Simplicispira hankyongi sp. nov., a novel denitrifying bacterium isolated from sludge

Response characteristics of the microbial community, metabolic pathways, and anti-resistance genes under high nitrate and sulfamethoxazole stress in a fluidized sulfur autotrophic denitrification process

The adaptability and microbial response mechanism of a sulfur autotrophic denitrification (SADN) biofilm under high nitrate (NO3--N) and sulfamethoxazole (SMX) stress through long-term operation of a fluidized bioreactor was evaluated. The SADN biofilm adapted to nitrate contents of up to 150 mg/L, and at 1 mg/L SMX, the nitrogen removal efficiency and SMX removal efficiency were as high as 85 % and 64 %, respectively. Microbial adaptation was driven by upregulated secretion of acyl-homoserine lactone (AHL) signal molecules, specifically 3OC6-HSL and 3OC8-HSL, which stabilized at concentrations of 575.7 ng/L and 579.9 ng/L, respectively. These molecules dynamically regulated the composition of extracellular polymeric substances, with total EPS content increasing from 113.37 mg/gVSS in the initial phase to 456.85 mg/gVSS under early SMX exposure, ensuring biofilm structural integrity. Under prolonged SMX stress, Simplicispira emerged as a key genus with a relative abundance of 21.20 %, utilizing apoptotic autotrophic denitrifiers and EPS metabolites as carbon sources for heterotrophic denitrification. This genus harbored critical nitrate reductase genes, including NarG, which accounted for 28.5 % of total functional gene abundance. In addition, SMX stress reduced the abundance of total anti-resistance genes (ARGs), with resistance mechanisms dominated by antibiotic efflux pumps, with the contribution increased from 63 % to 67 %. The relevance of this pump continuously increased, which hindered binding of SMX to cells and effectively reduced its toxicity. The results of this study provide scientific evidence for the application of SADN technology in a high-nitrate and antibiotically stressed environment. The results can further guide practical operations and provide technical support for increasing denitrification efficiency and antibiotic removal capacity in the SADN process.

Efficient nitrite accumulation in partial sulfide autotrophic denitrification (PSAD) system: insights of S/N ratio, pH and temperature

To provide the necessary nitrite for the Anaerobic Ammonium Oxidation (ANAMMOX) process, the effect of nitrite accumulation in the partial sulfide autotrophic denitrification (PSAD) process was investigated using an SBR reactor. The results revealed that the effectiveness of nitrate removal was unsatisfactory when the S/N ratio (mol/mol) fell below 0.6. The optimal conditions for nitrate removal and nitrite accumulation were achieved within the S/N ratio range of 0.7-0.8, resulting in an average Nitrate Removal Efficiency (NRE) of 95.84%±4.89% and a Nitrite Accumulation Rate (NAR) of 75.31%±6.61%, respectively. It was observed that the nitrate reduction rate was three times faster than that of nitrite reduction during a typical cycle test. Furthermore, batch tests were conducted to assess the influence of pH and temperature conditions. In the pH tests, it became evident that the PSAD process performed more effectively in alkaline environment. The highest levels of nitrate removal and nitrite accumulation were achieved at an initial pH of 8.5, resulting in a NRE of 98.30%±1.93% and a NAR of 85.83%±0.47%, respectively. In the temperature tests, the most favourable outcomes for nitrate removal and nitrite accumulation were observed at 22±1 ℃, with a NRE of 100.00% and a NAR of 81.03%±1.64%, respectively. Moreover, a comparative analysis of 16S rRNA sequencing results between the raw sludge and the sulfide-enriched culture sludge sample showed that Proteobacteria (49.51%) remained the dominant phylum, with Thiobacillus (24.72%), Prosthecobacter (2.55%), Brevundimonas (2.31%) and Ignavibacterium (2.04%) emerging as the dominant genera, assuming the good nitrogen performance of the system.

High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments

The tailwater from wastewater treatment plants serves as an important water resource in arid regions, alleviating the conflict between supply and demand. However, the effects of different tailwater discharge proportions on microbial community dynamics remain unclear. In this study, we investigated the effects of different tailwater discharge proportions on the water quality and microbial community characteristics of sediments in receiving water bodies under controlled conditions (WF-1, WF-2, WF-3, WF-4, and WF-5, containing 0% tailwater + 100% natural water, 25% tailwater + 75% natural water, 50% tailwater + 50% natural water, 75% tailwater + 25% natural water, and 100% tailwater + 0% natural water, respectively). Microbial co-occurrence networks and structural equation model were used to unveil the relationship between microbial communities and their shaping factors. Results showed that distinct microbial community compositions were found in the sediments with low- (< 50%) and high- (> 50%) proportions of tailwater. Specifically, WCHB1-41 and g_4-29-1, which are involved in organic degradation-related functions, were the key genera in the high-proportion cluster. A total of 21 taxa were more abundant in the low-proportion (< 50%) cluster than that in high-proportion (> 50%). Moreover, higher modularity was observed in the low-proportion. Total phosphorus directly affected while ammonia nitrogen indirectly affected the microbial community structure. Our findings support the distinct heterogeneity of microbial communities driven by tailwater discharge in receiving water bodies, and further confirmed that high-proportion tailwater depletes sensitive microbial communities, which may be avoided through scientific management.

From acidophilic to ornithogenic: microbial community dynamics in moss banks altered by gentoo penguins

Introduction

The study explores the indirect impact of climate change driven by gentoo's penguin colonization pressure on the microbial communities of moss banks formed by Tall moss turf subformation in central maritime Antarctica.

Methods

Microbial communities and chemical composition of the differently affected moss banks (Unaffected, Impacted and Desolated) located on Galindez Island and Сape Tuxen on the mainland of Kyiv Peninsula were analyzed.

Results

The native microbiota of the moss banks' peat was analyzed for the first time, revealing a predominant presence of Acidobacteria (32.2 ± 14.4%), followed by Actinobacteria (15.1 ± 4.0%) and Alphaproteobacteria (9.7 ± 4.1%). Penguin colonization and subsequent desolation of moss banks resulted in an increase in peat pH (from 4.7 ± 0.05 to 7.2 ± 0.6) and elevated concentrations of soluble nitrogen (from 1.8 ± 0.4 to 46.9 ± 2.1 DIN, mg/kg) and soluble phosphorus compounds (from 3.6 ± 2.6 to 20.0 ± 1.8 DIP, mg/kg). The contrasting composition of peat and penguin feces led to the elimination of the initial peat microbiota, with an increase in Betaproteobacteria (from 1.3 ± 0.8% to 30.5 ± 23%) and Bacteroidota (from 5.5 ± 3.7% to 19.0 ± 3.7%) proportional to the intensity of penguins' impact, accompanied by a decrease in community diversity. Microbial taxa associated with birds' guts, such as Gottschalkia and Tissierella, emerged in Impacted and Desolated moss banks, along with bacteria likely benefiting from eutrophication. The changes in the functional capacity of the penguin-affected peat microbial communities were also detected. The nitrogen-cycling genes that regulate the conversion of urea into ammonia, nitrite oxide, and nitrate oxide (ureC, amoA, nirS, nosZ, nxrB) had elevated copy numbers in the affected peat. Desolated peat samples exhibit the highest nitrogen-cycle gene numbers, significantly differing from Unaffected peat (p < 0.05).

Discussion

The expansion of gentoo penguins induced by climate change led to the replacement of acidophilic microbiomes associated with moss banks, shaping a new microbial community influenced by penguin guano's chemical and microbial composition.

Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery

A Gram-stain-negative, motile (by single polar flagellum) and rod-shaped bacterium, designated W1-6T, was isolated from a sediment of drainage ditch in winery in Guiyang, south-western China. Strain W1-6T showed the highest 16S rRNA gene sequence similarities with the type strain of Acidovorax wautersii (98.1%) and Simplicispira lacusdiani (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1-6T was placed adjacent to the members of the genus Simplicispira and formed a separat subclade. Cells showed oxidase and catalase negative reactions. The only respiratory quinone detected was ubiquinone-8 (Q-8). Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) were predominant cellular fatty acids (> 10%) of strain W1-6T. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unidentified phospholipids were found in the polar lipid extraction. The genomic DNA G + C content was 65.6%. Strain W1-6T shared the highest digital DNA-DNA hybridization [dDDH, (27.6%)] and average nucleotide identity [ANI (84.3%)] values with the type strain of S. lacusdiani. The dDDH and ANI values were below the cutoff level (dDDH 70%; ANI 95-96%) for species delineation. The polyphasic characteristics indicated that the strain W1-6T represents a novel species of the genus Simplicispira, for which the name Simplicispira sedimenti sp. nov. is proposed. The type strain is W1-6T (= CGMCC 1.16274T = NBRC 115624T).

Strategy for the formation of microalgae-bacteria aggregates in high-rate algal ponds

This work studied the formation of aggregates used for wastewater treatment in high-rate algal ponds (HRAP). For this, the establishment of microalgae-bacteria aggregates in these systems was evaluated, considering strategies for the inoculation and start-up. Two HRAP were operated in parallel, at first in batch mode and then in continuous flow. The wastewater treatment was efficient, with removal rates around 80% for COD and N-ammoniacal. Volatile suspended solids and chlorophyll for the culture grew continuously reached a concentration of 548 ± 11 mg L^-1 and 7.8 mg L^-1, respectively. Larger photogranules were observed when the system was placed in a continuous regime. The protein fraction of extracellular polymeric substances was identified as a determinant in photogranules formation. During the continuous regime, more than 50% of the biomass was higher than 0.2 mm, flocculation efficiency of 78 ± 6%, and the volumetric sludge index of 32 ± 5 mL g^-1. The genetic sequencing showed the growth of cyanobacteria in the aggregate and the presence of microalgae from the chlorophytes and diatoms groups in the final biomass.

Mixed culture of plants improved nutrient removal in constructed wetlands: response of microbes and root exudates

Root exudates are determined by plant species configuration and affect microbial community, which in turn affect purification efficiency of constructed wetlands (CWs). However, it is not well understood how plant configuration affects CW purification efficiency through specific root exudates. Herein, four mixed culture CWs were constructed; CW-G3 with Iris pseudacorus, Iris sibirica, Juncus effusus, and Hydrocotyle vulgaris showed the optimal diversity nutrients removal efficiency (TN: 94.2%, TP: 82.9%, COD: 74.7%). Highly increased antioxidant enzymes (peroxidase and catalase) reduced photosynthesis-negative enzyme (malondialdehyde) activity of plants in CW-G3, which ensured oxygen (O₂) and organic carbon (OC) production and successfully released to rhizosphere by well-developed root aeration tissues. Further, CW-G3 enriched higher abundance of genus Saccharimonadales and Flavobacterium, which benefited nitrogen removal. Moreover, as OC, higher contents of maltose in CW-G3 (6.6 ~ 11.1-fold of that in other three CWs), as well as lauramide, choline, triethylamine and urocanic acid contributed to microbial denitrifying. Differently, higher contents of unsaturated fatty acids (linoleic acid and oleic acid) in other three CWs inhibited microbial nitrifying as inhibitors, which also proved by co-occurrent network. Thereby, plant configuration in CW-G3 provided higher O₂ and OC contents for bacteria and reduced nitrifying inhibitors, which contributed to higher purifying efficiency. The study promoted the understanding about root exudates' effects on bacteria through plant configurations and improved the purification efficiency of CWs.

Field application of glycerol to enhance reductive dechlorination of chlorinated ethenes and its impact on microbial community

Chlorinated ethenes (CEs) are common and persistent contaminants of soil and groundwater. Their degradation is mostly driven by a process of bacterial reductive dechlorination (also called organohalide respiration) in anaerobic conditions. This study summarizes the outcomes of the long-term in-situ application of glycerol for the enhanced reductive dechlorination of CEs on a highly contaminated site. Glycerol injection resulted in an almost immediate increase in the abundance of fermentative Firmicutes, which produce essential sources of carbon (acetate) and electrons (H₂) for organohalide-respiring bacteria (OHRB) and change groundwater conditions to be suitable for OHRB growth. The decreased redox potential of groundwater promoted also the proliferation of sulfate-reducing bacteria, which compete for electron donors with OHRB but at the same time support their growth by producing essential corrinoids and acetate. A considerable increase in the abundance of OHRB Dehalococcoides, concurrently with vinyl chloride (VC) reductase gene levels, was revealed by real time polymerase chain reaction (qPCR) method. Consistent with the shifts in bacterial populations, the concentrations of pollutants tetrachloroethylene and trichloroethylene decreased during the monitoring period, with rising levels of cis-1,2-dichloroethylene, VC, and most importantly, the final CE degradation products: ethene and ethane. Our study implies the importance of syntrophic bacterial interactions for successful and complete CE degradation and evaluates glycerol as convenient substrate to enhance reductive dechlorination and as an effective source of electrons for OHRB.

Paludibacterium denitrificans sp. nov., a Novel Denitrifying Bacterium Isolated from Activated Sludge

A Gram-reaction-negative, facultatively aerobic, motile, non-spore-forming, rod-shaped, and denitrifying bacterium, designated dN18-1^T, was isolated from activated sludge, Republic of Korea. This bacterium was investigated via a polyphasic approach to reveal its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain dN18-1^T belongs to the genus Paludibacterium and is most closely related to P. purpuratum KCTC 42852^T (96.2% sequence similarity), P. yongneupense KACC 11601^T (96.1%), and P. paludis BCRC 80514^T (95.2%). The average nucleotide identity values and digital DNA-DNA hybridization values calculated between strain dN18-1^T and the closely related strains were 72.5-73.1% and 19.0-19.6%. The genome comprises of 3,347,996 bp with a G + C content of 57.3 mol%. Strain dN18-1^T possesses ubiquinone Q-8 as a predominant respiratory quinone, and summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), summed feature 8 (C_18:1 ω6c/C_18:1 ω7c), C_16:0 and C_12:0, as its major fatty acids (>5%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified aminophospholipids. The results of ANI calculation, digital DNA-DNA hybridization, physiological and biochemical tests allowed phenotypic differentiation of strain dN18-1^T from rephrase other genus Paludibacterium species with validly published names. Therefore, this isolate represents a novel species, for which the name Paludibacterium denitrificans sp. nov. (type strain dN18-1^T = KACC 19537^T = CGMCC 1.16961^T) is proposed.

Continuous anaerobic oxidation of methane: Impact of semi-continuous liquid operation and nitrate load on N2O production and microbial community

This work proves the feasibility of employing regular secondary activated sludge for the enrichment of a microbial community able to perform the anaerobic oxidation of methane coupled to nitrate reduction (N-AOM). After 96 days of activated sludge enrichment, a clear N-AOM activity was observed in the resulting microbial community. The methane removal potential of the enriched N-AOM culture was then studied in a stirred tank reactor (STR) operated in continuous mode for methane supply and semi-continuous mode for the liquid phase. The effect of applying nitrate loads of ∼22, 44, 66, and 88 g NO₃^- m^-3 h^-1 on (i) STR methane and nitrate removal performance, (ii) N₂O emission, and (iii) microbial composition was investigated. Methane elimination capacities from 21 ± 13.3 to 55 ± 12 g CH₄ m^-3 h^-1 were recorded, coupled to nitrate removal rates ranging from 6 ± 3.2 to 43 ± 14.9 g NO₃^- m^-3 h^-1. N₂O production was not detected under the three nitrate loading rates applied for the assessment of potential N₂O emission in the continuous N-AOM process (i.e. ∼22-66 g NO^-3 m^-3 h^-1). The lack of N₂O emissions during the process was attributed to the N₂O reducing capacity of the bacterial taxa identified and the rigorous control of dissolved O₂ and pH implemented (dissolved O₂ values ≤ 0.07 g m^-3 and pH of 7.6 ± 0.4). Microbial characterization showed that the N-AOM process was performed in absence of putative N-AOM archaea and bacteria (ANME-2d, M. oxyfera). Instead, microbial activity was driven by methane-oxidizing bacteria and denitrifying bacteria (Bacteroidetes, α-, and γ-proteobacteria).

Enhanced biostimulation coupled with a dynamic groundwater recirculation system for Cr(VI) removal from groundwater: A field-scale study

A large gap exists between laboratory findings and successful implementation of bioremediation technologies for the treatment of chromium (Cr)-contaminated sites. This work conducted the enhanced bioremediation of Cr(VI) in situ via the addition of organic carbon (ethanol) coupled with a dynamic groundwater recirculation (DGR)-based system in a field-scale study. The DGR system was applied to successfully (1) remove Cr(VI) from groundwater via enhanced flushing by the recirculation system and (2) deliver the biostimulant to the heterogeneous subsurface environment, including a sand/cobble aquifer and a fractured bedrock aquifer. The results showed that the combined extraction and bioreduction of Cr(VI) were able to reduce Cr(VI) concentrations from 1000 to 2000 mg/L to below the clean-up goal of 0.1 mg/L within the operation period of 52 days. The effectiveness of Cr(VI) bioremediation and the relationship between microbial communities and geochemical parameters were evaluated. Multiple-line of evidence demonstrated that the introduction of ethanol significantly stimulated a variety of bacteria, including those responsible for denitrification, sulfate reduction and reduction of Cr(VI), which contributed to the establishment of reducing conditions in both aquifers. Cr(VI) was removed from groundwater via combined mechanisms of physical removal through the DGR system and the bioreduction of Cr(VI) followed by precipitation. In particular, it was found competitive growth among Cr(VI)-reducing bacteria (such as the enrichment of Geobacter, along with the reduced relative abundance of Acinetobacter and Pseudomonas) was induced by ethanol injection. Furthermore, Cr(VI), total organic carbon, NO₂^-, and SO₄^2- played important roles in shaping the composition of the microbial community and its functions.

The cotreatment of old landfill leachate and domestic sewage in rural areas by deep subsurface wastewater infiltration system (SWIS): Performance and bacterial community☆

In this work, two deep subsurface wastewater infiltration systems (SWISs) were constructed and fed with domestic sewage (control system, S1) and mixed wastewater consisting of old landfill leachate and domestic sewage (experimental system, S2). S1 and S2 exhibited favorable removal efficiencies, with TP (98.8%, 98.7%), COD (87.6%, 86.9%), NH₄⁺-N (99.8%, 99.9%) and TN (99.2%, 98.9%). Even when increasing the pollutant load in S2 by adding old landfill leachate, the almost complete removal performance could be maintained in terms of low effluent concentrations and even increased in terms of load removal capabilities, which included COD (19.4, 25.9 g∙m^-2·d^-1), NH₄⁺-N (8.2, 19.9 g∙m^-2·d^-1), TN (8.9, 20.6 g∙m^-2·d^-1). To investigate the transformation of dissolved organic matter along depth, Three-Dimensional Excitation Emission Matrix fluorescence spectroscopy combined with Fluorescence Regional Integration analysis was applied. The results showed that P_Ⅰ,n and P_Ⅱ,n (the proportions of biodegradable fractions) increased gradually from 6.59% to 21.8% at S2_20 to 10.8% and 27.7% at S2_110, but P_Ⅲ,n and P_Ⅴ,n (the proportions of refractory organics) declined from 23.1% to 27.8% at S2_20 to 21.1% and 16.4% at S2_110, respectively. In addition, high-throughput sequencing technology was employed to observe the bacterial community at different depths, and the predicted functional potential of the bacterial community was analyzed by PICRUSt. The results showed that the genera Flavobacterium, Pseudomonas, Vogesella, Acinetobacter and Aquabacterium might be responsible for refractory organic degradation and that their products might serve as the carbon source for denitrifiers to achieve simultaneous nitrate and refractory organic removal. PICRUSt further demonstrated that there was a mutual response between refractory organic degradation and denitrification. Overall, the combined treatment of domestic sewage and old leachate in rural areas by SWIS is a promising approach to achieve comprehensive treatment.

Energy-Efficient Single-Stage Nitrite Shunt Denitrification with Saline Sewage through Concise Dissolved Oxygen (DO) Supply: Process Performance and Microbial Communities

Single-stage nitrite shunt denitrification (through nitrite rather than nitrate) with low dissolved oxygen (DO) supply is a better alternative in terms of energy-efficiency, short-footprint, and low C/N-ratio requirement. This study investigates the optimal DO level with temperature effect, with saline sewage at the fixed hydraulic and solids retention times of 8 h and 8 d, respectively. Moreover, 16S rRNA gene sequencing analysis corresponding with total nitrogen (TN) and chemical oxygen demand (COD) removals in each operating condition were performed. Results showed that DO of 0.3 mg/L at 20 °C achieved over 60.7% and over 97.9% of TN and COD removal, respectively, suggesting that such condition achieved effective nitrite-oxidizing bacteria inhibition and efficient denitrification. An unexpected finding was that sulfur-reducing Haematobacter and nitrogen-fixing Geofilum and Shinella were highly abundant with the copredominance of ammonia-oxidizing Comamonas and Nitrosomonas, nitrite-oxidizing Limnohabitans, and denitrifying Simplicispira, Castellaniella, and Nitratireductor. Further, canonical correspondence analysis (CCA) with respect to the operating conditions associated with phenotype prediction via R-based tool Tax4Fun was performed for a preliminary diagnosis of microbial functionality. The effects of DO, temperature, nitrite, and nitrate in various extents toward each predominant microbe were discussed. Collectively, DO is likely pivotal in single-stage nitrite shunt denitrification, as well as microbial communities, for energy-efficient saline sewage treatment.