Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems.

Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat. IMPORTANCE: Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.

A hybrid system for Nickel ions removal from synthesized wastewater using adsorption assisted with electrocoagulation.

The presence of heavy metal ions in water environments has raised significant concerns, necessitating practical solutions for their complete removal. In this study, a combination of adsorption and electrocoagulation (ADS + EC) techniques was introduced as an efficient approach for removing high concentrations of nickel ions (Ni2+) from aqueous solutions, employing low-cost sunflower seed shell biochar (SSSB). The combined techniques demonstrated superior removal efficiency compared to individual methods. The synthesized SSSB was characterized using SEM, FT-IR, XRD, N2-adsorption-desorption isotherms, XPS, and TEM. Batch processes were optimized by investigating pH, adsorbent dosage, initial nickel concentration, electrode effects, and current density. An aluminum (Al) electrode electrocoagulated particles and removed residual Ni2+ after adsorption. Kinetic and isotherm models examined Ni2+ adsorption and electrocoagulation coupling with SSSB-based adsorbent. The results indicated that the kinetic data fit well with a pseudo-second-order model, while the experimental equilibrium adsorption data conformed to a Langmuir isotherm under optimized conditions. The maximum adsorption capacity of the activated sunflower seed shell was determined to be 44.247 mg.g-1. The highest nickel ion removal efficiency of 99.98% was observed at initial pH values of 6.0 for ADS and 4.0 for ADS/EC; initial Ni2+ concentrations of 30.0 mg/L and 1.5 g/L of SSSB; initial current densities of 0.59 mA/cm2 and 1.32 kWh/m3 were also found to be optimal. The mechanisms involved in the removal of Ni2+ from wastewater were also examined in this research. These findings suggest that the adsorption-assisted electrocoagulation technique has a remarkable capacity for the cost-effective removal of heavy metals from various wastewater sources.

Fate of contaminants of emerging concern in two wastewater treatment plants after retrofitting tertiary treatment for reduction of nitrogen discharge.

More and more previously designed wastewater treatment plants (WWTPs) are upgraded to tertiary treatment to meet the higher effluent discharge standards of conventional pollutants. Contaminants of emerging concern (CECs) can cause adverse effects on organisms and usually flow into WWTPs along with urban sewage. How the retrofitted WWTPs targeting conventional pollutants will influence the treatment efficiency of CECs is seldom discussed. This study investigates the removal of CECs in two full-scale newly retrofitted WWTPs (CD and JM WWTPs), containing high-efficiency sedimentation tank and denitrification deep bed filter for enhancing total nitrogen removal. The overall CEC removal efficiencies in the CD and JM WWTPs were 73.79 % and 93.63 %, respectively. Mass balance results indicated that CD WWTP and JM WWTP release a total of 36.89 and 88.58 g/d of CECs into the environment through effluent and excess sludge, respectively. Analysis of the concentration of CECs along the treatment process revealed most CECs were removed in the biological treatment units. The incorporation of newly constructed tertiary treatment proved beneficial for CEC removal and removed 2.93 % and 2.36 % CECs, corresponding to CEC removal of 2.92 and 27.49 g/d in the CD and JM WWTPs, respectively. The data of this study were further used to evaluate the suitability of the SimpleTreat model for simulating the fate of CECs in WWTPs. The predicted fraction of CECs discharged through the biological treatment effluent were generally within ten-fold difference from the measured results, highlighting its potential for estimating CEC removal in WWTPs.

GLP-1 signaling-regulated SNAP25 is involved in improved insulin secretion in diabetic GK rats after Roux-en-Y gastric bypass surgery.

BACKGROUND: Roux-en-Y gastric bypass surgery (RYGB) improves glucose-stimulated insulin secretion (GSIS) in type 2 diabetes (T2D) patients. SNAP25 plays an essential role in GSIS. Clinical studies indicate that enhanced GLP-1 signaling is an important contributor to the improved ß-cell function in T2D. We aimed to explore whether GLP-1-regulated SNAP25 is involved in the enhanced secretory function of ß-cells in diabetic Goto-Kakizaki (GK) rats after RYGB. METHODS AND RESULTS: RYGB or sham surgery was conducted in GK rats. mRNA and protein expression of SNAP25 was assessed by qPCR and Western blot, respectively. Occupancy of CREB and acetyltransferase CBP and acetylation of histone H3 (ACH3) at the Snap25 promoter were determined using ChIP assay. RYGB led to increased SNAP25 expression and CREB phosphorylation in islets from GK rats. Increased SNAP25 improved GSIS in ß-cells cultured in high glucose conditions. Consistent with increased plasma GLP-1 after RYGB, GLP-1R agonist exendin4 increased SNAP25 expression and CREB phosphorylation in ß-cells. Mechanistically, exendin4 promoted the recruitment of CREB and CBP, thereby increasing ACH3 at the Snap25 promoter. Consistently, inhibition of CBP attenuated the effect of exendin4 on SNAP25 expression. Furthermore, the knockdown of SNAP25 diminished the increase of GSIS potentiated by chronic GLP-1 culture in INS-1 832/13 cells. CONCLUSIONS: Our findings unravel the novel mechanisms of RYGB-enhanced SNAP25 expression in ß-cells, and SNAP25 may contribute to the improved ß-cell secretory function induced by RYGB.

Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem.

BACKGROUND: Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms. RESULTS: We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions. CONCLUSIONS: Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.

Gut microbiota related response of Oryzias melastigma to combined exposure of polystyrene microplastics and tetracycline.

The co-existence of microplastics (MPs) and antibiotics in the coastal environment poses a combined ecological risk. Single toxic effects of MPs or antibiotics on aquatic organisms have been verified, however, the exploration of their combined toxic effects remains limited. Here, foodborne polystyrene microplastics (PS-MPs, 10 µm, 0.1 % w/w in food) and waterborne tetracyclines (TC, 50 µg/L) were used to expose an estuarine fish Oryzias melastigma for four weeks. We found that the aqueous availability of TC was not significantly altered coexisting with MPs. The fish body weight gain was significantly slower in TC alone or combined groups than the control group, consistent with the lower lipid content in livers. The body length gain was significantly inhibited by the combined presence compared to the single exposure. Both exposures led to a shift of gut microbiota composition and diversity. TC and the combined group possessed similar gut microbiota which is distinct from PS-MPs and the control group. The Firmicutes/Bacteroidetes (F/B) ratio in the TC and combined groups were significantly lower compared to the control, while the PS-MPs group showed no significant impact. Metabolomic analysis of the fish liver confirmed the shift of metabolites in specific pathways after different exposures. More, a number of gut microbiota-related metabolites on lipid metabolism was perturbed, which were annotated in arachidonic acid metabolism and linoleic acid metabolism. In all, TC modulates bacterial composition in the fish gut and disturbs their liver metabolites via the gut-liver axis, which led to the slower growth of O. melastigma. More, the adverse impact was aggravated by the co-exposure to foodborne PS-MPs.

Anti-inflammatory protein TSG-6 secreted by BMSCs attenuates silica-induced acute pulmonary inflammation by inhibiting NLRP3 inflammasome signaling in macrophages.

Silicosis is a severe occupational lung disease caused by inhalation of silica particles. Unfortunately, there are currently limited treatment options available for silicosis. Recent advances have indicated that bone marrow mesenchymal stem cells (BMSCs) have a therapeutic effect on silicosis, but their efficacy and underlying mechanisms remain largely unknown. In this study, we focused on the early phase of silica-induced lung injury to investigate the therapeutic effect of BMSCs. Our findings demonstrated that BMSCs attenuated silica-induced acute pulmonary inflammation by inhibiting NLRP3 inflammasome pathways in lung macrophages. To further understand the mechanisms involved, we utilized RNA sequencing to analyze the transcriptomes of BMSCs co-cultured with silica-stimulated bone marrow-derived macrophages (BMDMs). The results clued tumor necrosis factor-stimulated gene 6 (TSG-6) might be a potentially key paracrine secretion factor released from BMSCs, which exerts a protective effect. Furthermore, the anti-inflammatory and inflammasome pathway inhibition effects of BMSCs were attenuated when TSG-6 expression was silenced, both in vivo and in vitro. Additionally, treatment with exogenous recombinant mouse TSG-6 (rmTSG-6) demonstrated similar effects to BMSCs in attenuating silica-induced inflammation. Overall, our findings suggested that BMSCs can regulate the activation of inflammasome in macrophages by secreting TSG-6, thereby protecting against silica-induced acute pulmonary inflammation both in vivo and in vitro.

PacBio next-generation sequencing uncovers Apicomplexa diversity in different habitats.

The phylum Apicomplexa comprises a large group of intracellular protozoan parasites. These microorganisms are known to infect a variety of vertebrate and invertebrate hosts, leading to significant medical and veterinary conditions such as toxoplasmosis, cryptosporidiosis, theileriosis, and eimeriosis. Despite their importance, comprehensive data on their diversity and distribution, especially in riverine environments, remain scant. To bridge this knowledge gap, we utilized next-generation high-throughput 18S rRNA amplicon sequencing powered by PacBio technology to explore the diversity and composition of the Apicomplexa taxa. Principal component analysis (PCA) and principal coordinate analysis (PCoA) indicated the habitat heterogeneity for the physicochemical parameters and the Apicomplexa community. These results were supported by PERMANOVA (P < 0.001), ANOSIM (P < 0.001), Cluster analysis, and Venn diagram. Dominant genera of Apicomplexa in inlet samples included Gregarina (38.54%), Cryptosporidium (32.29%), and Leidyana (11.90%). In contrast, outlet samples were dominated by Babesia, Cryptosporidium, and Theileria. While surface water samples revealed 16% and 8.33% relative abundance of Toxoplasma and Cryptosporidium, respectively. To our knowledge, the next-generation high throughput sequencing covered a wide range of parasites in Egypt for the first time, which could be useful for legislation of the standards for drinking water and wastewater reuse.

Enforcing energy consumption promotes microbial extracellular respiration for xenobiotic bioconversion.

Extracellular electron transfer (EET) empowers electrogens to catalyse the bioconversion of a wide range of xenobiotics in the environment. Synthetic bioengineering has proven effective in promoting EET output. However, conventional strategies mainly focus on modifications of EET-related genes or pathways, which leads to a bottleneck due to the intricate nature of electrogenic metabolic properties and intricate pathway regulation that remain unelucidated. Herein, we propose a novel EET pathway-independent approach, from an energy manipulation perspective, to enhance microbial EET output. The Controlled Hydrolyzation of ATP to Enhance Extracellular Respiration (CHEER) strategy promotes energy utilization and persistently reduces the intracellular ATP level in Shewanella oneidensis, a representative electrogenic microbe. This approach leads to the accelerated consumption of carbon substrate, increased biomass accumulation and an expanded intracellular NADH pool. Both microbial electrolysis cell and microbial fuel cell tests exhibit that the CHEER strain substantially enhances EET capability. Analysis of transcriptome profiles reveals that the CHEER strain considerably bolsters biomass synthesis and metabolic activity. When applied to the bioconversion of model xenobiotics including methyl orange, Cr(VI) and U(VI), the CHEER strain consistently exhibits enhanced removal efficiencies. This work provides a new perspective and a feasible strategy to enhance microbial EET for efficient xenobiotic conversion.

Dissemination of antibiotic resistance genes from the Pearl River Estuary to adjacent coastal areas.

The spread of antibiotic resistance genes (ARGs) is a growing concern over the world's various environments. Coastal environments may receive pollutants from land runoffs via estuaries. However, the impact of ARG contamination from estuarine regions to coastal areas is rarely reported. This study used high-throughput quantitative PCR to examine the diversity and abundance of ARGs in Pearl River Estuary (PRE) and adjacent coastal areas. We found that the distribution of ARGs in seawater exhibited the distance-decay phenomenon from the estuary to coastal areas, while the sediment samples did not exhibit an obvious distribution pattern. The estuarine water was found to be the hotspot of ARGs, with 74 ARG species detected and absolute abundance being 5.93 × 105 copies per mL, on average, while less species and lower abundance of ARGs were detected in coastal waters. Ordination analysis showed that estuarine ARG communities were significantly different from coastal ARG communities for water samples. SourceTracker analysis revealed that ARGs from the estuarine environment contributed only a minor fraction of ARG contamination to downstream coastal areas (1.5%-7.4% for water samples, and 0.7-1.8% for sediment samples), indicating the strong dilution effect of seawater. Mantel tests, redundancy analysis and random forest model analysis identified salinity, nutrients, microbial community structure and mobile genetic elements (MGEs) as important factors influencing ARG distribution. Partial least squares-path model revealed that, among all environmental factors, MGEs directly affected the distribution of ARGs, while other factors indirectly contributed by affecting the MGEs assemblage. Our study provides insight into the dissemination of ARGs from the PRE to adjacent coastal areas.

Salipiger pentaromativorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from mangrove sediment.

Polycyclic aromatic hydrocarbons (PAHs) have been recognized as a potential health risk and are widespread in nature due to their intrinsic chemical stability and high recalcitrance to degradation. A taxonomic study was carried out on strain P9T, which was isolated from a PAH-degrading consortium, enriched from the mangrove sediment from Zhangzhou, PR China. The isolate was chemoheterotrophic, aerobic, Gram-stain-negative, short-rod shaped, and motile by one polar flagellum. Growth was observed at salinities from 0.5-6.0 % (optimum, 3 %), at pH 4-9 (optimum, pH 7) and at 10-41 °C (optimum, 25-30 °C). It did not synthesize bacteriochlorophyll a. Catalase and oxidase activities were positive. Acid was produced from starch, amygdalin, arbutin, cellobiose, d-fructose, maltose, d-mannitol, melezitose, melibiose, raffinose, d-ribose, sucrose, trehalose, d-xylose, aesculin ferric citrate, gentiobiose, glycogen, l-arabinose, l-rhamnose, methyl α-d-glucopyranoside, methyl ß-d-xylopyranoside, N-acetylglucosamine and salicin, and weakly positive for d-arabitol, d-galactose, lactose, turanose and glycerol. Phylogenetic analysis revealed that strain P9T fell within the clade comprising the type strains of Salipiger species and formed an independent cluster with Salipiger profundus, which was distinct from other members of the family Rhodobacteraceae. The 16S rRNA gene sequence comparisons showed that strain P9T was most closely related to Salipiger bermudensis HTCC 260T (96.7 %), and other species of the genus Salipiger (95.7-94.2 %). Strain P9T had the highest digital DNA-DNA hybridization value with S. profundus CGMCC 1.12377T (25.0 %) and the highest average nucleotide identity (ANIb and ANIm) values with S. profundus CGMCC 1.12377T(80.3 and 85.8 %, respectively). The sole respiratory quinone was quinone 10. The dominant fatty acids were C18 : 1 ω7c (61.4 %), C16 : 0 (17.5 %) and C19 : 0 ω8c cyclo (7.6 %). The G+C content of the chromosomal DNA was 65.8 mol%. In the polar lipid profile, phospholipid, phosphatidylglycerol, aminolipid, glycolipid and phosphatidylethanolamine were the major compounds. Based on the phenotypic and phylogenetic data, strain P9T represents a novel species of the genus Salipiger, for which the name Salipiger pentaromativorans sp. nov. is proposed. The type strain is P9T (=CCTCC AB 209290T=LMG 25701T=MCCC 1F01055T).

Response and recovery mechanisms of river microorganisms to gradient concentrations of estrogen.

As an important ecological system on the earth, rivers have been influenced by the rapid development of urbanization, industrialization, and anthropogenic activities. Increasingly more emerging contaminants, such as estrogens, are discharged into the river environment. In this study, we conducted river water microcosmic experiments using in situ water to investigate the response mechanisms of microbial community when exposed to different concentrations of target estrogen (estrone, E1). Results showed that both exposure time and concentrations shaped the diversity of microbial community when exposed to E1. Deterministic process played a vital role in influencing microbial community over the entire sampling period. The influence of E1 on microbial community could last for a longer time even after the E1 has been degraded. The microbial community structure could not be restored to the undisturbed state by E1, even if disturbed by low concentrations of E1(1 µg/L and 10 µg/L) for a short time. Our study suggests that estrogens could cause long-term disturbance to the microbial community of river water ecosystem and provides a theoretical basis for assessing the environmental risk of estrogens in rivers.

Insight into variation and controlling factors of dissolved organic matter between urban rivers undergoing different anthropogenic influences.

Dissolved organic matter (DOM), known as a key to the aquatic carbon cycle, is influenced by abiotic and biotic factors. However, the compositional variation and these factors' effects on fluorescence DOM (FDOM) in urban rivers undergoing different anthropogenic pressure are poorly investigated. Herein, using fluorescence excitation-emission matrix and parallel factor analysis (EEM-PARAFAC), four FDOM components (C1, C2, C3, and C4) were identified in a less urbanized north river (NR) and a more urbanized west river (WR) of Jiulong River Watershed in Fujian province, China. C1, C2, and C4 were related to humic-like substances (HLS) and C3 to protein-like substances (PLS). HLS (63.9% in WR and 36.4% in NR) and PLS (62.7% in WR and 37.3% in NR) exhibited higher fluorescence in the more urbanized river. We also found higher PLS in winter, but higher HLS in summer for both rivers. Although the coefficient of variation indicated a difference in FDOM components stability to some extent between the two rivers, the typhoon event that occurred in summer had a stronger disruptive impact on the CDOM and FDOM of a more urbanized river than that of a less urbanized river. We explore abiotic and biotic factors' effects on FDOM using the partial least squares path model (PLS-PM). PLS-PM results revealed higher significant influences of biotic factors on FDOM in the more urbanized river. This study enhances our understanding of FDOM dynamics of rivers with different anthropogenic pressure together with the abiotic and biotic factors driving them.

Impacts of a subtropical storm on nitrogen functional microbes and associated cycling processes in a river-estuary continuum.

Storms, in subtropical regions such as S.E. China, cause major changes in the physical and biogeochemical fluxes of anthropogenic N species through the river-estuary continuum to the coast. Two weeks continuous observations at a sampling station (Station E) in the upper Jiulong River Estuary (S.E. China) were conducted to track the changes of physical and biogeochemical parameters together with genomic identification of nitrogen cycling microbes through a complete storm event in June 2019. In conjunction with previous N flux measurements, it was found that there was greatly increased flux of N to and through the upper estuary during the storm. During the storm, the freshwater/brackish water boundary moved downstream, and previously deposited organic rich sediment was resuspended. During baseflow, anthropogenically derived ammonium was oxidised dominantly by the marine nitrifying (AOA) microbe Nitrosopelagicus. However, during the storm, the dominant ammonia-oxidizing archaea (AOA) at Station E changed to the riverine genus (Nitrosotenuis) while the marine genus, Nitrosopumilus decreased. At the same time the dominant ammonia-oxidizing bacteria (AOB) was still the marine genus (Nitrosomanas). Estuarine nitrifiers had higher abundance, weighted entropy and diversity during the Flood, suggesting that the high NH4-N and DO during the Rising period of the Flood resulted in a bloom of nitrifiers. The changing gene abundances of nitrifiers were reflected in changes in the concentration and isotopic composition of DIN confirming active nitrification in the oxygen-rich water column. During the storm the numbers of denitrifiers (narG, nirS and nod), DNRA (nrfA) and anammox (hzsB) were found in the water column increased, and the larger fraction was associated with the <22 µm free-living fraction. However it was not possible with the data obtained to estimate what fraction of these anaerobic bacteria were active in the dominantly oxic water column.

Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome.

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.

Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka.

Microplastics could accumulate and enrich antibiotics in the aquatic environment. Despite this, the joint effects of microplastics and antibiotics on aquatic organisms are not clear. Here, we investigated the changes of microbial interactions in both gill and gut of marine medaka exposed to polystyrene microbeads (PS) and/or tetracycline for 30 days by using co-occurrence network analysis based on 16S rRNA gene amplicon sequences. We found that the single and combined effects of PS and tetracycline were more profound on the gut than on the gill microbiome. SourceTracker analysis showed that the relative contributions from the gill microbiome to the gut microbiome increased under combined exposure. Moreover, the combined exposure reduced the complexity and stability of the gut microbial network more than those induced by any single exposure, suggesting the synergistic effects of PS and tetracycline on the gut microbiome. The PS and tetracycline combined exposure also caused a shift in the keystone taxa of the gut microbial network. However, no similar pattern was found for gill microbial networks. Furthermore, single and combined exposure to PS and/or tetracycline altered the associations between the gut network taxa and indicator liver metabolites. Altogether, these findings enhanced our understanding of the hazards of the co-occurring environmental microplastics and antibiotics to the fish commensal microbiome.

Zobellella iuensis sp. nov., an aerobic denitrifying bacterium isolated from activated sludge.

An aerobic denitrifying bacterium, designated as strain CPY4T, was isolated from activated sludge treating urban sewage under alternating aerobic/anaerobic conditions by an enrichment culture technique. Cells of strain CPY4T were Gram-stain-negative, aerobic, long rod-shaped, motile by means of single polar flagellum and capable of aerobic denitrification with citrate as the carbon source. Growth of strain CPY4T was observed at 10-45 °C (optimum, 30-35 °C), at pH 6.0-10.5 (optimum, pH 8.0-8.5) and in 0-5 % NaCl (optimum, 0-3 %; w/v). The 16S rRNA gene sequence of strain CPY4T showed the highest similarity to Zobellella denitrificans ZD1T (97.9 %), followed by Zobellella endophytica 59N8T (97.6 %), Zobellella aerophila JC2671T (97.2 %), Zobellella taiwanensis ZT1T (97.1 %) and Zobellella maritima 102-Py4T (96.3 %). Genome comparisons between CPY4T and other Zobellella species showed highest digital DNA-DNA hybridization with Z. denitrificans ZD1T (43.8 %) and highest average nucleotide identity (ANIb and ANIm) of genome nucleotide sequences with Z. denitrificans ZD1T(90.7 and 92 %, respectively). Phylogenetic analysis revealed that strain CPY4T fell within the clade comprising the type strains of Zobellella species and formed a phyletic line with them, which was distinct from other members of the family Aeromonadaceae. The sole respiratory ubiquinone was quinone 8. The predominant fatty acids (>10 % of the total fatty acids) of strain CPY4T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The genomic DNA G+C content was 62.7 mol %. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl ethanolamine, phospholipids and aminolipids were the major compounds. Based on the genotypic and phenotypic data, strain CPY4T represents a novel species of the genus Zobellella, for which the name Zobellella iuensis sp. nov. is proposed. The type strain is CPY4T (=JCM 34456T=CGMCC 1.18722T).

Effects of land-use patterns on the biogeography of the sediment bacteria in the Yarlung Tsangpo River.

Bacteria communities, as key drivers of energy flow and nutrient recycling in rivers, usually consist of a few abundant taxa and many rare taxa. During the last decades, rivers on the Tibetan Plateau have experienced dramatic land surface changes under climate change and anthropogenic disturbances. However, the responses of abundant and rare taxa to such changes and disturbances still remains unclear. In this study, we explored the biogeography and drivers of the abundant and rare bacteria in Yarlung Tsangpo River sediments on the Tibetan Plateau. Our study demonstrated that changes in surrounding land-use patterns, especially in forest land, bare land and cropland, had profound influences on the distribution of the abundant and rare sediment bacteria in the Yarlung Tsangpo River. Although both communities exhibited significant distance-decay patterns, dispersal limitation was the dominant process in the abundant community, while the rare community was mainly driven by heterogeneous selection. Our results also revealed that the abundant bacteria exhibited stronger adaptation across environmental gradients than the rare bacteria. The similar biogeographic patterns but contrasting assembly processes in abundant and rare communities may result from the differences in their environmental adaptation processes. This work provides valuable insights into the importance of land surface changes in influencing the biogeographic patterns of bacteria in fluvial sediments, which helps to predict their activities and patterns in Tibetan rivers under future global climate change and anthropogenic disturbances.

The Performance and Mechanism of Sludge Reduction by the Bioaugmentation Approach.

Millions of wastewater treatment plants (WWTPs) based on the activated sludge process have been established worldwide to help to purify wastewater. However, a vast amount of sludge is inevitably generated, and the cost of sludge disposal could reach over half of the total operation cost of a WWTP. Various sludge reduction techniques have been developed, including physicochemical, biological, and combinational methods. Micro-organisms that could reduce sludge by cryptic growth are vital to the biological approach. Currently, only limited functional bacteria have been isolated, and the lack of knowledge on the underlying mechanism hinders the technique development. Therefore, the present study is aimed at isolating sludge-reducing bacteria and optimizing the sludge reduction process through response surface methodology. Nineteen strains were obtained from sludge. The mix-cultures did not show a higher sludge reduction rate than the pure culture, which may be ascribed to the complicated interactions, such as competition and antagonistic effects. In total, 21.2% and 13.9% of total suspended and volatile suspended solids were reduced within 48 h after optimization. The three-dimensional excitation-emission matrix fluorescence spectrum and hydrolases test results revealed that the sludge reduction might be promoted by the strain mainly through hydrolysis via proteinase and amylase. The results obtained from the study demonstrate the potential of using micro-organisms for sludge reduction through cryptic growth.

Leachable Additives of Tire Particles Explain the Shift in Microbial Community Composition and Function in Coastal Sediments.

Massive microplastics are deposited in the coastal zone. Tire particles (TPs) are an important microplastic source, but little is known about how TPs affect the microbial community composition and function in coastal sediments and the role leachable additives play in TP toxicity. Here, a microcosm experiment was performed using coastal sediments amended with different doses of TPs and with their leachable additives to investigate their effects on the sediment microbial community composition and function. Environmentally relevant concentrations of TPs can change the microbial community structure, decrease community diversity, and inhibit nutrient cycling processes, including carbon fixation and degradation, nitrification, denitrification, and sulfur cycling in sediments. Notably, the raw TP and leachate treatments showed consistent effects. A variety of additives were found in the pore water of sediment, and they could explain over 90% of the variations of the community structure. Further modeling revealed that leachable additives not only directly influenced community function but also indirectly affected community diversity and function by shifting the community structure. In addition, rare taxa could be crucial mediators of ecological functions of sediment microbial community. Combined, this study provides novel insights into the role of TPs' leachable additives in affecting sediment microbial community and function.