Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies

Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.

Evaluating the low-rank coal degradation efficiency bioaugmented with activated sludge

Microbial bioaugmentation of coal is considered as a viable and ecologically sustainable approach for the utilization of low-rank coals (LRC). The search for novel techniques to derive high-value products from LRC is currently of great importance. In response to this demand, endeavors have been undertaken to develop microbially based coal solubilization and degradation techniques. The impact of supplementing activated sludge (AS) as a microbial augmentation to enhance LRC biodegradation was investigated in this study. The LRC and their biodegradation products were characterized using the following methods: excitation-emission Matrices detected fluorophores at specific wavelength positions (O, E, and K peaks), revealing the presence of organic complexes with humic properties. FTIR indicated the increased amount of carboxyl groups in the bioaugmented coals, likely due to aerobic oxidation of peripheral non-aromatic structural components of coal. The bacterial communities of LRC samples are primarily composed of Actinobacteria (up to 36.2%) and Proteobacteria (up to 25.8%), whereas the Firmicutes (63.04%) was the most abundant phylum for AS. The community-level physiological profile analysis showed that the microbial community AS had high metabolic activity of compared to those of coal. Overall, the results demonstrated successful stimulation of LRC transformation through supplementation of exogenous microflora in the form of AS.

Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality

Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.

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

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

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.

Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.

Applying Red Mud in Cadmium Contamination Remediation: A Scoping Review

Red mud is an industrial solid waste rarely utilized and often disposed of in landfills, resulting in resource waste and environmental pollution. However, due to its high pH and abundance of iron and aluminum oxides and hydroxides, red mud has excellent adsorption properties which can effectively remove heavy metals through ion exchange, adsorption, and precipitation. Therefore, red mud is a valuable resource rather than a waste byproduct. In recent years, red mud has been increasingly studied for its potential in wastewater treatment and soil improvement. Red mud can effectively reduce the migration and impact of heavy metals in soils and water bodies. This paper reviews the research results from using red mud to mitigate cadmium pollution in water bodies and soils, discusses the environmental risks of red mud, and proposes key research directions for the future management of red mud in cadmium-contaminated environments.

Co-influence of biochar-supported effective microorganisms and seasonal changes on dissolved organic matter and microbial activity in eutrophic lake

DOM (dissolved organic matter) play a crucial role in lakes' geochemical and carbon cycles. Eutrophication evolution would influence nutrient status of waters and investigating the DOM variation helps a better understanding of bioremediation on environmental behavior of DOM in eutrophic lakes. In our study, the contents, compositions and characteristics of systematic DOM&SOM (sediment organic matter) were greatly influenced by seasonal changes. But the effective bioremediations obviously reduced the DOM concentration and thus mitigated the eutrophication outbreak risks in water bodies due to the increased MBC (microbial biomass carbon), microbial activity and metabolism. In early summer, the overall DOM in each treatment were readily low levels and derived from both autochthonous and exogenous origins, dominated by fulvic acid-like. In midsummer, the DOM contents and characteristics in each treatment increased significantly as phytoplankton activity improved, and the majority of DOM were humic acid-like and mainly of biological origin. The greatest differences of enzymes, MBC, microbial metabolism and DOM&SOM removal among different treatments were observed in summer months. In autumn, the systematic DOM&SOM slightly reduced due to the deceased microbial activity, in which the microbial humic acids were main component and derived from endogenous sources. Additionally, the gradually decreased SOM with cultivated time in each treatment was a result of microbiological conversion of SOM into DOM. For various treatments, BE, BE.A, BE.C and BE.E increased the MBC, enzymatic and microbial activities due to the application of biochar-supported EMs. Among these, BE and BE.A, especially BE.A with oxygen supplement, achieved the most desirable effect on reducing systematic DOM&SOM levels and increasing enzymatic and microbial activities. The group of EM also reduced the levels of DOM&SOM as improved degradation of EMs for DOM. However, BC, BE.C and BE.E finally did not achieved the desirable effect on reducing DOM&SOM due to the suppression of microbial activities, respectively, from high dose of biochar, weakening of dominant species and additional introduction of EMs in low liveness.

A new strategy of using periphyton to simultaneously promote remediation of PAHs-contaminated soil and production of safer crops

Contaminated farmland leads to serious problems for human health through biomagnification in the soil-crop-human chain. In this paper, we have established a new soil remediation strategy using periphyton for the production of safer rice. Four representative polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (Phe), pyrene (Pyr), benzo[b]fluoranthene (BbF), and benzo[a]pyrene (BaP), were chosen to generate artificially contaminated soil. Pot experiments demonstrated that in comparison with rice cultivation in polluted soil with ΣPAHs (50 mg kg-1) but without periphyton, adding periphyton decreased ΣPAHs contents in both rice roots and shoots by 98.98% and 99.76%, respectively, and soil ΣPAHs removal reached 94.19%. Subsequently, risk assessment of ΣPAHs based on toxic equivalent concentration (TEQ), pollution load index (PLI), hazard index (HI), toxic unit for PAHs mixture (TUm), and incremental lifetime cancer risk (ILCR) indicated that periphyton lowered the ecological and carcinogenicity risks of PAHs. Besides, the role of periphyton in enhancing the rice productivity was revealed. The results indicated that periphyton alleviated the oxidative stress of PAHs on rice by reducing malondialdehyde (MDA) content and increasing total antioxidant capacity (T-AOC). Periphyton reduced the toxic stress of PAHs on the soil by promoting soil carbon cycling and metabolic activities as well. Periphyton also improved the soil's physicochemical properties, such as the percentage of soil aggregate, the contents of humic substances (HSs) and nutrients, which increased rice biomass. These findings confirmed that periphyton could improve rice productivity by enhancing soil quality and health. This study provides a new eco-friendly strategy for soil remediation and simultaneously enables the production of safe crops on contaminated land.

The Vertical Metabolic Activity and Community Structure of Prokaryotes along Different Water Depths in the Kermadec and Diamantina Trenches

Prokaryotes play a key role in particulate organic matter's decomposition and remineralization processes in the vertical scale of seawater, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity of the vertical distribution in the trenches. The composition and distribution of prokaryotes in the water columns and benthic boundary layers of the Kermadec Trench and the Diamantina Trench were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog EcoplateTM microplates culture to analyze the microbial metabolic activity. Microbial communities in both trenches were dominated by Nitrososphaera and Halobacteria in archaea, and by Alphaproteobacteria and Gammaproteobacteria in bacteria, and the microbial community structure was significantly different between the water column and the benthic boundary layer. At the surface water, amino acids and polymers were used preferentially; at the benthic boundary layers, amino acids and amines were used preferentially. Cooperative relationships among different microbial groups and their carbon utilization capabilities could help to make better use of various carbon sources along the water depths, reflected by the predominantly positive relationships based on the co-occurrence network analysis. In addition, the distinct microbial metabolic activity detected at 800 m, which was the lower boundary of the twilight zone, had the lowest salinity and might have had higher proportions of refractory carbon sources than the shallower water depths and benthic boundary layers. This study reflected the initial preference of the carbon source by the natural microbes in the vertical scale of different trenches and should be complemented with stable isotopic tracing experiments in future studies to enhance the understanding of the complex carbon utilization pathways along the vertical scale by prokaryotes among different trenches.

Analysis on metabolic functions of rhizosphere microbial communities of Pinus massoniana provenances with different carbon storage by Biolog Eco microplates

Introduction

Rhizosphere microorganisms are influenced by vegetation. Meanwhile, they respond to vegetation through their own changes, developing an interactive feedback system between microorganisms and vegetation. However, it is still unclear whether the functional diversity of rhizosphere soil microorganisms varies with different carbon storage levels and what factors affect the functional diversity of rhizosphere soil microorganisms.

Methods

In this study, the Biolog-Eco microplate technique was used to analyze the metabolic diversity of carbon source of rhizosphere soil microorganisms from 6 Pinus massoniana provenances with three levels of high, medium and low carbon storage.

Results

The results showed that the average well color development(AWCD) value of rhizosphere microorganisms was significantly positive correlated with carbon storage level of Pinus massoniana (p < 0.05). The AWCD value, Simpson and Shannon diversity of high carbon sequestrance provenances were 1.40 (144h incubation) 0.96 and 3.24, respectively, which were significantly higher (p < 0.05) than those of other P. massoniana provenances. The rhizosphere microbial AWCD, Shannon and Simpson diversity of the 6 provenances showed the same variation trend (SM>AY>QJ>SX>HF>SW). Similarly, microbial biomass carbon (MBC) content was positively correlated with carbon storage level, and there were significant differences among high, medium and low carbon storage provenances. The PCA results showed that the differences in the carbon source metabolism of rhizosphere microorganisms were mainly reflected in the utilization of amino acids, carboxylic acids and carbohydrates. Pearson correlation analysis showed that soil organic carbon (SOC), total nitrogen (TN) and pH were significantly correlated with rhizosphere AWCD (p < 0.05).

Conclusion

Soil properties are important factors affecting rhizosphere microbial carbon source metabolism. The study confirmed that the microorganisms of high carbon storage provenances had relatively high carbon metabolic activity. Among them, the carbon metabolic activity of rhizosphere microorganisms of SM provenance was the highest, which was the preferred provenances in effective ecological service function.

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.

The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice (Oryza sativa L.) Production

Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability.

The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids

Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.

Effects of rainfall amount and frequencies on soil net nitrogen mineralization in Gahai wet meadow in the Qinghai-Tibetan Plateau

Global climate change has led to a significant increase in the frequency of extreme rainfall events in the Qinghai-Tibetan Plateau (QTP), thus potentially increasing the annual rainfall amounts and, consequently, affecting the net soil nitrogen (N) mineralization process. However, few studies on the responses of the soil net N mineralization rates to the increases in rainfall amounts and frequencies in alpine wet meadows have been carried out. Therefore, the present study aims to assess the effects of rainfall frequency and amount changes on the N fixation capacity of wet meadow soils by varying the rainfall frequency and amount in the Gahai wet meadow in the northeastern margin of the QTP during the plant-growing season in 2019. The treatment scenarios consisted of ambient rain (CK) and supplementary irrigation at a rate of 25 mm, with different irrigation frequencies, namely weekly (DF1), biweekly (DF2), every three weeks (DF3), and every four weeks (DF4). According to the obtained results, the increased rainfall frequency and amount decreased the soil mineral N stock and increased the aboveground vegetation biomass (AB) amounts and soil water contents in the wet meadows of the QTP. Ammonium (NH4+-N) and nitrate N (NO3--N) contributed similarly to the mineral N contents. However, the ammonification process played a major role in the soil mineralization process. The effects of increasing rainfall amount and frequency on N mineralization showed seasonal variations. The N mineralization rate showed a single-peaked curve with increasing soil temperature during the rapid vegetation growth phase, reaching the highest value in August. In addition, the N mineralization rates showed significant positive correlations with soil temperatures and NH4+-N contents and a significant negative correlation with AB (P < 0.05). The results of this study demonstrated the key role of low extreme rainfall event frequencies in increasing the net soil N mineralization rates in the vegetation growing season, which is detrimental to soil N accumulation, thereby affecting the effectiveness of soil N contents.

Microbial metabolic activity in Amazon floodplain forest and agricultural soils

Microorganisms play an essential role in ecosystem functions. An increasingly used method for conducting functional analyses of a soil microbial community is based on the physiological profile at the community level. This method allows the metabolic capacity of microorganisms to be assessed based on patterns of carbon consumption and derived indices. In the present study, the functional diversity of microbial communities was assessed in soils from seasonally flooded-forest (FOR) and -traditional farming systems (TFS) in Amazonian floodplains flooded with black, clear, and white water. The soils of the Amazon floodplains showed differences in the metabolic activity of their microbial communities, with a general trend in activity level of clear water floodplain > black water floodplain > white water floodplain. The redundancy analysis (RDA) indicated that soil moisture (flood pulse) was the most important environmental parameter in determining the metabolic activity of the soil microbial communities in the black, clear, and white floodplains. In addition, the variance partitioning analysis (VPA) indicated that the microbial metabolic activity of the soil was more influenced by water type (41.72%) than by seasonality (19.55%) and land use type (15.28%). The soil microbiota of the white water floodplain was different from that of the clear water and black water floodplains in terms of metabolic richness, as the white water floodplain was mainly influenced by the low substrate use during the non-flooded period. Taken together, the results show the importance of considering soils under the influence of flood pulses, water types, and land use as environmental factors when recognizing functional diversity and ecosystem functioning in Amazonian floodplains.

Behind the plant-bacteria system: The role of zucchini and its secondary metabolite in shaping functional microbial diversity in MCPA-contaminated soil

MCPA (2-methyl-4-chlorophenoxyacetic acid) contamination is an emerging problem, especially in water reservoirs. The early removal of MCPA residues from soil can prevent its spread to untreated areas. It has been found that the growth of cucurbits and the addition of selected plant secondary metabolites (PSMs) can stimulate MCPA removal from soil. However, the effect of these treatments on soil microbial activity remains poorly studied. Hence, the aim of this research was to evaluate the influence of zucchini (C. pepo cv Atena Polka) and its characteristic PSM: syringic acid (SA) on the functional diversity of soil microorganisms in MCPA-contaminated soil using Biolog® EcoPlates™. It also examines soil physicochemical properties and the growth parameters of zucchini. Microbial activity was enhanced by both zucchini cultivation and SA. All unplanted variants showed significantly lower microbial activity (average well color development, AWCD, ranging from 0.35 to 0.51) than the planted ones (AWCD ranging from 0.77 to 1.16). SA also stimulated microbial activity in the soil: a positive effect was observed from the beginning of the experiment in the unplanted variants, but over a longer time span in the planted variants. SA ameliorated the toxic effect of MCPA on the studied plants, especially in terms of photosynthetic pigment production: the MCPA+SA group demonstrated significantly increased chlorophyll content (401 ± 4.83 μg/g), compared to the MCPA group without SA (338 ± 50.1 μg/g). Our findings demonstrated that zucchini and the amendment of soils with SA, the characteristic PSM of cucurbits, can shape functional diversity in MCPA-contaminated soil. The changes of soil properties caused by the application of both compounds can trigger changes in functional diversity. Hence, both SA and MCPA exert indirect and direct effects on soil microbial activity.

New insights into the effects of antibiotics and copper on microbial community diversity and carbon source utilization

Residual antibiotics (ABs) and heavy metals (HMs) are continuously released from soil, reflecting their intensive use and contamination of water and soil, posing an environmental problem of great concern. Relatively few studies exist of the functional diversity of soil microorganisms under the combined action of ABs and HMs. To address this deficiency, BIOLOG ECO microplates and the Integrated Biological Responses version 2 (IBRv2) method were used to comprehensively explore the effects of single and combined actions of copper (Cu) and enrofloxacin (ENR), oxytetracycline (OTC), and sulfadimidine (SM2) on the soil microbial community. The results showed that the high concentration (0.80 mmol/kg) compound group had a significant effect on average well color development (AWCD) and OTC showed a dose-response relationship. The results of IBRv2 analysis showed that the single treatment group of ENR or SM2 had a significant effect on soil microbial communities, and the IBRv2 of E1 was 5.432. Microbes under ENR, SM2, and Cu stress had more types of available carbon sources, and all treatment groups were significantly more enriched with microorganisms having D-mannitol and L-asparagine as carbon sources. This study confirms that the combined effects of ABs and HMs can inhibit or promote the function of soil microbial communities. In addition, this paper will provide new insights into IBRv2 as an effective method to evaluate the impacts of contaminants on soil health.

Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

Metagenomic study of carbon metabolism in black soil microbial communities under lead-lanthanum stress

Pollution of soil environments with heavy metals (HMs) and rare earth elements (REEs) cannot be ignored. We aimed to determine the effects of lead combined with lanthanum (Pb-La) on microbial community structure, carbon metabolism, and differences in carbon source utilization in black soils using EcoPlates™ and a macrogenomic approach. We found that Pb and La contents and the microbial community structure together influence and shape the response of soil carbon metabolism to Pb-La. Compared with controls, microorganisms under pollution stress preferentially use phenolic and carboxylic acids as growth carbon sources. Under Pb-La stress, the relative abundance of Proteobacteria significantly increased, thereby selectively displacing heavy metal-sensitive phyla, such as Chloroflexi, Acidobacteria, and Thaumarchaeota. Altered functional potential of the microbial carbon cycle manifested as differences in carbon metabolism, methane metabolism, and carbon fixation pathways. Furthermore, an appropriate concentration of La can reduce the environmental toxicity of Pb, whereas a high concentration of La has synergistic toxicity with Pb. These findings have important implications for understanding the impact of HM-REE contamination in microbial communities and the functions associated with carbon metabolism in black soils.

Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes

This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.

Environmental risk of microplastics after field aging: Reduced rice yield without mitigating yield-scale ammonia volatilization from paddy soils

Microplastics (MPs, <5 mm) are enriched in paddy ecosystems as emerging environmental pollutants. Biochar (BC) is a controversial recalcitrant carbon product that poses potential environmental risks. The presence of these two exogenous organic substances has been demonstrated to have impacts on soil nitrogen cycling and crop production. However, the after-effects of MPs and BC on soil ammonia (NH₃) volatilization and rice yield after field aging remain unexplored. In this study, two common MPs, including polyethylene (PE) and polyacrylonitrile (PAN), and BC were selected for rice growing season observations to study the impacts on soil NH₃ volatilization and rice yield after field aging. The results showed that the reduction of cumulative soil NH₃ losses by MPs was around 45% after one-year field aging, which was within the range of 40-57% in the previous rice season. Abatement of NH₃ volatilization by MPs mainly occurred in basal fertilization and was related to floodwater pH. Besides, the reduction rate of NH₃ volatilization by BC and MPs + BC was enhanced after field aging (63% and 50-57%) compared to that in the previous rice season (5% and 11-19%), with the abatement process occurring in the first supplementary fertilization. There was a significant positive correlation between cumulative NH₃ volatilization and soil urease activity. Notably, field aging removed the positive effect of MPs and MPs + BC in reducing yield-scale NH₃ losses in the previous rice season (∼62%). Furthermore, despite BC affecting rice yield insignificantly after field aging, the presence of MPs led to a significant 17-19% reduction in rice yield. Our findings reveal that differences in the after-effects of BC and MPs in field aging emerge, where the negative impacts of MPs on soil NH₃ abatement and crop yield are progressively becoming apparent and should be taken into serious consideration.

Coriander (Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning

The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

Metabolic activity and community structure of prokaryotes associated with particles in the twilight zone of the South China Sea

The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs) in the larger particles along the water depths, might be due to the fast sinking and major contribution of carbon flux of the larger particles from the euphotic layer. In addition to polymers as the major carbon source, carbohydrates and amino acids were preferentially used by microbial community at the upper and lower boundary, respectively. This could potentially be attributed to the metabolic capabilities of attached microbial groups in different particles, and reflected the initial preference of the carbon source by the natural microbes in the twilight zone as well. The microbial structure and carbon metabolic profiles could be complemented with metatranscriptomic analysis in future studies to augment the understanding of the complex carbon cycling pathways in the twilight zone.

Summary of research progress on separation and extraction of valuable metals from Bayer red mud

Bayer red mud is a strong alkaline solid waste discharged during alumina production. Due to large emissions and strong alkalinity, red mud is now mostly dammed or buried, which not only occupies huge land but also contaminates the surrounding ecosystem, causing the risk of collapse and landslide. In addition to its overall utilization in building materials, agriculture, the environment, and the chemical industry, red mud also contains valuable metals such as sodium, aluminum, iron, titanium, and scandium and is considered to be an important secondary resource. In this paper, the physicochemical properties and hazards of red mud are first introduced, and then, the overall utilization of red mud is summarized. Then, the latest research progress on the separation and extraction of valuable metals from red mud is reviewed in detail and a new comprehensive utilization method is recommended and evaluated. This paper also provides suggestions for the future development direction of the comprehensive utilization technology of red mud.

Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition

Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.

A review of comprehensive utilization of red mud

Red mud (RM) is a solid waste generated during the process of alumina production. RM has already posed a serious environmental threat with the development of the alumina refining industry. The comprehensive utilization of RM has attracted much attention due to its large-scale generation and harmful nature. This paper introduces the characteristics and state of RM and summarizes the relevant research on the comprehensive utilization of RM. The results show that comprehensive utilization of RM is mainly focused on the preparation of building materials, the extraction of valuable metals, catalyst synthesis and environmental protection. Besides, the article discusses the existing problems while utilizing RM. Prospects and suggestions for different utilization methods of RM are proposed.

Biorecovery of olive mill wastewater sludge from evaporation ponds

Olive mill wastewater (OMW) resulting from the olive oil extraction process is usually disposed of in evaporation ponds where it concentrates generating a sludge that pollutes the ponds nearby area. In this study, four bio-treatments were applied for the in-situ bioremediation and valorization of OMW sludge: Landfarming, phytoremediation, composting and vermicomposting. In all cases, the OMW sludge was added with organic residues (mushroom compost, rabbit manure, and chicken manure). The bio-treatments were carried out in duplicate, inoculated and non-inoculated, to determine the effect of a specialized fungal consortium (Aspergillus ochraceus H2 and Scedosporium apiospermum H16) on the efficacy of the bio-treatments. The evaluation of chemical parameters, toxicity, and functional microbial biodiversity revealed that the four techniques depleted the toxicity and favored the stimulation of functional microbiota. Landfarming and phytoremediation allowed the decontamination and improvement of soils. Composting and vermicomposting also offered high-quality products of agronomic interest. Inoculation improved the bioremediation effectiveness. Biological treatments are effective for the safe recovery of contaminated OMW sludge into high-quality services and products.

Advanced remediation of pyrene contaminated soil by double dielectric barrier discharge (DDBD) plasma and subsequent composting process

Due to increasing industrialization, soils are increasingly contaminated by polycyclic aromatics such as pyrene and need gentle treatment to keep the soil functioning. This study applied a double dielectric barrier discharge (DDBD) plasma reactor and composting reactor to remediate pyrene-contaminated soil. The effect of peak-to-peak applied voltages on the remediation efficiency of pyrene was investigated. The experimental results illustrate that pyrene remediation efficiency increased from 43% to 85% when the peak-to-peak applied voltage was increased from 28.0 to 35.8 kV. When using the combined method of DDBD and composting, 90-99% of pyrene could be removed, while a reduction of 76.5% was achieved using only composting, indicating the superiority of the combined system. Moreover, the authors could demonstrate that DDBD plasma treatment improves humification in the post-composting process as humic acid (HA) concentrations increased to 7.7 mg/g with an applied voltage of 35.8 kV; when composting was used as the sole treatment method, only 3.4 mg/g HA were produced. The microbial activity in the DDBD plasma-treated soil peaked on the 5th day and had a 2nd rise afterwards. The authors demonstrate that the combined technology of DDBD plasma and composting is a promising method for soil remediation with persistent organic pollutants. This treatment approach improves pollutant degradation efficiency and facilitates further humification, potentially restoring the function of contaminated soil. This approach could be considered a cost-effective and green strategy for soil remediation with persistent organic pollutants.

The evaluation of Hudson River sediment as a growth substrate - Microbial activity, PCB-degradation potential and risk assessment

The potential use of growth substrates prepared with an admixture of 10% to 75% Hudson River sediments was evaluated by analysis of changes in microbial activity (measured using Biolog Ecoplates) and molecular markers (presence of degradative tceA1 and bphA genes) as well as potential risks toward humans and the environment (health and environmental risk quotients). The highest microbial activity was found in growth substrate with 25% Hudson River sediments compared to unamended control soil. Significant differences were observed between samples amended with lower (0-10%) and higher (25-75%) proportion of sediment. Microbial activity increased with the proportion of sediment amendment (≥25% sediment); however, this increase in microbial activity was not affected by increasing pollutant concentrations (PCBs, Pb, Cr Ni and Zn) nor decreasing TOC content. The growth substrate amended with Hudson River sediments demonstrated a potential for PCB degradation, as evidenced by the presence of tceA1 and bphA genes responsible, respectively, for reductive dehalogenation and oxidation of a range of aromatic organic compounds including PCBs. An assessment of risk quotients showed that the growth substrates containing lower doses of Hudson River sediments (10-50%) meet the international requirements for use in agriculture/horticulture for the production of non-food crops. Nevertheless, due to the elevated content of some toxic metals and PCBs, the growth substrate prepared with the highest proportion of sediments (75%) was not suitable for agricultural/horticultural use.

Bauxite residue valorization - Soil conditioners production through composting with palm oil mill residual biomass

Bauxite residue (BR) is a by-product of Bayer process, which is applied for alumina production. Due to its inherent alkalinity and sodicity, the use of BR is globally limited to 23% of the 150 million tons (Mt) produced annually. Maximizing alternative and large-scale uses of BR is a game changer to promote the sustainability of the aluminum production chain. As a strategy for BR valorization, a soil conditioner composed of BR and palm oil residual biomass was proposed. Here we evaluate the BR (25%, 50% and 75%) batch composting with raw palm oil mill waste (POMW) and palm oil compost (POC). The pH, EC, total N and organic carbon, C:N ratio, water holding capacity (WHC), cation exchange capacity (CEC), granulometry and elemental composition were determined after 90 days of composting. Changes in temperature, pH and EC curves were observed during composting of soil conditioners for 90 days. Composting reduced the alkalinity and sodicity of BR, increasing CEC, moisture, organic carbon and total nitrogen. The formulation containing 25% of BR and 75% of POC showed WHC ≥ 60% and CEC ≥ 200 mmol_c·kg^-1, meeting the Brazilian legislation for production and commercialization of soil conditioners. This strategy could potentially consume 7.6% of all BR produced annually in the largest Brazilian alumina refinery. Concentrations of potentially toxic elements were far below the allowable levels in all formulations. Major and minor plant nutrients were present and the composting aggregated small particles in BR. Composting of BR is a new alternative for the valorization of mining tailings, allowing the development of an environmentally friendly and zero-waste product, which can be applied on a large scale in agriculture to improve soil fertility.

Rhizobacteria communities reshaped by red mud based passivators is vital for reducing soil Cd accumulation in edible amaranth

Red mud (RM) was constantly reported to immobilize soil cadmium (Cd) and reduce Cd uptake by crops, but few studies investigated whether and how RM influenced rhizobacteria communities, which was a vital factor determining Cd bioavailability and plant growth. To address this concern, high-throughput sequencing and bioinformatics were used to analyze microbiological mechanisms underlying RM application reducing Cd accumulation in edible amaranth. Based on multiple statistical models (Detrended correspondence analysis, Bray-Curtis, weighted UniFrac, and Phylogenetic tree), this study found that RM reduced Cd content in plants not only through increasing rhizosphere soil pH, but by reshaping rhizobacteria communities. Special taxa (Alphaproteobacteria, Gammaproteobacteria, Actinobacteriota, and Gemmatimonadota) associated with growth promotion, anti-disease ability, and Cd resistance of plants preferentially colonized in the rhizosphere. Moreover, RM distinctly facilitated soil microbes' proliferation and microbial biofilm formation by up-regulating intracellular organic metabolism pathways and down-regulating cell motility metabolic pathways, and these microbial metabolites/microbial biofilm (e.g., organic acid, carbohydrates, proteins, S^2-, and PO₄^3-) and microbial cells immobilized rhizosphere soil Cd via the biosorption and chemical chelation. This study revealed an important role of reshaped rhizobacteria communities acting in reducing Cd content in plants after RM application.

Enhanced production of polyhydroxyalkanoates in Pseudomonas putida KT2440 by a combination of genome streamlining and promoter engineering

Polyhydroxyalkanoates (PHAs), a class of bioplastics produced by a variety of microorganisms, have become the ideal alternatives for oil-derived plastics due to their superior physicochemical and material characteristics. Pseudomonas putida KT2440 can produce medium-chain-length PHA (mcl-PHA) from various substrates. In this study, a novel strategy of the large-scale deletion of genomic islands (GIs) coupling with promoter engineering was developed in P. putida KT2440 for constructing the minimal genome cell factories (MGF) capable of efficiently producing mcl-PHA. Firstly, P. putida KTU-U13, a 13 GIs- and upp-deleted mutant derived from the parental strain P. putida KT2440, was used as a starting strain for further deletion of GIs to generate a series of genome-reduced strains. Subsequently, the two minimal genome strains KTU-U24 and KTU-U27, which had a 7.19% and 8.35% reduction relative to the genome size of KT2440 and were advantageous over the strain KTU (KT2440∆upp) and KTU-U13 in several physiological traits such as the maximum specific growth rate, plasmid transformation efficiency, heterologous protein expression capacity and PHA production capacity, were selected as the chassis cells for PHA metabolic engineering. To prevent the formation of the by-product gluconic acid, the glucose dehydrogenase gene was deleted in KTU-U24 and KTU-U27, resulting in KTU-U24∆gcd and KTU-U27∆gcd. To enhance the transcriptional level of PHA synthase genes (phaC) and the supply of the precursor acetyl-CoA, a strong endogenous promoter P46 was inserted into upstream of the phaC operon and pyruvate dehydrogenase gene in the genome of KTU-U24∆gcd and KTU-U27∆gcd, to generate KTU-U24∆gcd-P46CA and KTU-U27∆gcd-P46CA, with the PHA yield of 50.5 wt% and 53.8 wt% (weight percent of PHA in cell dry weight). Finally, KTU-U27∆gcd-P46CA, the most minimal KT2440 chassis currently available, was able to accumulate the PHA to 55.82 wt% in a 5-l fermentor, which is the highest PHA yield obtained with P. putida KT2440 so far. This study suggests that genome streamlining in combination with promoter engineering may be a feasible strategy for the development of the MGF for the efficient production of high value products. Moreover, further streamlining of the P. putida KT2440 genome has great potential to create the optimal chassis for synthetic biology applications.

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.

Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.

Solidification performances of contaminants by red mud-based cementitious paste filling material and leaching behavior of contaminants in different pH and redox potential environments

Considering the urgent need for disposal of red mud and the comprehensive treatment of coal mined-out areas, this paper presented red mud-based cementitious paste filling material (RMFM) to achieve the purpose of green filling treatment. However, the solidification performance of alkaline RMFM for contaminants can be affected when in contact with acid goaf water in practice, which may in turn cause secondary pollution to the surroundings. The leaching tests of RMFM under different pH and redox potential (E_h) conditions were designed to investigate the effects of environmental elements on the solidification performance of RMFM, and primarily investigated the treatment effectiveness of RMFM on goaf water. The test results manifest that the acidic and oxidizing environments could damage the hydration products generated by alkali and sulfate activation, thus affecting the solidification performance, while the alkaline and reducing environments could effectively prevent the release of the contaminants by enhancing the degree of alkali activation and inhibiting oxidation acid forming process. In the possible exposure environment, RMFM could effectively stabilize its own pollutants without secondary pollution. In addition, the powder RMFM samples had significant removal effects on heavy metals, the values of Cu, Pb, and As removal efficiency all reached more than 96.15%.

Increasing acid rain frequency promotes the microbial community dissimilarities of forest soil rather than agricultural soil in southern China

Soil microbial community drives the terrestrial carbon (C) cycling by C sources metabolism (i.e., organic C decomposition), however, the microbial response to changing acid rain frequency remains less studied, thus hampering global warming projection. Here, we manipulated a simulated experiment to decipher the impact of acid rain frequency (0, 30%, and 100%) on microbial community and C sources metabolism in the agricultural and forest soils of southern China, based on the phospholipid fatty acids (PLFAs) analysis and BIOLOG method, respectively. We found that changing acid rain frequency did not affect the microbial biomass and community structure of agricultural soil during the whole experiment period, while the 30% and 100% acid rain frequencies significantly decreased the microbial biomass, and altered the microbial community structure of forest soil at the early stage. However, changing acid rain frequency did not influence the microbial C sources metabolism in the agricultural soil, but 30% acid rain frequency significantly reduced the microbial utilization of carboxylic acids in the forest soil. Moreover, increasing acid rain frequency promoted the microbial community dissimilarities of forest soil. The microbial community structure and C sources utilization of agricultural soil were significantly related to soil available phosphorus content, while that of forest soil correlated with the soil available potassium content and temperature. Changes in soil environmental condition, soil acidification parameters and soil nutrients explained most of the variance of microbial community and C sources utilization (81% and 57%, respectively) in the forest soil, whereas great uncertainties of microbial community and C sources utilization existed in the agricultural soil with the explanatory proportion being 20% and 10%, respectively. Our findings suggest that the microbial community of forest soil is more sensitive to changing acid rain frequency than that of agricultural soil in a short term. These results support the prediction of microbes-driven C cycling dynamics in specific soil ecosystems in the context of changing acid rain frequency.

Influence of lead on the activity of soil microorganisms in two Beskidy landscape parks

The aim of the study was to assess the potential impact of lead on soil metabolism in two landscape parks localized in the Beskid Śląski and Beskid Żywiecki mountains which were affected, among others, by air pollution from the Upper Silesian Industrial Region, the largest industrial zone in Poland. The study was carried out in six locations with different lead levels in the soil environment. Each plot was equipped with four pairs of vacuum ceramic lysimeters to assess the mobility of Pb in the soil. The metabolic activity was assessed by measuring: soil enzyme activity, soil respiration and by studying community-level physiological profiling (CLPP) using Biolog EcoPlates technique. The soil to the examination was collected near the stands with the lysimeters from two soil horizons (A and B layer). The analyses carried out showed that the factors that had the greatest influence on lead mobility were the organic carbon content and the soil pH. The elevated lead level in the topsoil (layer A) could affect the functional biodiversity of soil microorganisms, but low soil pH was a more likely limiting factor. In the subsoil (layer B), lower lead content was found and its probable effect on soil microbial activity was small. In summary, it can be concluded that the assessment of the influence of heavy metals on soil metabolism is not easy, and the Biolog system has proven to be a sensitive tool for assessing the potential impact of heavy metals on the soil environment.

Effect of Commercial Amendments on Immobilization of Arsenic, Copper, and Zinc in Contaminated Soil: Comprehensive Assessing to Plant Uptake Combined with a Microbial Community Approach

Identifying the proper chemical and biological materials as soil amendments is a great concern because they replace soil properties and subsequently change the soil quality. Hence, this study was conducted to evaluate the effects of a diverse range of soil amendments including bentonite (B), talc (T), activated carbon (AC), and cornstarch (CS) in form of sole and composite on the immobilization and bioavailability of As, Cu, and Zn. The amendments were characterized by SEM, FT-IR, and XRF, and applied at 2% (w/w) in the experimental pots with an Asteraceae (i.e., lettuce) for 45 days to monitor plant growth parameters and soil microbial community. Soil pH from 6.1 ± 0.02 significantly increased in the amended soils with the maximum value found for TAC (7.4 ± 0.04). The results showed that soil amendments reduced easily in an exchangeable fractionation of As, Cu, and Zn with the maximum values found for BAC by 66.4%, AC by 84.2%, and T by 89.7% respectively. Adding B, T, AC, and their composites induced dry biomass of lettuce >40 wt.%, while CS and its composites did not affect the dry biomass of the plant. The average content of Cu and Zn in plant tissues decreased >45 wt.% in B, AC, and their composites amended soils; meanwhile, AC and its composites mitigated As uptake by >30 wt.% in lettuce. The results of Biolog Ecoplate showed that the amending soils improved the microbial community, especially for composites (e.g., TCS). The results demonstrated that adding composites amendments provided an efficient method for the immobilization of metals and metalloids, and also induced plant growth parameters and microbial community.

Evaluating the metabolic functional profiles of the microbial community and alfalfa (Medicago sativa) traits affected by the presence of carbon nanotubes and antimony in drained and waterlogged sediments

Antimony (Sb) is the ubiquitous re-emerging contaminant greatly accumulated in sediments which has been revealed risky to ecological environment. However, the impacts of Sb (III/V) on microbes and plants in sediments, under different water management with presence of engineering materials are poorly understood. This study conducted sequential incubation of sediments (flooding, draining and planting) with presence of multiwall carbon nanotubes (MWCNTs) and Sb to explore the influence on microbial functional diversity, Sb accumulation and alfalfa traits. Results showed that water management and planting led to greater impacts of sediment enzyme activities and microbial community metabolic function and bioavailable Sb fractions (defined as sum of acid-soluble fraction and reducible fraction, F1 + F2). Available fractions of Sb (V) showed higher correlation to microbial metabolism (r = 0.933) than that of Sb (III) (r = -0.480) in planting stage. MWCNTs with increasing concentrations (0.011%, w/w) positively correlated to microbial community metabolic function in planting stage whereas resulted in decreasing of Sb (III/V) concentrations in alfalfa, although 0.01% MWCNT led to increase of Sb (V) and decrease of Sb (V) by 50.97% and 32.68% respectively. This study provided information for investigating combined ecological impacts of heavy metal and engineering materials under different water managing sediments.

Effect of Municipal Solid Waste Compost on Antimony Mobility, Phytotoxicity and Bioavailability in Polluted Soils

The effect of a municipal solid waste compost (MSWC), added at 1 and 2% rates, on the mobility, phytotoxicity, and bioavailability of antimony (Sb) was investigated in two soils (SA: acidic soil; SB: alkaline soil), spiked with two Sb concentrations (100 and 1000 mg kg−1). The impact of MSWC on microbial activity and biochemical functioning within the Sb-polluted soils was also considered. MSWC addition reduced water-soluble Sb and favored an increase in residual Sb (e.g., by 1.45- and 1.14-fold in SA-100 and SA-1000 treated with 2% MSWC, respectively). Significant increases in dehydrogenase activity were recorded in both the amended soils, as well as a clear positive effect of MSWC on the metabolic activity and catabolic diversity of respective microbial communities. MSWC alleviated Sb phytotoxicity in triticale plants and decreased Sb uptake by roots. However, increased Sb translocation from roots to shoots was recorded in the amended soils, according to the compost rate. Overall, the results obtained indicated that MSWC, particularly at a 2% rate, can be used for the recovery of Sb-polluted soils. It also emerged that using MSWC in combination with triticale plants can be an option for the remediation of Sb-polluted soils, by means of assisted phytoextraction.

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Measurement and modeling of hormesis in soil bacteria and fungi under single and combined treatments of Cd and Pb

Heavy metals are considered major environmental pollutants. Soil microorganisms represent a predominant component of soils ecosystems, yet there is little information regarding hormetic responses of soil microorganisms to single and combined exposures to heavy metals. In the present study, to explore and predict the hormetic response of soil microorganisms, dose-response relationships of bacterial and fungal populations to single and combined treatments of cadmium (Cd) and lead (Pb) were evaluated. The results revealed hormetic responses of bacterial and fungal populations to both single and combined Cd and Pb treatments. The maximum stimulation (M_max; relative to control treatment with no metals) of bacterial and fungal populations was 40% at 2 mg Cd/kg and 60% at 160 mg Pb/kg. An enhanced M_max occurred in bacterial (50%) and fungal (75%) populations in the presence of the binary mixtures of 0.6 mg Cd/kg + 160 mg Pb/kg and 4.0 mg Cd/kg + 200 mg Pb/kg, suggesting positive additivity. This study showed that the hormetic effects of the mixtures were related to the independent effect of Cd and Pb, but they could not be predicted by the single effect of Cd or Pb. These new findings of the hormetic response of soil microorganisms to single treatments of Cd and Pb and their binary mixtures can facilitate the determination and minimization of ecological risks in heavy metal-polluted soils.

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

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

Red mud with other waste materials as artificial soil substitute and its effect on Sinapis alba

Despite efforts to utilise bauxite residue, the amount of red mud stored in reservoirs is increasing. This paper aims to evaluate the potential of red mud and other sludge waste types as a soil substitute by monitoring plant development. Pot experiments were carried out testing two types of mixtures: dredging sludge from Lake Balaton mixed with garden soil and the sewage sludge and soil blend. These were then treated with red mud (15 and 30% w/w). The plants were under-, while the roots were more developed in the sewage sludge mix than the dredging sludge blend and the control soil. In the sewage amendment, the phosphorous content increased while the calcium content was lower than in the other soil types and the optimum. The metals uptake of the plants was a factor of the red mud quantity. Lead, nickel, titanium and silicon had elevated concentrations parallel to higher red mud content, but only the nickel exceeded the threshold of the Hungarian legislation. Silicon and titanium were beneficial for plant growth, compensating for the potentially toxic effects of lead and nickel. Results suggest that the red mud in a mixture with either sewage sludge or dredging sludge can act as catalysts for the growth rate of test plants, allowing their utilisation as secondary raw materials.

Applications of red mud as an environmental remediation material: A review

Red mud is an alkaline by-product produced by alumina plants. The accumulation of red mud is becoming an increasingly serious problem with the growth of the aluminum industry. Various waste treatment methods utilizing red mud as an environmental remediation material have been developed. Red mud environmental remediation materials (RM-ERMs) are environmental remediation materials prepared by activating red mud, synergistically using red mud and other ingredients, or by extracting effective components from red mud. There are three general categories of use for RM-ERMs: for waste water purification, waste gas purification and soil remediation. As well as providing an opportunity to improve the environment through purification technologies, the highly alkaline red mud is consumed in the production of RM-ERMs. The use of RM-ERMs has been shown to be a promising strategy for the simultaneous treatment of various wastes. In this paper, the developregeneration characteristics of various red mud granularent status of RM-ERMs is described, the physical and chemical properties of red mud are introduced, and the active mechanism of RM-ERMs on target pollutants in waste water, waste gas and soil is summarized. Moreover, a discussion on the current existing problems of RM-ERMs provides important tips and suggestions for future research on RM-ERMs.

Acetobacter orientalis XJC-C with a high lignocellulosic biomass-degrading ability improves significantly composting efficiency of banana residues by increasing metabolic activity and functional diversity of bacterial community

Banana residues are an important energy resource after fruit harvesting. The optionally dumping and burning causes severely environmental problems. Traditional compost efficiency was limited by lignocellulosic composition of banana residues. Inoculation with cellulase-producing microbes provides an efficient strategy for improving degradation of lignocellulosic materials. In our study, a newly isolated cellulolytic bacterium Acetobacter orientalis XJC-C with a salt and high temperature resistance was identified from a marine soft coral. By contrast, the strain can biodegrade different lignocellulosic agricultural residues, especially banana straw. The highest cellulolytic and ligninolytic enzyme activities were detected during composting at 40 days. Compared with the negative and positive control groups, the lignin degradation rate reached 76.24% in the A. orientalis XJC-C group, increased by 47.08% and 21.85%, respectively. Moreover, the strain improved significantly the metabolic activity and functional diversity of bacterial community. Hence, A. orientalis XJC-C will be a promising candidate for degrading lignocellulosic agricultural residues.

Microbial communities of the olive mill wastewater sludge stored in evaporation ponds: The resource for sustainable bioremediation

Olive Mill Wastewater (OMW) is a polluting residue from the olive oil industry. It is usually stored in open-air unprotected evaporation ponds where their sediments accumulate. This study compares the characteristics of OMW sludges stored for long-time in evaporation ponds and assesses their impact on the underlying soil layer. Physicochemical parameters, toxicity bioassays, and full characterization of the microbial community were analyzed. The extension of the polluting effects was assessed by analysis of toxicity, microbial biomass carbon, and respiration. Geostatistics was used to predict their spatial distribution. Organic matter and polyphenol content besides toxicity levels determine variations between OMW sludges and have a high impact on the microbiota they contain. The microbial community was abundant, diverse, and functionally active. However, the biodegradability of the sludges was hindered by the toxicity levels. Toxicity and biomass carbon were higher on the surface of the ponds than in the soil layer revealing a reduced leach flow and depletion of contaminants. The natural microbiota might be biostimulated by means of applying sustainable and feasible biological treatments in order to favor the OMW sludges bioremediation. These results open up the possibility of solving the environmental concern caused by its storage in similar scenarios, which are common in olive oil-producing countries.