Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns

Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation

Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. ENVIRONMENTAL IMPLICATION: Parabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.

Synergistic binding mechanisms of co-contaminants in soil profiles: Influence of iron-bearing minerals and microbial communities

In contaminated soil sites, the coexistence of inorganic and organic contaminants poses a significant threat to both the surrounding ecosystem and public health. However, the migration characteristics of these co-contaminants within the soil and their interactions with key components, including Fe-bearing minerals, organic matter, and microorganisms, remain unclear. This study involved the collection of a 4.3-m-depth co-contaminated soil profile to investigate the vertical distribution patterns of co-contaminants (namely, arsenic, cadmium, and polychlorinated biphenyls (PCBs)) and their binding mechanisms with environmental factors. The results indicated a notable downward accumulation of inorganic contaminants with increasing soil depth, whereas PCBs were predominantly concentrated in the uppermost layer. Chemical extraction and synchrotron radiation analysis highlighted a positive correlation between the abundance of reactive iron (FeCBD) and both co-contaminants and microbial communities in the contaminated site. Furthermore, Mantel tests and structural equation modeling (SEM) demonstrated the direct impacts of FeCBD and microbial communities on co-contaminants within the soil profile. Overall, these results provided valuable insights into the migration and transformation characteristics of co-contaminants and their binding mechanisms mediated by minerals, organic matter, and microorganisms.

Distinct microbial characteristics of the robust single-stage coupling system during the conversion from anammox-denitritation to anammox-denitratation patterns

Simultaneous anammox-denitrification is effectively operated in two types, i.e., the anammox-denitritation (SAD pattern) and the anammox-denitratation (PDA pattern). The nitrate derived from inevitable nitrite oxidization likely determines the practical operational pattern of the coupling system, while little information is available regarding the microbial characteristics during the pattern conversion. Here, the single-stage bioreactor coupling anammox with denitrification was operated under conditions with a changed ratio of influent nitrite and nitrate. Results showed that the bioreactor exhibited a robust performance during the conversion from SAD to PDA patterns, corresponding with the total nitrogen removal efficiency ranging from 89.5% to 92.4%. Distinct community structures were observed in two patterns, while functional bacteria including the genera Denitratisoma, Thauera, Candidatus Brocadia, and Ca. Jettenia steadily co-existed. Meanwhile, the high transcription of hydrazine synthase genes demonstrated a stable anammox process, while the up-regulated transcription of nitrite and nitrous oxide reductase genes indicated that the complete denitrification process was enhanced for total nitrogen removal during the PDA pattern. Ecologically, stochastic processes dominantly governed the community assembly in two patterns. The PDA pattern improved the interconnectivity of communities, especially for the cooperative behaviors between dominant denitrifying bacteria and low-abundant species. These findings deepen our understanding of the microbial mechanism underlying the different patterns of the coupling system and potentially expand its engineering application.

Effects of single and combined contamination of total petroleum hydrocarbons and heavy metals on soil microecosystems: Insights into bacterial diversity, assembly, and ecological function

Deciphering the impact of single and combined contamination of total petroleum hydrocarbons (TPH) and heavy metals on soil microecosystems is essential for the remediation of contaminated habitats, yet it remains incompletely understood. In this study, we employed high-throughput sequencing to investigate the impact of single TPH contamination, single metal contamination, and their co-contamination on soil microbial diversity, assembly mechanisms, composition, ecological function, and resistome. Our results revealed that contamination led to a reduction in alpha diversity, with single contamination displaying lower diversity compared to co-contamination, depending on the concentration of pollutants. Community beta diversity was primarily driven by turnover rather than nestedness, and narrower ecological niches were detected under pollution conditions. The neutral community model suggested that homogenizing dispersal played a significant role in the community assembly process under single TPH or co-contamination, while homogeneous selection dominated under heavy metals pollution. Procrustes analysis demonstrated a correlation between community composition and functional divergence, while Mantel tests linked this divergence to concentrations of Cr, Cr6+, Pb, and TPH. Interestingly, soils co-polluted with TPH and heavy metals exhibited similar genera, community functions, and resistomes as soils contaminated with only metals, highlighting the significant impact of heavy metals. Ecological functions related to carbon (C), nitrogen (N), and sulfur (S) cycles were enhanced under TPH pollution but impaired under heavy metals stress. These findings enhance our understanding of soil microecosystems subjected to TPH, heavy metals, and their co-contamination, and carry significant implications for environmental microecology and pollutant risk assessment.

Soil core microbiota drive community resistance to mercury stress and maintain functional stability

Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.

Adaptive Evolution Laws of Biofilm under Emerging Pollutant-Induced Stress: Community Assembly-Driven Structure Response

The widely used biofilm process in advanced wastewater treatment is currently challenged by numerous exotic emerging pollutants (EPs), and the underlying principle of the challenge is the adaptive evolution laws of biofilm under EP stress. However, there is still a knowledge gap in exploration of the biofilm adaptive evolution theory. Herein, we comprehensively analyzed the morphological variation, community succession, and assembly mechanism of biofilms to report the mechanism underlying their adaptive evolution under sulfamethoxazole and carbamazepine stress for the first time. The ecological role of the dominant species was driven as a pioneer and assembly hub by EP stress, and the deterministic processes indicated the functional basis of the transformation. In addition, the characteristic responses of dispersal limitation and homogenizing dispersal adequately revealed the assembly pathways in adaptive evolution and the resulting structural variation. Therefore, the "interfacial exposure-structural variation-mass transfer feedback" mechanism was inferred to underly the adaptive evolution process of biofilms. Overall, this study highlighted the internal drivers of the adaptive evolution of the biofilm at the phylogenetic level and deepened our understanding of the mechanism of biofilm development under EP stress in advanced wastewater purification.

Integrated fixed-film activated sludge systems in continuous-flow and batch mode acclimated from low to high aniline concentrations: Performance, mechanism and metabolic pathways

Integrated fixed-film activated sludge (IFAS) system has considerable advantages in treating aniline wastewater economically and efficiently. However, the response mechanism of IFAS to aniline needs further study. Herein, IFAS in continuous-flow (CF-IFAS) and batch mode (B-IFAS) were set up to investigate it. The removal efficiency of aniline exceeded 99% under different stress intensities. At low stress intensity (aniline ≈ 200 mg/L), the total nitrogen removal efficiency of B-IFAS was approximately 37.76% higher than CF-IFAS. When the stress intensity increased (aniline ≥ 400 mg/L), both were over 82%. CF-IFAS was restrained by denitrification while nitrification in B-IFAS. The legacy effect of perturbation of B-IFAS made microflora quickly reach new stability. The closer interspecific relationship in B-IFAS and more key species: Leucobacter, Rhodococcus, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Ellin6067 and norank_f_NS9_marine_group. Metabolic and Cell growth and death were the most abundant metabolic pathways, resulting both systems the excellent pollutant removal and stability under high stress intensity.

Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity

Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C₈-C₁₆ medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.

Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response

Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used ¹⁴C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.

Synergistic analysis of performance, functional genes, and microbial community assembly in SNDPR process under Zn(II) stress

One of the most prevalent heavy metals found in rural sewage is Zn(II), while its effect on simultaneous nitrification, denitrification and phosphorus removal (SNDPR) remains unclear. In this work, the responses of SNDPR performance to long-term Zn(II) stress were investigated in a cross-flow honeycomb bionic carrier biofilm system. The results indicated that Zn(II) stress at 1 and 5 mg L^-1 could increase nitrogen removal. Maximum ammonia nitrogen, total nitrogen, and phosphorus removal efficiencies of up to 88.54%, 83.19%, and 83.65% were obtained at Zn(II) concentration of 5 mg L^-1. The functional genes, such as archaeal amoA, bacterial amoA, NarG, NirS, NapA, and NirK, also reached the highest value at 5 mg L^-1 Zn(II), with the absolute abundances of 7.73 × 10⁵, 1.57 × 10⁶, 6.68 × 10⁸, 1.05 × 10⁹, 1.79 × 10⁸, and 2.09 × 10⁸ copies·g^-1 dry weight, respectively. The neutral community model demonstrated that deterministic selection was responsible for the system's microbial community assembly. Additionally, response regimes with extracellular polymeric substances and cooperation among microorganisms facilitated the stability of the reactor effluent. Overall, the findings of this paper contribute to improving the efficiency of wastewater treatment.

Enhanced carbon emission driven by the interaction between functional microbial community and hydrocarbons: An enlightenment for carbon cycle

Soil microbial communities are usually regarded as one of the key players in the global element cycling. Moreover, an important consequence of oil contamination altering the structure of microbial communities is likely to result in an increased carbon emission. However, understanding of the complex interactions between environmental factors and biological communities is clearly lagging behind. Here it showed that the flux of carbon emissions increased in oil-contaminated soils, up to 13.64 g C·(kg soil)^-1·h^-1. This phenomenon was mainly driven by the enrichment of rare degrading microorganisms (e.g., Methylosinus, Marinobacter, Pseudomonas, Alcanivorax, Yeosuana, Halomonas and Microbulbifer) in the aerobic layer, rather than the anaerobic layer, which is more conducive to methane formation. In addition, petroleum hydrocarbons and environmental factors are equally important in shaping the structure of microbial communities (the ecological stability) and functional traits (e.g., fatty acid metabolism, lipid metabolism and amino acid metabolism) due to the different ecological sensitivities of microorganisms. Thus, it can be believed that the variability of rare hydrocarbon degrading microorganisms is of greater concern than changes in dominant microorganisms in oil-contaminated soil. Undoubtedly, this study could reveal the unique characterization of bacterial communities that mediate carbon emission and provide evidence for understanding the conversion from carbon stores to carbon gas release in oil-contaminated soils.

Electrokinetic-Enhanced Bioremediation of Trichloroethylene-Contaminated Low-Permeability Soils: Mechanistic Insight from Spatio-Temporal Variations of Indigenous Microbial Community and Biodehalogenation Activity

Electrokinetic-enhanced bioremediation (EK-Bio), particularly bioaugmentation with injection of biodehalogenation functional microbes such as Dehalococcoides, has been documented to be effective in treating a low-permeability subsurface matrix contaminated with chlorinated ethenes. However, the spatio-temporal variations of indigenous microbial community and biodehalogenation activity of the background matrix, a fundamental aspect for understanding EK-Bio, remain unclear. To fill this gap, we investigated the variation of trichloroethylene (TCE) biodehalogenation activity in response to indigenous microbial community succession in EK-Bio by both column and batch experiments. For a 195 day EK-Bio column (∼1 V/cm, electrolyte circulation, lactate addition), biodehalogenation activity occurred first near the cathode (<60 days) and then spread to the anode (>90 days), which was controlled by electron acceptor (i.e., Fe(III)) competition and microbe succession. Amplicon sequencing and metagenome analysis revealed that iron-reducing bacteria (Geobacter, Anaeromyxobacter, Geothrix) were enriched within initial 60 d and were gradually replaced by organohalide-respiring bacteria (versatile Geobacter and obligate Dehalobacter) afterward. Iron-reducing bacteria required an initial long time to consume the competitive electron acceptors so that an appropriate reductive condition could be developed for the enrichment of organohalide-respiring bacteria and the enhancement of TCE biodehalogenation activity.

Stochastic processes drive the soil fungal communities in a developing mid-channel bar

Intricate associations between rhizosphere microbial communities and plants play a critical role in developing and maintaining of soil ecological functioning. Therefore, understanding the assembly patterns of rhizosphere microbes in different plants and their responses to environmental changes is of great ecological implications for dynamic habitats. In this study, a developing mid-channel bar was employed in the Yangtze River to explore the assembly processes of rhizosphere fungal communities among various plant species using high-throughput sequencing-based null model analysis. The results showed a rare significant variation in the composition and alpha diversity of the rhizosphere fungal community among various plant species. Additionally, the soil properties were found to be the primary drivers instead of plant species types. The null model analysis revealed that the rhizosphere fungal communities were primarily driven by stochastic processes (i.e., undominated processes of ecological drift), and the predominance varied with various plant species. Moreover, the assembly processes of rhizosphere fungal communities were significantly related to the changes in soil properties (i.e., soil total carbon, total nitrogen, organic matter, and pH). The co-occurrence network analysis revealed that many keystone species belonged to unclassified fungi. Notably, five network hubs were almost unaffected by the measured soil properties and aboveground plant traits, indicating the effect of stochastic processes on the rhizosphere fungal community assembly. Overall, these results will provide insights into the underlying mechanisms of fungal community assembly in the rhizosphere soils, which are significant for maintaining the functional stability of a developing ecosystem.

A novel cross-flow honeycomb bionic carrier promotes simultaneous nitrification, denitrification and phosphorus removal in IFAS system: Performance, mechanism and keystone species

Simultaneously achieving efficient nitrogen (N) and phosphorus (P) removal without adding external carbon source is vital for carbon-neutral wastewater treatment. In this study, a novel cross-flow honeycomb bionic microbial carrier (CF) was developed to improve the efficiency of simultaneous nitrification, denitrification, and P removal (SNDPR) in an integrated fixed-film activated sludge (IFAS) system. A parallel laboratory-scale sequencing batch reactor with the commercialized microbial carriers (CM) (CM-IFAS) was performed as the comparative system for over 233 d The results demonstrated that CF-IFAS exhibited a more consistent N removal efficiency and better performance than CM-IFAS. In the CF-IFAS, the highest N and P removal efficiencies were 95.40% and 100%, respectively. Typical cycle analysis revealed that nitrate was primarily removed by the denitrifying glycogen-accumulating organisms in the CF-IFAS and by denitrifying phosphate-accumulating organisms in the CM-IFAS. The neutral community model showed that the microbial community assembly in both the reactors was driven by deterministic selection rather than stochastic factors. Compared to those in CM-IFAS, the microorganisms in CF-IFAS were more closely related to each other and had more keystone species: norank_f_norank_o_norank_c_OM190, SM1A02, Defluviicoccus, norank_f_ Saprospiraceae, and norank_f_Rhodocyclaceae. The absolute contents of the genes associated with N removal (bacterial amoA, archaeal amoA, NarG, NapA, NirS, and NirK) were higher in CF-IFAS than in CM-IFAS; the N cycle activity was also stronger in the CF-IFAS. Overall, the microecological environment differed between both systems. This study provides novel insights into the potential of bionic carriers to improve SNDPR performance by shaping microbial communities, thereby providing scientific guidance for practical engineering.

Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.