Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

Long-term microbial functional responses in soil contaminated with biofuel/fossil fuel blends triggered by different bioremediation treatments

The use of biofuel blends with fossil fuels is widespread globally, raising concerns over novel contamination types in environments impacted by these mixtures. This study investigates the microbial functional in soils contaminated by biofuel and fossil fuel blends and subjected to various bioremediation treatments. Using metagenomic analysis, it was compared hydrocarbon degradation functional profiles across areas polluted with ethanol/gasoline and biodiesel/diesel blends. Results indicate that long-term natural attenuation areas exhibited distinct functional profiles compared to actively bioremediated areas. However, same hydrocarbon degradation genes were enriched across all areas, highlighting functional redundancy despite taxonomic variation in hydrocarbon-degrading microbes. Finally, several of the keystone species found were hydrocarbon degraders, such as members of the families Clostridiaceae and Comamonadaceae, representing potential targets for biostimulation in future remediation efforts. This long-term, field-scale study uniquely focuses on the functional profiles of microbial communities, offering new insights into the bioremediation of complex biofuel/fossil fuel contaminants in situ.

Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils

This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Assembly patterns and key taxa of bacterial communities in the rhizosphere soil of moso bamboo (Phyllostachys pubescens) under different Cd and Pb pollution

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future.

Evaluating groundwater ecosystem dynamics in response to post in-situ remediation of mixed chlorinated volatile organic compounds (CVOCs): An insight into microbial community resilience, adaptability, and metabolic functionality for sustainable remediation and ecosystem restoration

The in-situ remediation of groundwater contaminated with mixed chlorinated volatile organic compounds (CVOCs) has become a significant global research interest. However, limited attention has been given in understanding the effects of these remediation efforts on the groundwater microbial communities, which are vital for maintaining ecosystem health through their involvement in biogeochemical cycles. Hence, this study aimed to provide valuable insights into the impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, employing high-throughput sequencing coupled with functional and physiological assays. The results showed that both bioremediation and chemical remediation methods adversely affected microbial diversity and abundance compared to non-polluted sites. Certain taxa such as Pseudomonas, Acinetobacter, and Vogesella were sensitive to these remediation methods, while Aquabacterium exhibited greater adaptability. Functional annotation unveiled the beneficial impact of bioremediation on the sulfur cycle and specific taxa such as Cellvibrio, Massilia, Algoriphagus, and Flavobacterium which showed a significant positive relationship with dark oxidation of sulfur compounds. In contrast, chemical remediation showed adverse impacts on the nitrogen cycle with a reduced abundance of nitrogen and nitrate respiration along with a reduced utilization of amines (nitrogen rich substrate). The findings of this study offer valuable insights into the potential impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, emphasizing the need for meticulous consideration to ensure the implementation of effective and sustainable remediation strategies that safeguard ecosystem health and function.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach

This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.

Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change

Petroleum biodegradation is of importance for the mitigation of secondary pollutants from soil chemical remediation. Describing the gene abundance change of the petroleum degradation emerged as an important practice for success. In this study, an indigenous consortium with targeting-enzyme was utilized to develop a degradative system that was later subjected to metagenomic analysis on the soil microbial community. Centering on ko00625 pathway, abundance change of dehydrogenase gene was firstly found increasing from groups D, DS to DC in turn, just in an opposite direction with that of oxygenase. In addition, gene abundance of responsive mechanism went rising with degradative process as well. This finding sufficiently promoted that equal attention should be paid to both degradative and responsive processes. Hydrogen donor system was innovatively built on the consortium-used soil to satisfy the demand of dehydrogenase gene tendency and to sustain further petroleum degradation. Anaerobic pine-needle soil was supplemented to this system, bi-functionally serving as dehydrogenase substrate with nutrients and hydrogen donor. In doing so, two successive degradations optimally achieved the total removal rate 75.6-78.7% for petroleum hydrocarbon. The conception on the gene abundance changes and its corresponding supplement helps industries of concern to develop geno-tag guided framework.

Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially heterogeneous habitats for microbial communities to develop. However, an understanding of the assembly processes and the functional profile of microbes at the aggregate level remain largely rudimentary, particularly for those active members in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and predictive functional profile of active bacteria in aggregates of different sizes using H₂¹⁸O-based DNA stable isotope probing (SIP) and 16S rRNA gene sequencing. Most of the bacterial reads were active with 91 % of total reads incorporating labelled water during the incubation. The active microbial community belonged mostly of Proteobacteria and Actinobacteria, with a relative abundance of 55.32 % and 28.12 %, respectively. Assembly processes of the active bacteria were more stochastic than total bacteria, while the assembly processes of total bacteria were more influenced by deterministic processes. Furthermore, many functional profiles such as environmental information processing increased in active bacteria (19.39 %) compared to total bacteria (11.22 %). After incubation, the diversity and relative abundance of active bacteria of certain phyla increased, such as Proteobacteria (50.70 % to 59.95 %), Gemmatimonadetes (2.63 % to 4.11 %), and Bacteroidetes (1.50 % to 2.84 %). In small macroaggregates (SMA: 0.25-2 mm), the active bacterial community and its assembly processes differed from that of other soil aggregates (MA: microaggregates, <0.25 mm; LMA: large macroaggregates, 2-4 mm). For functional profiles, the relative abundance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with incubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community of active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance of dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.

Polyethylene mulching film degrading bacteria within the plastisphere: Co-culture of plastic degrading strains screened by bacterial community succession

As an ecological niche close to the polymer, microorganisms in the plastisphere possess the advantage of degrading plastics. This study aims to investigate the bacterial community succession and obtain degrading bacteria in the plastisphere, as well as identify the most efficient degradation combination by co-culture of multiple strains. The findings demonstrate the alpha-diversity indices of the plastisphere bacterial community are significantly lower, and the community structure is regularly and significantly altered. With the time of culture, the plastisphere community composition alters regularly, and the hydrocarbon-degrading genera become the core members. Functional prediction of community reveals the potential for Xenobiotics Biodegradation and Metabolism of plastisphere, and the apparent variations detections of polyethylene mulching film (PMF) indicating the PMF degrading ability of plastisphere. Besides, three PMF-degrading bacterial strains, Rhodopseudomonas sp. P1 (P), Rhodanobacter sp. Rs (R) and Microbacterium sp. M1 (M), are screened for co-culture with PMF degrading strain Bacillus aryabhattai 5-3 (B). By considering bacterial growth, biofilm adhesion, and apparent degradation of different samples, RB (R. sp. Rs + B. aryabhattai 5-3) is ultimately selected as the best PMF degradation combination. This study provides a new possibility for plastisphere-related research from the perspective of mitigating plastic pollution on agricultural land.

Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation

Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.

Coupled effect of porous network and water content on the natural attenuation of diesel in unsaturated soils

The natural attenuation potential of a vadose zone against diesel is critical for optimizing remedial actions and determining groundwater vulnerability to contamination. Here, diesel attenuation in unsaturated soils was systematically examined to develop a qualitative relationship between physical soil properties and the natural attenuation capacity of a vadose zone against diesel. The uniformity coefficient (C_u) and water saturation (S_w, %) were considered as the proxies reflecting the degree of effects by porous network and water content in different soils, respectively. These, in turn, are related to the primary diesel attenuation mechanisms of volatilization and biodegradation. The volatilization of diesel was inversely proportional to C_u and S_w, which could be attributed to effective pore channels facilitating gas transport. Conversely, biodegradation was highly proportional to C_u under unsaturated conditions (S_w = 35-71%), owing to nutrients typically associated with fine soil particles. The microbial community in unsaturated soils was affected by S_w rather than C_u. The overall diesel attenuation including volatilization and biodegradation was optimized at S_w = 35% for all tested soils.

Does bacterial community succession within the polyethylene mulching film plastisphere drive biodegradation?

Agricultural fields are severely contaminated with polyethylene mulching film (PMF) and this plastic in the natural environment can be colonized by biofilm-forming microorganisms that differ from those in the surrounding environment. In this study, we investigated the succession of the soil microbial communities in the PMF plastisphere using an artificial micro-ecosystem as well as exploring the degradation of PMF by plastisphere communities. The results indicated a significant and gradual decrease in the alpha diversity of the bacterial communities in the plastisphere and surrounding liquid. The community compositions in the plastisphere and surrounding liquid differed significantly from that in agricultural soil. Phyla and genera with the capacity to degrade polyethylene and hydrocarbon were enriched in the plastisphere, and some of these microorganisms were core members of the plastisphere community. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis detected increases in metabolism pathways for PMF plastisphere Xenobiotics Biodegradation and Metabolism, thereby suggesting the possibility of polyethylene degradation in the plastisphere. Observations by scanning electron microscopy (SEM) and confocal laser scanning microscopy demonstrated the formation of biofilms on the incubated PMF. SEM, atomic force microscopy, Fourier transform infrared spectroscopy and water contact angle detected significant changes in the surface microstructure, chemical composition and hydrophobicity change of the films, thereby suggesting that the plastisphere community degraded PMF during incubation. In conclusion, this study provides insights into the changes in agricultural soil microorganisms in the PMF plastisphere and the degradation of PMF.

Paenibacillus sp. Strain OL15 Immobilized in Agar as a Potential Bioremediator for Waste Lubricating Oil-Contaminated Soils and Insights into Soil Bacterial Communities Affected by Inoculations of the Strain and Environmental Factors

Waste lubricating oil is a widespread common soil pollutant. In this study, the waste lubricating oil degraders were isolated from the oil-contaminated soil. The bacterial strains OL6, OL15, and OL8, which tolerated a high concentration (10%) of waste lubricating oil, presented the degradation efficiency values (measured in culture broth) of 15.6 ± 0.6%, 15.5 ± 1%, and 14.8 ± 1%, respectively, and belonged to the genera Enterobacter, Paenibacillus, and Klebsiella, respectively. To maintain long survival, immobilization of a promising bioremediator, Paenibacillus sp. strain OL15, in agar exhibited the significantly highest number of surviving cells at the end of a 30-day incubation period, as compared to those in alginate and free cells. Remarkably, after being introduced into the soil contaminated with 10% waste lubricating oil, the strain OL15 immobilized in agar conferred the highest degradation percentage up to 45 ± 3%. Due to its merit as a promising soil pollutant degrader, we investigated the effect of an introduction of the strain OL15 on the alterations of a bacterial community in the oil-contaminated soil environments using 16S rRNA amplicon sequencing. The result revealed that the Proteobacteria, Acidobacteriota, Firmicutes, and Actinobacteriota were predominant phyla. The introduction of the strain affected the soil bacterial community structures by increasing total bacterial diversity and richness. The proportions of the genera Pseudomonas, Vibrio, Herbaspirillum, Pseudoalteromonas, Massilia, Duganella, Bacillus, Gordonia, and Sulfurospirillum were altered in response to the strain establishment. Soil pH, EC, OM, total N, P, Mg, Fe, and Zn were the major factors influencing the bacterial community compositions in the oil-contaminated soils.

Microbial diversity drives pyrene dissipation in soil

Soil microbial diversity is an essential driver of multiple ecosystem functions and services. However, the role and mechanisms of microbial diversity in the dissipation of persistent organic pollutants in soil are largely unexplored. Here, a gradient of soil microbial diversity was constructed artificially by a dilution-to-extinction approach to assess the role of soil microbial diversity in the dissipation of pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), in a 42-day microcosm experiment. The results showed that pyrene dissipation (98.1%) and the abundances of pyrene degradation genes (the pyrene dioxygenase gene nidA and the gram-positive PAH-ring hydroxylating dioxygenase gene PAH-RHDα GP) were highest in soils with high microbial diversity. Random-forest machine learning was combined with linear regression analysis to identify a range of keystone taxa (order level) associated with pyrene dissipation, including Sphingobacteriales, Vampirovibrionales, Blastocatellales, Myxococcales, Micrococcales and Rhodobacterales. The diversity of these keystone taxa was significantly and positively correlated with the abundance of pyrene degradation genes and the removal rate of pyrene. According to (partial) Mantel tests, keystone taxa diversity was the dominant factor determining pyrene dissipation compared with total microbial diversity. Moreover, co-occurrence network analysis revealed that diverse keystone taxa may drive pyrene dissipation via more positive interactions between keystone species and with other species in soil. Taken together, these findings provide new insights on the regulation of keystone taxa diversity to promote the dissipation of PAH in soil.

Ecological Insights Into Community Interactions, Assembly Processes and Function in the Denitrifying Phosphorus Removal Activated Sludge Driven by Phosphorus Sources

The microbial characteristics in the wastewater treatment plants (WWTPs) strongly affect their optimal performance and functional stability. However, a cognitive gap remains regarding the characteristics of the microbial community driven by phosphorus sources, especially co-occurrence patterns and community assembly based on phylogenetic group. In this study, 59 denitrifying phosphorus removal (DPR) activated sludge samples were cultivated with phosphorus sources. The results suggested that homogeneous selection accounted for the largest proportion that ranged from 35.82 to 64.48%. Deterministic processes dominated in 12 microbial groups (bins): Candidatus_Accumulibacter and Pseudomonas in these bins belonged to phosphate-accumulating organisms (PAOs). Network analysis revealed that species interactions were intensive in cyclic nucleoside phosphate-influenced microbiota. Function prediction indicated that cyclic nucleoside phosphates increased the activity of enzymes related to denitrification and phosphorus metabolism and increased the α-diversity of microorganism but decreased the diversity of metabolic function. Based on these results, it was assumed that cyclic nucleoside phosphates, rather than inorganic phosphates, are the most available phosphorus source for majority microorganisms in DPR activated sludge. The study revealed the important role of phosphorus source in the construction and assembly of microbial communities and provided new insights about pollutant removal from WWTPs.

Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress

The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.

Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic

The present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria-Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella-and fungi-Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.

How sediment bacterial community shifts along the urban river located in mining city

Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.

Engineering complex communities by directed evolution

Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.

Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater

Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.

Mining of two novel aldehyde dehydrogenases (DHY-SC-VUT5 and DHY-G-VUT7) from metagenome of hydrocarbon contaminated soils

Background

Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications.

Results

Fifteen fosmid clones with hydrocarbon degrading potential were functionally screened to identify dehydrogenase enzymes. Accordingly, the fosmid insert of the positive clones were sequenced using PacBio next generation sequencing platform and de novo assembled using CLC Genomic Work Bench. The 1233 bp long open reading frame (ORF) for DHY-SC-VUT5 was found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli. The 1470 bp long ORF for DHY-G-VUT7 was found to share a protein sequence similarity of 23.9% to glycine dehydrogenase (decarboxylating) (EC 1.4.4.2) from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus). The in silico analyses and blast against UNIPROT protein database with the stated similarity show that the two dehydrogenases are novel. Biochemical characterization revealed, that the highest relative activity was observed at substrate concentrations of 150 mM and 50 mM for DHY-SC-VUT5 and DHY-G-VUT7, respectively. The K_m values were found to be 13.77 mM with a V_max of 0.009135 μmol.min^− 1 and 2.832 mM with a V_max of 0.005886 μmol.min^− 1 for DHY-SC-VUT5 and DHY-G-VUT7, respectively. Thus, a potent and efficient enzyme for alkyl aldehyde conversion to carboxylic acid.

Conclusion

The microorganisms overexpressing the novel aldehyde dehydrogenases could be used to make up microbial cocktails for biodegradation of alkanes. Moreover, since the discovered enzymes are novel it would be interesting to solve their structures by crystallography and explore the downstream applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-021-00677-8.

Fungal and Bacterial Diversity Patterns of Two Diversity Levels Retrieved From a Late Decaying Fagus sylvatica Under Two Temperature Regimes

Environmental fluctuations are a common occurrence in an ecosystem, which have an impact on organismic diversity and associated ecosystem services. The aim of this study was to investigate how a natural and a species richness-reduced wood decaying community diversity were capable of decomposing Fagus sylvatica dead wood under a constant and a fluctuating temperature regime. Therefore, microcosms with both diversity levels (natural and species richness-reduced) were prepared and incubated for 8 weeks under both temperature regimes. Relative wood mass loss, wood pH, carbon dioxide, and methane emissions, as well as fungal and bacterial community compositions in terms of Simpson‘s diversity, richness and evenness were investigated. Community interaction patterns and co-occurrence networks were calculated. Community composition was affected by temperature regime and natural diversity caused significantly higher mass loss than richness-reduced diversity. In contrast, richness-reduced diversity increased wood pH. The bacterial community composition was less affected by richness reduction and temperature regimes than the fungal community composition. Microbial interaction patterns showed more mutual exclusions in richness-reduced compared to natural diversity as the reduction mainly reduced abundant fungal species and disintegrated previous interaction patterns. Microbial communities reassembled in richness-reduced diversity with a focus on nitrate reducing and dinitrogen-fixing bacteria as connectors in the network, indicating their high relevance to reestablish ecosystem functions. Therefore, a stochastic richness reduction was followed by functional trait based reassembly to recover previous ecosystem productivity.

Long-Term Exposure to Azo Dyes from Textile Wastewater Causes the Abundance of Saccharibacteria Population

Discharge of untreated wastewater is one of the major problems in various countries. The use of azo dyes in textile industries are one of the key xenobiotic compounds which effect both soil and water ecosystems and result in drastic effect on the microbial communities. Orathupalayam dam, which is constructed over Noyyal river in Tamil Nadu, India has become a sink of wastewater from the nearby textile industries. The present study had aimed to characterize the bacterial diversity and community profiles of soil collected from the vicinity of the dam (DS) and allied agricultural field (ALS) nearby the catchment area. The soil dehydrogenase and cellulase activities were significantly lower in DS compared to ALS. Additionally, the long-term exposure to azo dye compounds resulted in higher relative abundance of Saccharibacteria (36.4%) which are important for degradation of azo dyes. On the other hand, the relative abundance of Proteobacteria (25.4%) were higher in ALS. Interestingly, the abundance of Saccharibacteria (15.2%) were also prominent in ALS suggesting that the azo compounds might have deposited in the agricultural field through irrigation. Hence, this study revealed the potential bacterial phyla which can be key drivers for designing viable technologies for degradation of xenobiotic dyes.

Bacterial diversity in aqueous/sludge phases within diesel fuel storage tanks

Diesel fuel storage tanks are not hostile environments for microorganisms and tend to form sludges in the water deposited at the bottom of the tanks. The lack of nutrient, carbon and energy limitations within these habitats boost the abundance and the metabolic activity of microorganisms providing microbial hotspots with high growing rates of diesel degradation (0.10 ± 0.021 d^-1). Five different Phyla (Thermotogae, Spirochaetes, Firmicutes, Bacteroidetes Proteobacteria) were identified within the aqueous/sludge phase from in situ diesel storage tanks, by cultured independent molecular surveys using the 16S rDNA gene fragment. The identified dominant strains were Geotoga aestuarianus, Flavobacterium ceti, Spirochaeta thermophila, Propionispira arboris, Sporobacterium olearium and Dysgonomonas genera. The altitude where the storage tanks are located and the organic carbon concentration within the aqueous/sludge phases affected the bacterial diversity. Therefore, the more diverse the microbial communities are, the more probability of the presence of bacteria with capacity to metabolized diesel and eliminate organic matter. Despite, only phosphate showed an effect on the bacterial distribution within the storage tanks, there was an apparent lack of deterministic process in structuring microbial communities. Consequently, preventative protocols are a priority to avoid the microbial growth within diesel fuel storage tanks. A new focus of this worldwide problem within the oil industry would be to explore deeply the wide range of metabolic and adaptive capacities of these microorganisms. These microbial consortia are potential tools with new specific services to apply in bioremediation among others.

Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake

Aquatic bacterial communities play crucial roles in the circulation of nutrients in watershed ecosystems. However, the interaction between bacterial communities and chromophoric dissolved organic matter (CDOM) in freshwater ecosystems has not been studied in depth. In our study, we examined the constitution and interactions of CDOM with the bacterial community in Lake Chaohu and its inflow rivers under the influence of different exogenous pollutants. The results revealed that the bacterial community diversity in the inflow rivers was significantly lower than that in the lake sites. Clustering of different types of polluted inflow rivers integrated with the most abundant genera observed in specific areas indicated that environmentally guided species selection had a large impact on the composition of aquatic bacterial communities. Moreover, our study suggests that communities in lake environments may be more susceptible to interference through a variety of physiologies or via functional redundancy, allowing them to preserve their community structure. Through linear discriminant analysis effect size (Lefse) methods, we revealed that some taxa (from phylum to genus) were consistently enriched in the lake sites. Based on correlation network analysis results, the supersession niches of bacterial community members related to different CDOM in the biogeochemical process was determined. This study provides an ecological basis for the control of external pollution and the protection of the water environment in watershed ecosystems.

Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils

Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.

Petroleum Depletion Property and Microbial Community Shift After Bioremediation Using Bacillus halotolerans T-04 and Bacillus cereus 1-1

Bioremediation of crude oil contaminated environments is an economical, low-maintenance, environmentally friendly technology and has attracted increasing attention in recent years. In the present study, two efficient crude oil degrading bacteria strains were isolated from soils contaminated with crude oil. Phylogenetic analysis suggested they belonged to genus Bacillus, and were designated as Bacillus cereus T-04 and Bacillus halotolerans 1-1. The crude oil depletion of each strain under different conditions was tested. The optimum conditions for both strains' oil degradation was pH 7, 15-20 g/L NaCl concentration, and 5-15 g/L original oil concentration. The crude oil depletion rate could reach to 60-80% after 20 days of treatment. The crude oil bioremediation simulation tests revealed that the bioremediation promoted the depletion of crude oil to a large extent. The inoculum group with inorganic medium showed the highest crude oil depletion (97.5%) while the crude oil depletion of control group was only 26.6% after 180 days of treatment. High-throughput sequencing was used to monitor the changes of microbial community using different treatments. In all groups, Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla. After contaminated with crude oil, the relative abundance of phylum Actinobacteria was dramatically increased and occupied 81.8%. Meanwhile although strains of Bacillus were added in the bioaugmentation groups, the relative abundance of genus Bacillus was not the most abundant genus at the end of simulation tests. The crude oil contamination dramatically decreased the soil microbial diversity and bioremediation could not recover the microbial community in the short term.

Use of Phosphatase and Dehydrogenase Activities in the Assessment of Calcium Peroxide and Citric Acid Effects in Soil Contaminated with Petrol

The objective of the study was to compare the effect of calcium peroxide and citric acid on the activity of acid phosphatase (ACP), alkaline phosphatase (ALP), and dehydrogenases (DHA) in uncontaminated soil and soil contaminated with petrol. The experiment was carried out on samples of loamy sand under laboratory conditions. Petrol was introduced to soil samples at a dose of 0 and 50 g·kg 1 DM, as well as calcium peroxide or citric acid at a dose of 0, 50, 100, or 150 mg·kg 1 DM. The humidity of the samples was brought to 60% maximum water holding capacity, and the samples were incubated at 20°C for 8 weeks. Enzyme activity was determined on days 1, 14, 28, and 56. The obtained results demonstrated that the addition of calcium peroxide and citric acid did not result in significant changes in the activity of the determined enzymes in uncontaminated soil. However, it was observed that the application of calcium peroxide, particularly at the dose of 150 mg·kg 1 DM, largely alleviated the impact of petrol on the enzymatic activity of the soil contaminated with petrol. Moreover, among the determined enzymes, the activity of DHA was found to be the best indicator of the effect of calcium peroxide on the soil ecosystem.

Use of plant materials for the bioremediation of soil from an industrial site

Bioremediation is one of the existing techniques applied for treating oil-contaminated soil, which can be improved by the incorporation of low-cost nutritional materials. This study aimed to assess the addition of two low-cost plant residues, sugarcane bagasse (SCB) and leaf litter (LL) of the forest leguminous Mimosa caesalpiniifolia plant (sabiá), either separately or combined, to a contaminated soil from a petroleum refinery area, analyzed after 90 days of treatment. Individually, both amounts of SCB (20 and 40 g kg^-1) favored the growth of total heterotrophic bacteria and total fungi, while LL at 20 g kg^-1 better stimulated the hydrocarbon-degrading microorganism's activity in the soil. However, no TPH removal was observed under any of these conditions. Higher microbial growth was detected by the application of both plant residues in multicontaminated soil. The maximum TPH removal of 30% was achieved in amended soil with 20 g kg^-1 SCB and 20 kg^-1 LL. All the experimental conditions revealed changes in the microbial community structure, related to the handling of the soil, with abundance of Alphaproteobacteria. This study demonstrates the effectiveness of the plant residues SCB and LL as low-cost nutritional materials for biodegradation of hydrocarbon in real oil contaminated soil by indigenous populations.

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10-9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.

High abundance of Vibrio in tarball-contaminated seawater from Vagator beach, Goa, India

Tarballs are semi-solid remnants of crude oil and they are formed in marine environment after oil-spill incidents. They are composed of diverse hydrocarbons; some of which are recalcitrant in nature. Recent studies based on amplicon sequencing of 16S rRNA gene suggested that tarballs support hundreds of bacterial genera and provided insights into their role as hydrocarbon degraders and potential human pathogens. In this study, bacterial composition of tarball-contaminated seawater from Vagator beach, Goa, India was characterized by amplicon sequencing of V₃-V₄ regions of 16S rRNA gene. The DNA data revealed an unusual surge of Vibrio in sea-water contaminated with tarballs in May 2018 (16.16% OTUs), compared to tarball-free seawater samples collected in March 2018 (no detectable OTUs) and September 2018 (0.17% OTUs). Further studies are required to investigate if Vibrio species form biofilms on tarballs which may act as good reservoirs for their survival and transmission success.

The distinct response of phenanthrene enriched bacterial consortia to different PAHs and their degradation potential: a mangrove sediment microcosm study

Understanding the microbial community succession to polycyclic aromatic hydrocarbons (PAHs) and identification of important degrading microbial groups are crucial for the designing of appropriate bioremediation strategies. In the present study, two distinct phenanthrene enriched bacterial consortia were treated against high molecular weight (Pyrene, Benzo (a) pyrene and Benzo (a) fluoranthene) and the response was studied in term of taxonomic variations by using High Throughput Illumina sequencing and qPCR analysis. Overall, the type of PAHs significantly affected the composition and the relative abundance of bacterial communities while no obvious difference was detected between bacterial communities of benzo (a) pyrene and benzo (a) fluoranthene treatments. Genera, Novosphingobium, Pseudomonas, Flavobacterium, Mycobacterium, Hoeflae, and Algoriphagus dominated all PAHs treatment groups indicating that they could be the key PAHs degrading phylotypes. Due to the higher abundance of gram-negative PAH-ring hydroxylating dioxygenase gene than that of gram-positive bacteria in all treated groups, we speculated that gram-negative bacteria may contribute more in the PAH degradation. The studied sediments harbored rich PAHs degrading bacterial assemblages involved in both low and high molecular weight PAHs and these findings provided new insight into the perspective of microbial PAHs bioremediation in the mangrove ecosystem.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste

Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day-1 and 7.8 mg day-1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day-1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.

Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion

Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.

Sex-Specific Linkages Between Taxonomic and Functional Profiles of Tick Gut Microbiomes

Ticks transmit the most diverse array of disease agents and harbor one of the most diverse microbial communities. Major progress has been made in the characterization of the taxonomic profiles of tick microbiota. However, the functional profiles of tick microbiome have been comparatively less studied. In this proof of concept we used state-of-the-art functional metagenomics analytical tools to explore previously reported datasets of bacteria found in male and female Ixodes ovatus, Ixodes persulcatus, and Amblyomma variegatum. Results showed that both taxonomic and functional profiles have differences between sexes of the same species. KEGG pathway analysis revealed that male and female of the same species had major differences in the abundance of genes involved in different metabolic pathways including vitamin B, amino acids, carbohydrates, nucleotides, and antibiotics among others. Partial reconstruction of metabolic pathways using KEGG enzymes suggests that tick microbiome form a complex metabolic network that may increase microbial community resilience and adaptability. Linkage analysis between taxonomic and functional profiles showed that among the KEGG enzymes with differential abundance in male and female ticks only 12% were present in single bacterial genera. The rest of these enzymes were found in more than two bacterial genera, and 27% of them were found in five up to ten bacterial genera. Comparison of bacterial genera contributing to the differences in the taxonomic and functional profiles of males and females revealed that while a small group of bacteria has a dual-role, most of the bacteria contribute only to functional or taxonomic differentiation between sexes. Results suggest that the different life styles of male and female ticks exert sex-specific evolutionary pressures that act independently on the phenomes (set of phenotypes) and genomes of bacteria in tick gut microbiota. We conclude that functional redundancy is a fundamental property of male and female tick microbiota and propose that functional metagenomics should be combined with taxonomic profiling of microbiota because both analyses are complementary.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg^-1 dry sediment day^-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg^-1 dry sediment day^-1. The denitrification gene abundances of the N-cycling genes were 10⁷-10⁸ orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 10⁵-10⁶ orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Implications of Soil Pollution with Diesel Oil and BP Petroleum with ACTIVE Technology for Soil Health

Grass Elymus elongatus has a potential in phytoremediation and was used in this study in a potted experiment, which was performed to determine the effect of polluting soil (Eutric Cambisol) with diesel oil (DO) and unleaded petroleum (P) on the diversity of soil microorganisms, activity of soil enzymes, physicochemical properties of soil, and on the resistance of Elymus elongatus to DO and P, which altogether allowed evaluating soil health. Both petroleum products were administered in doses of 0 and 7 cm3 kg-1 soil d.m. Vegetation of Elymus elongatus spanned for 105 days. Grasses were harvested three times, i.e., on day 45, 75, and 105 of the experiment. The study results demonstrated a stronger toxic effect of DO than of P on the growth and development of Elymus elongatus. Diesel oil caused greater changes in soil microbiome compared to unleaded petroleum. This hypothesis was additionally confirmed by Shannon and Simpson indices computed based on operational taxonomic unit (OTU) abundance, whose values were the lowest in the DO-polluted soil. Soil pollution with DO reduced the counts of all bacterial taxa and stimulated the activity of soil enzymes, whereas soil pollution with P diminished the diversity of bacteria only at the phylum, class, order, and family levels, but significantly suppressed the enzymatic activity. More polycyclic aromatic hydrocarbons (PAHs) were degraded in the soil polluted with P compared to DO, which may be attributed to the stimulating effect of Elymus elongatus on this process, as it grew better in the soil polluted with P than in that polluted with DO.

Using QC-Blind for Quality Control and Contamination Screening of Bacteria DNA Sequencing Data Without Reference Genome

Quality control for next generation sequencing (NGS) has become increasingly important with the ever increasing importance of sequencing data for omics studies. Tools have been developed for filtering possible contaminants from species with known reference genome. Unfortunately, reference genomes for all the species involved, including the contaminants, are required for these tools to work. This precludes many real-life samples that have no information about the complete genome of the target species, and are contaminated with unknown microbial species. In this work we proposed QC-Blind, a novel quality control pipeline for removing contaminants without any use of reference genomes. The pipeline merely requires the information about a few marker genes of the target species. The entire pipeline consists of unsupervised read assembly, contig binning, read clustering, and marker gene assignment. When evaluated on in silico, ab initio and in vivo datasets, QC-Blind proved effective in removing unknown contaminants with high specificity and accuracy, while preserving most of the genomic information of the target bacterial species. Therefore, QC-Blind could serve well in situations where limited information is available for both target and contamination species.

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity

Organic and inorganic amendments with equivalent nutrient content may have comparable fertilizer effects on crop yield, but their effects on the soil microbial community and subsequent plant-soil-microbe interactions in this context are unknown. This experiment aimed to understand the relationship between soil microbial communities, soil physicochemical characteristics and crop performance after addition of amendments to soil. Poultry litter and synthetic fertilizer with balanced total nitrogen (N) content equivalent to 1,200 kg ha⁻¹ were added to the topsoil (0–10 cm) or subsoil layer (20–30 cm) of repacked soil columns. Wheat plants were grown until maturity. Soil samples were taken at Zadoks 87–91 (76 days after sowing) for analysis of bacterial and fungal communities using 16S and ITS amplicon sequencing. The interaction between amendment type and placement depth had significant effects on bacterial and fungal community structure and diversity in the two soil layers. Addition of poultry litter and fertilizer stimulated or suppressed different taxa in the topsoil and subsoil leading to divergence of these layers from the untreated control. Both amendments reduced microbial community richness, diversity and evenness in the topsoil and subsoil compared to the nil-amendment control, with these reductions in diversity being consistently negatively correlated with plant biomass (root and shoot weight, root length, grain weight) and soil fertility (soil NH₄⁺, shoot N). These results indicate that in this experimental system, the soil microbial diversity was correlated negatively with plant productivity.

Next-Generation Metagenomics: Methodological Challenges and Opportunities

Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.

Influence of salinity on the degradation of xenobiotic compounds in rhizospheric mangrove soil

Mangroves are highly productive tropical ecosystems influenced by seasonal and daily salinity changes, often exposed to sewage contamination, oil spills and heavy metals, among others. There is limited knowledge of the influence of salinity on the ability of microorganisms to degrade xenobiotic compounds. The aim of this study were to determine the salinity influence on the degradation of xenobiotic compounds in a semi-arid mangrove in La Guajira-Colombia and establish the more abundant genes and degradation pathways. In this study, rhizospheric soil of Avicennia germinans was collected in three points with contrasting salinity (4H, 2 M and 3 L). Total DNA extraction was performed and shotgun sequenced using the Illumina HiSeq technology. We annotated 507,343 reads associated with 21 pathways and detected 193 genes associated with the degradation of xenobiotics using orthologous genes from the KEGG Orthology (KO) database, of which 16 pathways and 113 genes were influenced by salinity. The highest abundances were found in high salinity. The degradation of benzoate showed the highest abundance, followed by the metabolism of the drugs and the degradation of chloroalkane and chloroalkene. The majority of genes were associated with phase I degradation of xenobiotics. The most abundant genes were acetyl-CoA C-acetyltransferase (atoB), catalase-peroxidase (katG) and GMP synthase (glutamine-hydrolysing) (guaA). In conclusion, the metagenomic analysis detected all the degradation pathways of xenobiotics of KEGG and 59% of the genes associated with these pathways were influenced by salinity.

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa

Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit.

Rhizobacterial Community Assembly Patterns Vary Between Crop Species

Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments

Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area.