Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet.

The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.

Electronic configuration regulation of single-atomic Mn sites mediated by Mo/Mn clusters for an efficient hydrogen evolution reaction.

Tuning the electron distribution of metal single-atom active sites via bimetallic clusters is an effective way to enhance their hydrogen evolution reaction (HER) activity, but remains a great challenge. A biochar-based electrocatalyst (BCMoMn800-2) with both MnN4 active sites and Mo2C/Mn7C3 clusters was synthesized using in situ enriched Mo/Mn biomass as a precursor to trigger the HER. Various characterization and density functional theory (DFT) calculation results indicated that the presence of Mo2C/Mn7C3 clusters in BCMoMn800-2 effectively induced the redistribution of charges at MnN4 sites, reducing the energy of H* activation during the HER. In 0.5 M H2SO4, the overpotential was 27.4 mV at a current density of 10 mA cm-2 and the Tafel slope was 31 mV dec-1, and its electrocatalytic performance was close to that of Pt/C. The electrocatalyst also exhibited excellent electrocatalytic stability and durability. This work might provide a new strategy for solid waste recycling and constructing efficient HER electrocatalysts.

A comprehensive study on microbial-surfactants from bioproduction scale-up toward electrokinetics remediation of environmental pollutants: Challenges and perspectives.

Currently, researchers have focused on electrokinetic (EK) bioremediation due to its potential to remove a wide-range of pollutants. Further, to improve their performance, synthetic surfactants are employed as effective additives because of their excellent solubility and mobility. Synthetic surfactants have an excessive position in industries since they are well-established, cheap, and easily available. Nevertheless, these surfactants have adverse environmental effects and could be detrimental to aquatic and terrestrial life. Owing to social and environmental awareness, there is a rising demand for bio-based surfactants in the global market, from environmental sustainability to public health, because of their excellent surface and interfacial activity, higher and stable emulsifying property, biodegradability, non- or low toxicity, better selectivity and specificity at extreme environmental conditions. Unfortunately, challenges to biosurfactants, like expensive raw materials, low yields, and purification processes, hinder their applicability to large-scale. To date, extensive research has already been conducted for production scale-up using multidisciplinary approaches. However, it is still essential to research and develop high-yielding bacteria for bioproduction through traditional and biotechnological advances to reduce production costs. Herein, this review evaluates the recent progress made on microbial-surfactants for bioproduction scale-up and provides detailed information on traditional and advanced genetic engineering approaches for cost-effective bioproduction. Furthermore, this study emphasized the role of electrokinetic (EK) bioremediation and discussed the application of BioS-mediated EK for various pollutants remediation.

Using bioelectrohydrogenesis left-over residues as a future potential fertilizer for soil amendment.

In this current research, the left-over residues collected from the dark fermentation-microbial electrolysis cells (DF-MEC) integrated system solely biocatalyzed by activated sludge during the bioconversion of the agricultural straw wastes into hydrogen energy, was investigated for its feasibility to be used as a potential alternative biofertilizer to the commonly costly inorganic ones. The results revealed that the electrohydrogenesis left-over residues enriched various plant growth-promoting microbial communities including Enterobacter (8.57%), Paenibacillus (1.18%), Mycobacterium (0.77%), Pseudomonas (0.65%), Bradyrhizobium (0.12%), Azospirillum (0.11%), and Mesorhizobium (0.1%) that are generally known for their ability to produce different essential phytohormones such as indole-3-acetic acid/indole acetic acid (IAA) and Gibberellins for plant growth. Moreover, they also contain both phosphate-solubilizing and nitrogen-fixing microbial communities that remarkably provide an adequate amount of assimilable phosphorus and nitrogen required for enhanced plants or crop growth. Furthermore, macro-, and micronutrients (including N, P, K, etc.) were all analyzed from the residues and detected adequate appreciate concentrations required for plant growth promotions. The direct application of MEC-effluent as fertilizer in this current study conspicuously promoted plant growth (Solanum lycopersicum L. (tomato), Capsicum annuum L. (chilli), and Solanum melongena L. (brinjal)) and speeded up flowering and fruit-generating processes. Based on these findings, electrohydrogenesis residues could undoubtedly be considered as a potential biofertilizer. Thus, this technology provides a new approach to agricultural residue control and concomitantly provides a sustainable, cheap, and eco-friendly biofertilizer that could replace the chemical costly fertilizers.

Evaluation of di-rhamnolipid biosurfactants production by a novel Pseudomonas sp. S1WB: Optimization, characterization and effect on petroleum-hydrocarbon degradation.

Rhamnolipid biosurfactants are multifunctional compounds that can play an indispensable role in biotechnological, biomedical, and environmental bioremediation-related fields, and have attracted significant attention in recent years. Herein, a novel strain Pseudomonas sp. S1WB was isolated from an oil-contaminated water sample. The biosurfactants produced by this strain have capabilities to reduce surface tension (SFT) at 32.75 ± 1.63 mN/m and emulsified 50.2 ± 1.13 % in liquid media containing 1 % used engine oil (UEO) as the sole carbon source. However, the lowest SFT reduction (28.25 ± 0.21), highest emulsification index (60.15 ± 0.07), and the maximum yields (900 mg/L) were achieved under optimized conditions; where, the glucose/urea and glycerol/urea combinations were found efficient carbon and nitrogen substrates for improved biosurfactants production. Biosurfactants product was characterized using ultra-high performance liquid chromatography-mass spectrometry (UHPLC- MS) and detected various di- rhamnolipids congeners. In addition, the di-rhamnolipids produced by S1WB strain was found highly stable in terms of surface activity and EI indices at different environmental factors i.e. temperature, pH and various NaCl concentrations, where, emulsifying property was found high stable till 30 days of incubation. Moreover, the stain was capable to degrade hydrocarbon at 42.2 ± 0.04 %, and the Gas chromatography- mass spectrometry (GC-MS) profile showed the majority of peak intensities of hydrocarbons have been completely degraded compared to control.

Gut region induces gastrointestinal microbiota community shift in Ujimqin sheep (Ovis aries): from a multi-domain perspective.

Gastrointestinal (GI) microbiota is one of the most complicated microbial ecosystems and is vital in regulating biological processes associated with nutrient absorption and homeostatic maintenance. Although several efforts have been achieved in characterizing bacterial communities across gut regions, the variation of non-bacterial communities across GI tracts is still largely unexplored. To address this, we investigated microbial biogeography throughout the whole GI tracts of Ujimqin sheep (Ovis aries) by amplicon sequencing which targeted bacteria, fungi, and archaea. The results indicated that the community structures of all three domains were significantly distinguished according to GI tracts (stomach, small intestine, and large intestine), and a more strong and efficient species interaction was detected in small intestine based on cross-domain network analysis. Moreover, a between-domain difference in microbial assembly mechanism of among-GI regions was revealed here, wherein bacterial community is dominantly governed by variable selection (explaining ~62% of taxa turnover), while fungal and archaeal communities mainly governed by homogenizing dispersal (explaining ~49% and 60% of the turnover, respectively). Overall, these data highlight the GI section- and domain-dependence of GI microbial structure and assembly mechanism, suggesting that multi-domain should be explicitly considered when evaluating the influences of GI selection on gut microbial communities.

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons.

It is important to track fecal sources from humans and animals that negatively influence the water quality of rural rivers and human health. In this study, microbial source tracking (MST) methods using molecular markers and the community-based FEAST (fast expectation-maximization microbial source tracking) program were synergistically applied to distinguish the fecal contributions of multiple sources in a rural river located in Beijing, China. The performance of eight markers were evaluated using 133 fecal samples based on real-time quantitative (qPCR) technique. Among them, six markers, including universal (BacUni), human-associated (HF183-1 and BacH), swine-associated (Pig-2-Bac), ruminant-associated (Rum-2-Bac), and avian-associated (AV4143) markers, performed well in the study. A total of 96 water samples from the river and outfalls showed a coordinated composition of fecal pollution, which revealed that outfall water might be a potential input of the Fsq River. In the FEAST program, bacterial 16S rRNA genes of 58 fecal and 12 water samples were sequenced to build the "source" library and "sink," respectively. The relative contribution (<4.01% of sequence reads) of each source (i.e., human, swine, bovine, or sheep) was calculated based on simultaneous screening of the operational taxonomic units (OTUs) of sources and sinks, which indicated that community-based MST methods could be promising tools for identifying fecal sources from a more comprehensive perspective. Results of the qPCR assays indicated that fecal contamination from human was dominant during dry weather and that fecal sources from swine and ruminant were more prevalent in samples during the wet season than in those during the dry season, which were consistent with the findings predicted by the FEAST program using a very small sample size. Information from the study could be valuable for the development of improved regulation policies to reduce the levels of fecal contamination in rural rivers.

Carbon dots enhance the recovery of microalgae bioresources from wastewater containing amoxicillin.

The cultivation of microalgae using wastewater could bring some major economic benefits; however, the toxics in wastewater typically lead to a reduction in bioresource production. In this study, carbon dots (CDs) could enhance the photosynthetic activity of Chlorella under antibiotic stress because they might optimize photoluminescence by red-shifting incident light. Adding of 1 mg/L CDs increased the specific growth rate of Chlorella by 36.0% (day 8-13) and 52.7% (day 14-18) and significantly increased photosystems II activity. This treatment also increased amoxicillin removal by 18.6%. Thus, the toxicity of residuals was significantly eliminated (P < 0.05). The removal of nitrogen and phosphorous was increased by 14.6% and 9.9%, respectively. The production of pigments, lipids and proteins was increased by 16.6%, 19.5% and 24.8%, respectively. This work provided a new strategy of using CDs to mediate the coupling of microalgal bioresources production and toxic wastewater purification.

Bioprospecting of rhamnolipids production and optimization by an oil-degrading Pseudomonas sp. S2WE isolated from freshwater lake.

The present study revealed biosurfactants production by a novel oil-degrading Pseudomonas sp. S2WE isolated from hydrocarbon enriched water sample, where the genus Pseudomonas (48.65%) was dominated amongst several other genera. Biosurfactants produced by this strain showed the great potential for surface tension reduction (SFT) and emulsification. The extracted crude biosurfactants were characterized using ultra-high-performance liquid chromatography-Mass Spectrometry (UHPLC-MS) and identified various mono-and di-rhamnolipids homologs from the mixture. Moreover, the lowest SFT 33.05 ± 0.1 mN/m and highest emulsification of 60.65 ± 0.64% were achieved from rhamnolipids produced from glycerol with urea. Compared to initial screening, almost (>87%) higher emulsification was observed. In addition, the biosurfactants were found highly stable at different environmental factors i.e. temperature (4 °C-121 °C), pH (3-10) and NaCl conc. (1-9%). The high stable rhamnolipids produced by new Pseudomonas sp. S2WE in this study could widely be used in enormous industrial as well as environmental applications.

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation.

Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.

Using easy-to-biodegrade co-substrate to eliminate microcystin toxic on electrochemically active bacteria and enhance bioelectricity generation from cyanobacteria biomass.

Cyanobacterial biomass is a promising natural resource for power generation, through the reactions bio-catalyzed by electrochemically active bacteria (EAB). However, the major limitation is the involvement of Microcystin-LR (MC-LR) in inhibiting EAB activation. In this work, toxic M. aeruginosa biomass was employed as analyte of a microbial fuel cell (MFC), and sodium acetate was applied as easy-to-biodegrade co-substrate to alleviate the MC-LR stress on EAB survival. The running stability was continuously enhanced with the increment of co-substrate concentration. The sufficient co-substrate supply (6.0 mM) eliminated the negative effects of MC-LR on the cyanobacteria biomass fed-MFC performance; it contributed 12.7% extension on the electric cyclic terms and caused the productions of the power density which was comparable and even 3.8% higher than its corresponding control (MFC treated with acetate alone). The co-substrate addition also increased coulombic efficiency by 60.1%, microcystin-LR removal efficiency increased by 64.7%, and diversified the microbial community with more species able to biodegrade the MC-LR, bio-transforming the metabolites and EAB. Microcystin-degrading bacteria, such as Sphingopyxis sp., Burkholderia-Paraburkholderia, and Bacillus sp., were remarkably increased, and EAB, including Shewanella sp., Desulfovibrio desulfuricans, Aeromonas hydrophila, were also much more enriched in co-substrate use protocol. Therefore, this study verified a co-substrate strategy for simultaneously eliminating MC-LR toxin and enhancing bioelectricity generation from cyanobacterial biomass via an MFC.

Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel.

Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.

Production and characterization of surfactin-like biosurfactant produced by novel strain Bacillus nealsonii S2MT and it's potential for oil contaminated soil remediation.

BACKGROUND: Biosurfactants, being highly biodegradable, ecofriendly and multifunctional compounds have wide applications in various industrial sectors including environmental bioremediation. Surfactin, a member of lipopeptide family, which is considered as one of the most powerful biosurfactants due to its excellent emulsifying activities as well as environmental and therapeutic applications. Therefore, the aim of this study was to investigate the newly isolated bacterial strain S2MT for production of surfactin-like biosurfactants and their potential applications for oil-contaminated soil remediation. RESULTS: In this study, the strain S2MT was isolated from lake sediment and was identified as Bacillus nealsonii based on transmitted electron microscopy (TEM) and 16S rRNA ribo-typing. The strain S2MT produced biosurfactant that reduced the surface tension (34.15 ± 0.6 mN/m) and displayed excellent emulsifying potential for kerosene (55 ± 0.3%). Additionally, the maximum biosurfactant product yield of 1300 mg/L was achieved when the composition of the culture medium was optimized through response surface methodology (RSM). Results showed that 2% glycerol and 0.1% NH4NO3 were the best carbon/nitrogen substrates for biosurfactant production. The parameters such as temperature (30 °C), pH (8), agitation (100 rpm), NH4NO3 (0.1%) and NaCl (0.5%) displayed most significant contribution towards surface tension reduction that resulted in enhanced biosurfactant yield. Moreover, the extracted biosurfactants were found to be highly stable at environmental factors such as salinity, pH and temperature variations. The biosurfactants were characterized as cyclic lipopeptides relating to surfactin-like isoforms (C13-C15) using thin-layer chromatography (TLC), Ultra high performance liquid chromatography and mass spectrometry (UHPLC-MS). The crude biosurfactant product displayed up to 43.6 ± 0.08% and 46.7 ± 0.01% remediation of heavy engine-oil contaminated soil at 10 and 40 mg/L concentrations, respectively. CONCLUSION: Present study expands the paradigm of surfactin-like biosurfactants produced by novel isolate Bacillus nealsonii S2MT for achieving efficient and environmentally acceptable soil remediation as compared to synthetic surfactants.

Bioelectricity generation using microalgal biomass as electron donor in a bio-anode microbial fuel cell.

In this study, microalgal biomass waste (Chlorella regularis) was treated while simultaneously producing bioelectricity in a microbial fuel cell (MFC). Algal biomass was the sole electron donor and was enriched with easily biodegradable proteins (46%) and carbohydrates (22%). The generated power density was 0.86 W/m2 and the columbic efficiency reached ∼61.5%.The power generation could be further increased to 1.07 W/m2 by using a biomass waste concentration enhancement strategy with maximum chemical oxygen demand (COD) removal of ∼65.2%. Via direct comparison, the power generation and COD removal capability of the algal-fed MFC was close to that of the commercial acetate-fed MFC. The algae-fed MFC presented superior electrochemical characteristics that were attributed to the complicated composition of the biomass anolyte. It possessed a multiple anode respiring bacterial group and diverse microbial community. Hence, this study provides a new strategy for the utilization of microalgal biomass as a bioresource.

Acceleration of saturated porous media clogging and silicon dissolution due to low concentrations of Al(III) in the recharge of reclaimed water.

The recharge of reclaimed water is an effective strategy for addressing the issues of water quality deterioration and groundwater level decline simultaneously. Residual Al coagulants are normally remained in the recovered water at low concentrations, and may induce clogging problems during the recharging process. However, this issue has been ignored in the past. In this study, we investigated the mechanisms of Al(III)-induced aquifer bio-clogging, the role of Al(III) in quartz sand media (SiO2) dissolution and re-precipitation in the series of aquifer columns. We determined that Al(III) resulted in serious clogging in ∼140 h at low concentrations that satisfied the national drinking water standard of China. The corresponding hydraulic conductivity decreased by more than ∼90% in the bacteria-containing aquifer, which was ∼30% greater than that for the bacteria-free trials. The enhanced Al(III)-related clogging was caused by modifying quartz sand to form Si-O-Al(OH)n and improving microbes attachment. Microbes retention kinetic coefficients (k) of the Al recharged simulated aquifer could increase by 3.0-8.3 times. The Al(III) also enhanced biomass production and clogging by binding to microbial extracellular polymeric substances. In turn, the greater amount of biomass accelerated the Si dissolution and re-precipitation, this may potentially damage the stability of aquifer structure. The results showed that reclaimed water treated with Al coagulation should be employed with caution for recharging.