The key monooxygenase involved in phenanthrene degradation of Ruegeria sp. PrR005.

As a typical polycyclic aromatic hydrocarbon (PAH), phenanthrene is often present in diverse environments, leading to severe environmental contamination. However, bacterial degradation plays a crucial role in remediating phenanthrene contamination and has been widely adopted. The widely distributed marine Roseobacter-clade bacteria are frequently found in phenanthrene-contaminated environments, but their catalyzing ability and related molecular mechanism have been rarely elucidated. Our previous work showed Ruegeria sp. PrR005 isolated from the Pearl River Estuary sediment could degrade phenanthrene and other PAHs. Integrated approaches including multi-omics and biochemical analysis were applied here to explore its catabolism mechanism. The genomic and transcriptomic analysis indicated that six new P450 monooxygenase proteins could be closely associated with phenanthrene degradation. Heterologous expression of P450 monooxygenase candidates revealed that PrR005_00615, PrR005_04282, PrR005_04577 have considerable activity in phenanthrene removal, with PrR005_00615 being the primary contributor. Further, the biochemical and metabolic analysis revealed that PrR005_00615 could catalyze phenanthrene to phenanthrene-9,10-epoxide by introducing an oxygen atom at 9,10-carbon positions, which functioned as a monooxygenase. The present study provides compelling evidences of a novel enzyme responsible for catalyzing the initial step of phenanthrene transformation in PrR005. These findings hold significant importance in unraveling the mechanism behind phenanthrene degradation by Roseobacter-clade bacteria.

A sonication-filtration method for acquisition of integrated bacterial communities from phycosphere.

Bacteria in phycosphere engage in intricate interactions with microalgae by exchanging organic and inorganic matter. However, elucidating the primary roles of bacteria in phycosphere has been a big challenge, due to the lack of adequate methods for separating tightly associated bacteria from microalgal cells. In this study we evaluated several isolation methods including centrifugation, filtration, sonication combined with filtration, and tween lysis followed by sonication and filtration, aiming to efficiently acquire complete bacterial communities from phycosphere. The results demonstrated that the sonication-filtration approach maximally preserves the original characteristics of the bacterial communities. This method will facilitate the acquisition and further analysis of future experimental data.

Revolutionizing sanitation: Valorizing fecal slags through co-digesting food waste at high-solid content and dosing metallic nanomaterials for anaerobic digestion stability.

To achieve the UN Sustainable Development Goals (SDGs) and the China Toilet Revolution on a global scale, it is crucial to implement a decentralized sanitation management system in developing countries. Fecal slags (FS) generated from septic tanks of toilets pose a challenge for remote villages. This study sought to resourcefully utilize FS through co-digesting with food waste (FW) under high-solid anaerobic co-digestion (HSAD). Besides, two metallic nanomaterials, nano-zerovalent iron (nZVI) and magnetite (Fe3O4), were employed to demonstrate the practical improvement of HSAD. The results showed that nZVI-dosed digesters produced the highest cumulative methane of 295.72 mL/gVS, 371.36 mL/gVS, 360.53 mL/gVS and 296.64 mL/gVS in 10%, 15%, 20% and 25% TS content, respectively, which was 1.15, 1.22, 1.16, 1.12 times higher than Fe3O4 dosed digesters. This increment could be ascribed to the simultaneous production of H2 from Fe2+ release from nZVI and the enrichment of homoacetogen. Changes in carbon degradation and methanogenic pathways, which facilitated stability under high TS contents, were observed. At low solid digestion (10% TS), Syntrophomonas cooperated with Methanosarcina and Methanobacterium to metabolize butyrate and propionate. However, due to the buildup of total ammonia nitrogen and volatile fatty acids, acetoclastic methanogens were inhibited in the high-solid digesters (15%, 20% and 25% TS). Consequently, a more resilient and highly tolerant Syntrophaceticus, alongside hydrogenotrophic methanogens such as Methanoculleus and Methanobrevibacter, maintained stability in the harsh environment.

The novel application of violacein produced by a marine Duganella strain as a promising agent for controlling Heterosigma akashiwo bloom: Algicidal mechanism, fermentation optimization and agent formulation.

Controlling harmful algal blooms with algicidal bacteria is thought to be an efficient and eco-friendly way but lack of comprehensive studies from theory to practice limited the field application. Here we presented a purple bacterial strain Duganella sp. A3 capable of killing several harmful algae, including Heterosigma akashiwo, a world-wide fish-killing microalga. A bioactivity-guided purification and identification approach revealed the major algicidal compound of A3 as the pigment violacein, which was never reported for its algicidal potential before. Violacein rapidly disrupted cell permeability, caused long-term oxidative stress, but mildly affected algal photosystem, which might explain its highly species-specific activity against unarmored H. akashiwo. To explore the application potential of violacein, a fermentation optimization approach combing single-factor and multi-factor experiments was conducted to increase the violacein yield, which finally reached 0.4199 g/L just using a simple medium formula beneficial for compound purification. Finally, taking advantages of the physical and chemical stabilities, we successfully developed the novel application of violacein as a sustained-releasing and easy-to-preserve algicidal agent using alginate-acacia-gum-chitosan encapsulation, which paved the path for its future application in controlling H. akashiwo bloom.

Nutrient-dependent interactions between a marine copiotroph Alteromonas and a diatom Thalassiosira pseudonana.

IMPORTANCE: As the major producers and consumers, phytoplankton and bacteria play central roles in marine ecosystems and their interactions show great ecological significance. Whether mutualistic or antagonistic, the interaction between certain phytoplankton and bacterial species is usually seen as a derivative of intrinsic physiological properties and rarely changes. This study demonstrated that the interactions between the ubiquitously co-occurring bacteria and diatom, Alteromonas and Thalassiosira pseudonana, varied with nutrient conditions. They overcame hardship together in oligotrophic seawater but showed antagonistic effects against each other under nutrient amendment. The contact-dependent algicidal behavior of Alteromonas based on protease activity solved the paradox among bacterial proliferation, nutrient viability, and algal demise haunting other known non-contact-dependent algicidal processes and might actually trigger the collapse of algal blooms in situ. The chemotactic and swarming movement of Alteromonas might also contribute greatly to the breakdown of "marine snow," which could redirect the carbon sequestration pathway in the ocean.

Local environment, surface characteristics and stochastic processes shape the dynamics of urban dustbin surface microbiome.

Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community assembly on dustbin surfaces. Here, surface samples were collected from three sampling zones (business building, commercial street and residential community) with different types (kitchen waste, harmful waste, recyclables, and others) and materials (metallic and plastic); and distribution pattern and assembly of microbial communities were investigated by high-throughput sequencing. Bacterial and fungal communities showed the distinct community variations across sampling zones and waste sorting. Core community and biomarker species were significantly correlated with the spatial distribution of overall community. The detection of pathogens highlighted the potential risk of surface microbiome. Human skin, human feces and soil biomes were the potential source environments of the surface microbiomes. Neutral model prediction suggested that microbial community assembly was significantly driven by stochastic processes. Co-association patterns varied with sampling zones and waste types, and neutral amplicon sequence variants (ASVs) that fall within the 95 % confidence intervals of neutral model were largely involved in the stability of microbial networks. These findings improve our understanding of the distribution pattern and the underlying assembly of microbial community on the dustbin surface, thus enabling prospective prediction and assessment of urban microbiomes and their impacts on human health.

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees.

tvBOT is a user-friendly and efficient web application for visualizing, modifying, and annotating phylogenetic trees. It is highly efficient in data preparation without requiring redundant style and syntax data. Tree annotations are powered by a data-driven engine that only requires practical data organized in uniform formats and saved as one table file. A layer manager is developed to manage annotation dataset layers, allowing the addition of a specific layer by selecting the columns of a corresponding annotation data file. Furthermore, tvBOT renders style adjustments in real-time and diversified ways. All style adjustments can be made on a highly interactive user interface and are available for mobile devices. The display engine allows the changes to be updated and rendered in real-time. In addition, tvBOT supports the combination display of 26 annotation dataset types to achieve multiple formats for tree annotations with reusable phylogenetic data. Besides several publication-ready graphics formats, JSON format can be exported to save the final drawing state and all related data, which can be shared with other users, uploaded to restore the final drawing state for re-editing or used as a style template for quickly retouching a new tree file. tvBOT is freely available at: https://www.chiplot.online/tvbot.html.

Opacimonas viscosa gen. nov., sp. nov., a novel bacterium isolated from phycosphere.

A novel strain of a member of the family Alteromonadaceae was isolated from the phycosphere of a diatom and designated as LMIT007T. LMIT007T could form milk-white, opaque, circular and smooth colonies on 2216E marine agar. LMIT007T cells were around 1.0-1.8 µm long, 0.8-1.8 µm wide, round or oval shaped and had polar flagella but were non-motile. Optimum conditions for growth were 25 °C, pH 7.0 and 6 % (w/v) NaCl. The results of 16S rRNA gene-based analysis indicated that LMIT007T had the highest similarity with the type strains Aestuaribacter halophilus JC2043T (95.95 %), Alteromonas lipolytica JW12T (95.60 %) and Alteromonas halophila KCTC 22164T (94.21 %). Furthermore, the results of phylogenetic analysis based on 16S rRNA gene sequences and of phylogenomic analysis indicated that LMIT007T could be clustered into the family Alteromonadaceae but formed a separate branch. The genome size of the strain was 2.95 Mbp and the DNA G+C content was 41.6 %. The average nucleotide identity (ANI) values of orthologous genes between LMIT007T and species of other closely related genera within the family Alteromonadaceae ranged from 66.9 to 69.2 %, and the average amino acid identity (AAI) values ranged from 60.0 to 65.7 %. The main respiratory quinone was ubiquinone-8. The major fatty acids were summed feature 3 (C16 : 1ω7c / C16 : 1ω6c) and C16 : 0. The polar lipid profile contain phosphatidylethanolamine, phosphatidylglycerol, aminolipid, two phospholipid and an unknown polar lipid. On the basis of the results of the polyphasic analysis, strain LMIT007T is suggested to represent a novel genus and species within the family Alteromonadaceae, for which the name Opacimonas viscosa gen. nov., sp. nov. is proposed. The type strain is LMIT007T (=MCCC 1K08161T=KCTC 92597T).

Eliminating the ecological hazards of Heterosigma akashiwo bloom by a microbial algicide: removal of nitrite contamination, redirection of carbon flow and restoration of metabolic generalists.

Harmful algal blooms (HABs) attracted much attention due to their extensive ecological hazards and the increasing influences on global biogeochemical cycles with the intensification of human impact and global warming. Lysing algal cells with species-specific microbial algicide seemed to be promising to eliminate HABs, but the potential ecotoxicity was rarely studied. In this study, microcosms simulating Heterosigma akashiwo blooms were established to reveal the influences of a microbial algicide from Streptomyces sp. U3 on the biological, physicochemical parameters and bacterial community. The results showed that H. akashiwo bloom accumulated nitrite to a lethal dose, produced bio-labile DOM with widespread influences and enriched pathogenic Coxiella to a high abundance. Lysing H. akashiwo cells by microbial algicide induced a bacterial bloom, eliminated nitrite contamination, enhanced the recalcitrance of DOM, and restored bacterial population from a Gammaproteobacteria-dominant community during bloom back to an Alphaproteobacteria-dominant community similar to the non-bloom seawater. Succession of bacterial genera further suggested that the variation from algal exudates to lysates promoted the restoration of metabolic generalists, which redirected the carbon flow to a less ecologically impactive path. This study revealed the benefits of using microbial algicide to remediate the ecological hazards of HABs, which provided references for future application.

[Adsorption of Mn2+ by Modified Biochar Fixed Bed in Simulated Lakes and Reservoir Waters].

Lakes and reservoirs are important water resources for human survival and sustainable development. The seasonal excess of manganese ions (Mn2+) in drinking water in lakes and reservoirs has become an important factor threatening human life in health and social safety in production. Firstly, a batch study of NaOH-modified biochar was carried out. The effects of pyrolysis temperature (400, 500, and 600℃) and modification conditions (unmodified, pre-alkali modified, and post-alkali modified) on the adsorption performance of biochar were investigated. The results showed that the alkali pretreatment could improve the adsorption capacity of biochar, and the maximum adsorption capacity of the modified biochar obtained by alkali pretreatment at 400℃ was 41.06 mg·g-1. Additionally, the dynamic adsorption characteristics of Mn2+in the application on the fixed bed were investigated. The results showed that the stronger the adsorption capacity of biochar in the batch experiment, the longer its breakthrough point (ct/c0=0.1) and saturation point (ct/c0=0.9) in the dynamic adsorption process. In addition, when the initial concentration of Mn2+ and the influent flow rate were increased, the breakthrough point of the fixed bed was shortened from 360 min to 160 min and 200 min, respectively, and the saturation point was shortened from 865 min to 700 min and 600 min, respectively. The Thomas model could better fit the adsorption process of the fixed bed, indicating that the removal of Mn2+ by biochar was also dominated by chemical adsorption. This outcome can provide theoretical guidance for actual operations.

Inoculating indoleacetic acid bacteria promotes the enrichment of halotolerant bacteria during secondary fermentation of composting.

The secondary fermentation stage is critical for stabilizing composting products and producing various secondary metabolites. However, the low metabolic rate of mesophilic bacteria is regarded as the rate-limiting stage in composting process. In present study, two indoleacetic acid (IAA)-producing bacteria (Bacillus safensis 33C and Corynebacterium stationis subsp. safensis 29B) were inoculated to strengthen the secondary fermentation stage to improve the plant-growth promoting potential of composting products. The results showed that the addition of IAA-producing bacteria promoted the assimilation of soluble salt, the condensation and aromatization of humus, and the accumulation of dissolved organic nitrogen (DON) and dissolved organic carbon (DOC). The bioaugmentation strategy also enabled faster microbial community succession during the medium-late phase of secondary fermentation. However, the colonization of Bacillus and Corynebacterium could not explain the disproportionate increase of IAA yield, which reached up to 5.6 times compared to the control group. Deeper analysis combined with physicochemical properties and microbial community structure suggested that IAA-producing bacteria might induce the increase of salinity, which enriched halotolerant bacteria capable of producing IAA, such as Halomonas, Brachybacterium and Flavobacterium. In addition, the results also proved that it was necessary to shorten secondary fermentation time to avoid IAA degradation without affecting composting maturity. In summary, enhancing secondary fermentation of composting via adding proper IAA-producing bacteria is an efficient strategy for upgrading the quality of organic fertilizer.

Semi-solid anaerobic co-digestion of source-separated fecal slag and food waste: focusing on methane production, ecological risk assessment, and quality evaluation as fertilizer.

Toilet revolution is driven by the urgent need for solutions to improve sanitation and access to high-quality organic fertilizer for rural areas, which is tagged "resource recovery from human waste." This study provides a possible solution via semi-solid anaerobic co-digestion (Aco-D) of source-separated fecal slag (SFS) and food waste (FW) (3:1). A comprehensive investigation of Aco-D at different inoculum/substrate ratios (ISR) was conducted. Results revealed that the reactor with ISR of 1:4 reached the highest methane yield (255.05 mL/gVS), which enhanced Methanosaetaceae, Methanomicrobiales, and Syntrophomonas. Additionally, the reactor with low feedstock (ISR of 1:2) showed higher removal efficiency of antibiotics (74.75%). The ecological risk of digestate decreased to an insignificant hazard quotient level, and the contents of nutrients and heavy metals were in line with the standard requirement for fertilizer. This study could serve as an alternative technology to support further research in SFS management and digestate utilization as fertilizer.

Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting.

Composting, as an effectively bio-oxidative process, has been widely used for converting organic waste to organic fertilizer. However, the low fertilizer efficiency of composting product limited its application in agriculture. To improve the growth-promoting effect of composting product, the present study investigated the bioaugmentation strategy of inoculating indole-3-acetic-acid (IAA)-producing bacteria. Firstly, two IAA-producing bacteria (Bacillus safensis 33C and Rhodococcus rhodochrous YZ) were isolated from composting products with high IAA yields of 39.18 and 16.32 µg mL-1, respectively. Secondly, the microbial inoculants were prepared with 33C, YZ and a previously isolated IAA-producing strain Corynebacterium stationis 29B. To increase the accumulation of microbial secondary metabolites, microbial inoculants were amended at the secondary fermentation stage of composting. Physicochemical characterization showed that the maturity of composting product was significantly promoted by inoculating microbial inoculants prepared with 33C and 29B (single and combined inoculants). Finally, bioaugmentation with 33C and 29B increased the IAA contents of composting products by 2.9-5.2 times, which benefited the germination and early vegetative growth of plants. In summary, inoculating proper IAA-producing bacteria during secondary fermentation of composting could improve the quality of composting product and expand its application.

pH and hydraulic retention time regulation for anaerobic fermentation: Focus on volatile fatty acids production/distribution, microbial community succession and interactive correlation.

Enriching suitable fermentative products by optimizing operation conditions could effectively improve the efficiency of anaerobic digestion. In the present study, pH (5.0-6.0) and hydraulic retention time (HRT) (2 h-12 h) were regulated for volatile fatty acids (VFAs) production during glucose fermentation in acidogenic continuous stirred tank reactor (CSTR). Results showed that acetate and butyrate dominated during pH regulation. HRT reduction favored butyrate production and formate retainment. Maximum total VFAs production with highest acetate content was achieved at pH of 6.0 and HRT of 6 h. Microbial analysis revealed that Clostridium_sensu_stricto_1 was predominant butyrate producer during pH regulation, and Bacteroides was main contributor when HRT shorter than 6 h. In addition to acetyl-CoA pathway, acetate could also be produced via homoacetogenesis by Parabacteroides, UCG-004 and norank_f__Acidaminococcaceae. These results would give guidance for enhancing targeted VFAs products by optimizing operational parameters or bio-augmentation with specific bacteria.

Multi-functional biochar preparation and heavy metal immobilization by co-pyrolysis of livestock feces and biomass waste.

Biomass waste is a desirable additive in livestock feces biochar preparation due to its easy access, better moisture adjustment, and abundant organic content. In the present study, co-pyrolysis of livestock feces (PM: pig manure, CM: chicken manure) and biomass wastes (WC: wood chips, BS: bamboo sawdust, RH: rice husk, and CH: chaff) with different blending ratios was conducted at 600 °C to investigate the biochar characteristic and Cu/Zn immobilization performances. The results showed that WC and BS have more significant effect on the increase in fixed carbon content and heating value and the decrease in ash content of biochar. The biochar with lower pH and electrical conductivity is obtained from co-pyrolysis of manure with RH and CH. Compared with CM-based biochar, PM-based biochar presented better potential as fuel and soil remediation considering the higher heating value and lower aromatic H/C ratio. Specially, the residual fractions of Cu and Zn in PM biochar increased from 73.09% and 65.54% to 90.68% and 72.31% after 10 wt% BS addition and those in CM biochar increased from 81.07% and 73.57% to 88.87% and 84.11% after 10 wt% WC addition, which induced the lowest environmental risk of biochar. This work provided a strategy and direction for targeted enhancement in biochar characteristics with selective biomass addition during manure pyrolysis, which is beneficial to the local treatment and utilization of farm wastes.

Carbon- and metal-based mediators modulate anaerobic methanogenesis and phenol removal: Focusing on stimulatory and inhibitory mechanism.

In this study, anaerobic batch experiments were conducted to investigate the effect of carbon-based (biochar) and metal-based (nanoscale zero-valent iron, NZVI and zero valent iron, ZVI) mediators on the AD process treating phenolic wastewater. Fresh apricot shell- and wood-derived biochar (BiocharA, BiocharB) could remove the phenol efficiently (77.1% and 86.2%), suggesting that biodegradation cooperated with adsorption had advantage in phenol removal. BiocharB, NZVI and ZVI enhanced the methane production by 17.6%, 23.7% and 23.2%, respectively. Apart from serving as carrier for microbial growth, BiocharB might promote the direct interspecies electron transfer (DIET) since the Anaerolineaceae/Clostridium sensu stricto, which have potential for DIET, were enriched. NZVI and ZVI added systems mainly enhanced the abundance of Clostridium sensu stricto (24.5%, 37.6%) and Methanosaeta. Interestingly, BiocharA inhibited the methanogenesis completely. An inhibitory mechanism was proposed: the exposure of absorbed microbes on the BiocharA to the highly concentrated phenol in biochar' pores resulted in the inhibition of methanogens, especially for Methanosarcina. In conclusion, this study showed that suitable biochar (BiocharB) could serve as an alternative redox mediator for realizing simultaneously the efficient phenol removal and methane production.

Novel insights into the anaerobic digestion of propionate via Syntrophobacter fumaroxidans and Geobacter sulfurreducens: Process and mechanism.

The accumulation of volatile fatty acids, particularly propionic acid, significantly inhibits the efficiency of the anaerobic digestion system. In propionate degradation metabolism, the unfavorable thermodynamics of syntrophic reactions, strict ecological niche of syntrophic priopionate oxidizing bacteria, and slow metabolic rate of methanogens are regarded as major limitations. In this study, Geobacter sulfurreducens was co-cultured with Syntrophobacter fumaroxidans in bioelelectrochemical cells to analyze the propionate degradation process, impact factor, mechanism metabolic pathways, and electron transfer comprehensively. The results revealed that the syntroph S. fumaroxidans and syntrophic partner G. sulfurreducens achieved more efficient propionate degradation than the control group, comprising S. fumaroxidans and methanogens. Moreover, the carbon resource concentration and pH were both significantly correlated with propionate degradation (P < 0.01). The results further confirmed that G. sulfurreducen strengthened the consumption of H2 and acetate via direct interspecific electron transfer in propionate degradation. These findings indicate that G. sulfurreducens plays an unidentified functional role in propionate degradation.

Deeper investigation on methane generation from synthetic wastewater containing oxytetracycline in a scale up acidic anaerobic baffled reactor.

Acidic anaerobic digestion attracted much attention and interest due to its significant advantage in wastewater treatment. In the present study, methanogenic fermentation was successfully operated under acidic condition during treating wastewater containing oxytetracycline (OTC) in a scale up anaerobic baffled reactor (ABR). After start-up process, the pH value in the first compartment was 4.60 with high activity of methanogenesis. After stabilization, different OTC loading of 1.0, 3.3 and 5.0 g/m3/d was added in the influent for OTC removal. The resulted showed that OTC addition had little impact on the methane generation with whole COD and OTC removal rate of 95% and 60%, respectively. The microbial analysis, OTC addition could significantly influence the bacteria and archaea communities. To be more specific, Methanosaeta showed the highest relative abundance and tolerance to OTC under acidic condition. The present work supplied deeper insights into methane generation from acidic condition during wastewater containing OTC treatment.

Syntrophic butyrate-oxidizing methanogenesis promoted by anthraquinone-2-sulfonate and cysteine: Distinct tendencies towards the enrichment of methanogens and syntrophic fatty-acid oxidizing bacteria.

Interspecies electron transfer (IET) between syntrophic fatty-acid oxidizing bacteria (SFOBs) and methanogens decided the performance of anaerobic digestion. Electron shuttles, as potential IET accelerators, were controversial concerning their influences on methanogenesis. In this study, concentration-dependent effects of anthraquinone-2-sulfonate (AQS) and cysteine on glucose digestion were firstly demonstrated: low dosage of AQS and cysteine (50 and 100 µM, respectively) had highest methane yield (133.5% and 148.6%, respectively). Using butyrate as substrate, distinct tendencies towards the enrichment of methanogenic community were further revealed. Cysteine just acted as a reductant which lowered ORP quickly and enriched most methanogens. It benefited methanogenesis right until methanogenic substrates accumulated. AQS, however, showed characteristic features of electron shuttles: it was firstly oxidized by SFOBs and then reduced by hydrogenotrophic methanogens, which accelerated methanogenic butyrate degradation. This study showed wide spectrum of SFOBs and methanogens benefited from the addition of electron shuttles, which laid foundation for future application.