference soil groups (RSG) (Luvisols, Gleysols and Stagnosols). Four soil profiles were excavated at different sites that are located in two mesoregions of the South Baltic Lake District (central Poland) in fields with alfalfa (Medicago sativa L.) in the fourth year of its cultivation. Using the soil samples collected in June 2019, we assessed the oxidoreductase activity (DHA – dehydrogenases, POX – phenol oxidase, PER – peroxidase), the fluorescein diacetate hydrolysis (FDAH) rate, the microbial biomass carbon and nitrogen (MBC, MBN) content, the number of microbial groups and the related physico-chemical properties. The community-level physiological profiles of the soil microorganisms were evaluated using the Biolog EcoPlate™ method. In general, the highest level of enzymatic activity per soil mass unit was found in the Ap horizons, whereas the dehydrogenases activity and FDAH decreased gradually with depth, while the phenol oxidase and peroxidase activity revealed no consistent trends between the sub-surface horizons. The specific enzymatic activity, expressed per unit of soil TOC and MBC, was more variable in response to profile depth than the enzymatic activity, which was expressed per soil mass, and this did not allow for clear trends to be determined. Also, the specific activity was different with regard to the intracellular and extracellular enzymes. The DHA/MBC ratio was markedly higher in the Ap horizons (all profiles) and generally decreased with depth. The phenol oxidase and peroxidase activities, expressed in the terms of the MBC content, did not exhibit any clear trends in the studied profiles, however, they reached their highest levels in the deepest layers in all of them. The abundance of all of the microbial groups was generally highest in the Ap horizon and decreased sharply with depth. A greater abundance of microbial groups was found in the gleyic horizons of the Gleysols and Stagnosols as compared to the upper and lower horizons. The highest average well color development (AWCD) under aerobic conditions was observed in the Ap genetic horizons (with the exception of the Haplic Luvisol profile), while the highest values of AWCD in anaerobic conditions were found in the illuvial and gleyic horizons. In contrast to the AWCD, the Shannon diversity index (H) and Shannon evenness index (S) (equal usage of compounds) indices were more similar in the compared horizons. Our findings suggest that the studied microbial properties in the Ap horizons were primarily determined by the TOC content, while their activity in the sub-surface layers was also affected by factors associated with soil-forming processes.

Evidence of functional and structural changes in the microbial community beneath a succulent invasive plant in coastal dunes

Abstract Coastal dunes represent priority habitats for conservation due to the provision of valuable ecosystem services such as land protection, water supply or biodiversity conservation. Soil microbial communities are of crucial importance to maintain plant diversity due to harsh environmental conditions, water limitation and nutrient scarcity. Invasive alien plants represent a major threat to ecosystem conservation. Here, we explored different impacts of Carpobrotus edulis, a succulent plant invading coastal areas worldwide, on the function and structure of bacterial communities. Sand represents a challenging substrate due to low organic matter content and limited microbial activity. We optimized bacterial extraction for functional evaluation before assessing ecosystem impacts produced by C. edulis. We compared 12 extracting procedures combining different soil storage, sample amount and extracting solutions on the functional activity of sand communities through the community-level physiological profile. We further explored the function (using Biolog Ecoplates) and structure [using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE)] of bacterial communities from dunes invaded by C. edulis. Saline solution consistently increased bacterial cells detected by cytometry (P ≤ 0.001). Principal component analysis suggested a limited temporal framework (0–24 h) in which community function can be explored without significant alterations in C substrate consumption. Changes under C. edulis invasion exhibited a different pattern of C substrate utilization comparing native and non-native zones (interspecific), but also between native zones (intraspecific), suggesting that functional impacts are site-dependent. Complementary, results obtained from PCR-DGGE indicated that the bacterial community structure of native dunes significantly differed from dunes invaded by C. edulis.

Short-Term Resilience of Soil Microbial Communities and Functions Following Severe Environmental Changes

Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) content, hydrolase activities involved in the mineralization of organic C, N, P and S, and microbial community-level physiological profiles (CLPPs)) during the microbial recolonization of three heat-sterilized forest soils followed by cross- or self-reinoculation and incubation for 1, 7 and 30 days. Soil ATP content, biochemical activities and CLPP were annihilated by autoclaving, whereas most of the hydrolase activities were reduced to varying extents depending on the soil and enzyme activity considered. During the incubation period, the combination of self- and cross-reinoculation of different sterilized soils produced rapid dynamic changes in enzymatic activity as well as in microbial structure and catabolic activity. Physicochemical properties of the original soils exerted a major influence in shaping soil functional diversity, while reinoculation of sterilized soils promoted faster and greater changes in bacterial community structure than in fungal communities, varying with incubation period and soil type. Our results also confirmed the importance of microbial richness in determining soil resilience under severe disturbances. In particular, the new microbial communities detected in the treated soils revealed the occurrence of taxa which were not detected in the original soils. This result confirmed that rare microbial taxa rather than the dominant ones may be the major drivers of soil functionality and resilience.

Recovery of microbial community in strongly alkaline bauxite residues after amending biomass residue

The aim of this study was to characterize the effects of cornstalk biomass amendments on microbial communities in bauxite residues (BRs) by phylogenetic analysis. Improvements in soil geochemical, physical, and biological properties were assessed to identify the major factors controlling microbial community development in BRs. After one year of incubation, the salinity and structure of the amended BRs had gradually improved, with pH dropping from 11.39 to 9.89, the exchangeable sodium percentage (ESP) dropping from 86.3% to 35.2%, and the mean weight diameter (MWD) rising from 0.12 mm to 0.38 mm. Further analysis of community level physiological profiles (CLPP) showed that the microbial utilization of different carbohydrates had shifted significantly, in addition to increases in the diversity index H′ (0.7–7.34), U (2.16–3.14), and the average well color development (0.059–1.08). Over the one-year outside incubation, the dominant fungal phyla in the BRs had shifted gradually from Ascomycota (85.64%) to Ascomycota (52.07%) and Basidiomycota (35.53%), while the dominant bacterial phyla had shifted from Actinobacteria (38.47%), Proteobacteria (21.39%), and Gemmatimonadetes (12.72%) to Actinobacteria (14.87%), Proteobacteria (23.53%), and Acidobacteria (14.37%). Despite these shifts, microbial diversity remained lower in the amended BRs than in the natural soil. Further redundancy analysis indicated that pH was the major factor driving shifts in the bacterial community, while aggregates were the major factor driving shifts in the fungal community. This study demonstrated that amendment with cornstalk biomass shifted the microbial community in the BRs from halophilic groups to acidogenic groups by improving the soil environmental conditions.

Can the Biological Activity of Abandoned Soils Be Changed by the Growth of Paulownia elongata × Paulownia fortunei?—Preliminary Study on a Young Tree Plantation

Bioenergy crops play an ecologically and economically fundamental role as an alternative to agri-food productions and as renewable energy sources. Thus far, less attention has been given to assessing microbiological indicators of soil quality in bioenergy crops on abandoned land. The current study assessed microbial and biochemical properties of two soils with different textures in agroforestry plantations of Paulownia elongata × Paulownia fortunei, with regard to the analysis of potential for the reclamation and redevelopment of abandoned lands. The soil samples were characterised by measuring microbial biomass C and N, key enzyme activities, and determining the community-level physiological profiles (CLPP) using Biolog EcoPlates. Soil texture, sampling time (June and October), and distance of sampling (0.1 m and 1 m from a tree) had significant effects on microbiological properties. Moreover, dehydrogenases and acid phosphatase activities as well as microbial biomass C and N decreased with distance from the trees, and were significantly higher in the October than in the June. The community-level physiological profiles (CLPP) and diversity indices showed a similar trend to other parameters of biological activity. The results showed that there were significant differences in the AWCD (average well-colour development) of all carbon sources among the Paulownia microbial communities (p < 0.05). In summary, already after one year of tree planting, a statistically significant increase in microbial activity was found, regardless of soil texture, when evaluated by various methods. This proves the value of the Paulownia as fast-growing plant for recultivation and improvement of soil quality on abandoned land.

Unraveling the mystery of subsurface microorganisms in bioremediation

Microorganisms are the key players in biogeochemical processes in the shallow subsurface for bioremediation. Estimation of genetic diversity, microbial activity, and their metabolic functions are the most applicable methods to explore the biodegradation processes in the subsurface. Several techniques such as community-level physiological profiling, sequencing, metagenomics, enzyme assay, and culture-based methods are used to investigate the metabolic potential, functional diversity, and genetic diversity of inherent microbial communities. These studies help to understand the metabolic pathways and biodegradation patterns in the subsurface, however, the interspecies microbial interactions and their transport mechanism in the porous media toward bioremediation of subsurface pollutants are still not well understood. Despite the advanced characterization methods for microbes, multiple crucial knowledge gaps of the dynamic subsurface microbial community remain unraveled. A detailed understanding of subsurface microbial interactions, mineral-metal-microbial correlation, transport mechanism, and degradation pathways will help in the optimization and design of in-situ bioremediation in the future. There is a need for detail-oriented exploration of these fundamental microbial processes to gain a greater understanding of microbial dynamics to facilitate the advanced bioremediation processes sustainably.