Pure Culture Studies Research Articles

Comprehensive model for predicting toxic equivalents (TEQ) reduction due to dechlorination of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/F congeners)

Remediation-focused predictive tools for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) rely on transformation models to evaluate the reduction in total contaminant load and toxic equivalency (TEQ). In this study, a comprehensive model predicting the profiles of PCDD/F congeners and the associated TEQs was developed. The model employs first-order kinetics to describe the transformation of 256 reactions for 75 PCDD congeners and 421 reactions for 135 PCDF congeners. It integrates the growth of anaerobic microbial guilds using Monod kinetics on hydrogen release compounds and stoichiometric growth for Dehalococcoides sp. The effects of temperature, salinity, pH, and availability of vitamin B12 (a cofactor) were also integrated. The PCDD/F congeners model was used to extract the first-order dechlorination rate constants from a number of pure culture and mixed microbial microcosm studies. Simulations for the transformation of PCDD/F congeners at concentrations representative of the Tittabawassee or Saginaw Rivers and watershed in MI, USA were carried out. For a starting TEQ of 5000 ng per kg dry sediment (ppt), the model predicted a decrease in the overall TEQ to below 2000 ppt after 2.6 years and below 250 ppt after ∼21 years. The developed model may be used for extracting rates from microcosm studies and to evaluate the effect of engineering interventions on TEQ reduction.

Distribution of extracellular adhesins in environmental biofilms and flocs: Reimagining the microbial structure

Extracellular cellular adhesins facilitate microbial aggregation; however, most of the information about extracellular adhesins is based on pure culture studies. In this study, we characterized the hydrophobic characteristics and distribution of the extracellular adhesins in environmental biofilms and flocs. The hydrophobic characteristics of the extracellular adhesins were studied by sonicating the microbial aggregates to disperse the cells and by fractionating them using the microbial adhesion to the hydrocarbon method. Furthermore, we probed environmental biofilms and flocs using immunohistochemistry coupled with confocal laser scanning microscopy for reimaging the microbial aggregates based on extracellular adhesins. Small flocs have a relatively dispersed distribution of extracellular adhesins (flagella, fimbriae, pili, and amyloid adhesins). The stratified distribution of extracellular adhesins was observed in environmental biofilms. It was observed that the pili and amyloid adhesins were predominantly present in the core of biofilms, whereas flagella and fimbriae were present in the outer layer of the microbial aggregates. The dispersion of microbial aggregates is one of the limiting factors that challenge the sustainable application of wastewater treatment processes. Greater attention to the components of extracellular protein (such as the adhesins) is required to understand the aggregation of dispersible environmental microbial aggregates.

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria.

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

Relationships among bacterial cell size, diversity, and taxonomy in rumen.

The rumen microbial community plays a crucial role in the digestion and metabolic processes of ruminants. Although sequencing-based studies have helped reveal the diversity and functions of bacteria in the rumen, their physiological and biochemical characteristics, as well as their dynamic regulation along the digestion process in the rumen, remain poorly understood. Addressing these gaps requires pure culture studies to demystify the intricate mechanisms at play. Bacteria exhibit morphological differentiation associated with different species. Based on the difference in size or shape of microorganisms, size fractionation by filters with various pore sizes can be used to separate them. In this study, we used polyvinylidene difluoride filters with pore sizes of 300, 120, 80, 40, 20, 8, 6, 2.1, and 0.6 μm. Bacterial suspensions were successively passed through these filters for the analysis of microbial population distribution using 16S rRNA gene sequences. We found that bacteria from the different pore sizes were clustered into four branches (> 120 μm, 40-120 μm, 6-20 μm, 20-40 μm, and < 0.6 μm), indicating that size fractionation had effects on enriching specific groups but could not effectively separate dominant groups by cell size alone. The species of unclassified Flavobacterium, unclassified Chryseobacterium, unclassified Delftia, Methylotenera mobilis, unclassified Caulobacteraceae, unclassified Oligella, unclassified Sphingomonas, unclassified Stenotrophomonas, unclassified Shuttleworthia, unclassified Sutterella, unclassified Alphaproteobacteria, and unclassified SR1 can be efficiently enriched or separated by size fractionation. In this study, we investigated the diversity of sorted bacteria populations in the rumen for preliminary investigations of the relationship between the size and classification of rumen bacteria that have the potential to improve our ability to isolate and culture bacteria from the rumen in the future.

Constraining activity and growth substrate of fungal decomposers via assimilation patterns of inorganic carbon and water into lipid biomarkers.

Fungi are among the few organisms on the planet that can metabolize recalcitrant carbon (C) but are also known to access recently produced plant photosynthate. Therefore, improved quantification of growth and substrate utilization by different fungal ecotypes will help to define the rates and controls of fungal production, the cycling of soil organic matter, and thus the C storage and CO2 buffering capacity in soil ecosystems. This pure-culture study of fungal isolates combined a dual stable isotope probing (SIP) approach, together with rapid analysis by tandem pyrolysis-gas chromatography-isotope ratio mass spectrometry to determine the patterns of water-derived hydrogen (H) and inorganic C assimilated into lipid biomarkers of heterotrophic fungi as a function of C substrate. The water H assimilation factor (αW) and the inorganic C assimilation into C18:2 fatty acid isolated from five fungal species growing on glucose was lower (0.62% ± 0.01% and 4.7% ± 1.6%, respectively) than for species grown on glutamic acid (0.90% ± 0.02% and 7.4% ± 3.7%, respectively). Furthermore, the assimilation ratio (RIC/αW) for growth on glucose and glutamic acid can distinguish between these two metabolic modes. This dual-SIP assay thus delivers estimates of fungal activity and may help to delineate the predominant substrates that are respired among a matrix of compounds found in natural environments.IMPORTANCEFungal decomposers play important roles in food webs and nutrient cycling because they can feed on both labile and more recalcitrant forms of carbon. This study developed and applied a dual stable isotope assay (13C-dissolved inorganic carbon/2H) to improve the investigation of fungal activity in the environment. By determining the incorporation patterns of hydrogen and carbon into fungal lipids, this assay delivers estimates of fungal activity and the different metabolic pathways that they employ in ecological and environmental systems.

Elucidation of the complete degradation mechanism of N,N-dimethylformamide (DMF) and substrate preference within a synthetic bacterial consortium (DMFsyn) formed via a “top-down” strategy

The challenge posed by the chemical stability of N,N-dimethylformamide (DMF) renders its biological treatment a complex endeavor. Despite the isolation and characterization of numerous DMF-degrading bacterial strains, their limited adaptability to diverse environments has resulted in suboptimal efficacy in the treatment of actual DMF-containing wastewater. This research aims to address this predicament by employing a “top-down” approach to engineer a synthetic bacterial community termed DMFsyn. The mineralization of 0.5 % (v/v) DMF (∼4725 mg L−1) was efficiently carried out by DMFsyn within 4 days. Notably, robust DMF degradation capabilities across a broad spectrum of environmental conditions were observed. In scenarios where N,N-dimethylacetamide (DMAC) and N-methylpyrrolidone (NMP) coexisted with DMF, degradation followed a sequential pattern: NMP > DMAC > DMF. Through 16S rRNA gene sequencing, and metagenomic analysis, potential functional genes and species responsible for DMF degradation were unveiled. The active DMF degraders in DMFsyn, including Paracoccus aminovorans bin8, Hyphomicrobium sulfonivorans bin2, Hyphomicrobium zavarzinii bin0, Paracoccus zhejiangensis bin23, and Aquamicrobium lusatiense bin4, were substantiated by metaproteomic analysis. Furthermore, another DMF-mineralizing bacterium Aminobacter niigataensis DMFA1 was isolated from DMFsyn. Molecular dynamics simulations indicated that the preference for DMAC over DMF at the community level is dictated by the substrate specificity of DMFases from Sphingosinicella microcystinivorans bin6. By harnessing a multi-omics approach, conducting pure culture studies, and employing molecular simulations, an intricate mechanism governing DMF degradation and substrate preference within the DMFsyn was elucidated.

Fate of Shiga Toxin-Producing Escherichia coli (STEC) and Salmonella during Kosher Processing of Fresh Beef

Traditional kosher meat processing involves the following steps after slaughtering: soaking with water to remove blood, salting to help draw out more blood, and rinsing to remove salt. However, the impact of the salt used on foodborne pathogens and beef quality is not well understood. The objectives of the current study were to determine the effectiveness of salt in reducing pathogens in a pure culture model, on surfaces of inoculated fresh beef during kosher processing, and the effect of salt on beef quality. The pure culture studies indicated that the reduction of E. coli O157:H7, non-O157 STEC, and Salmonella increased with increasing salt concentrations. With salt concentrations from 3 to 13%, salt reduced E. coli O157:H7, non-O157 STEC, and Salmonella ranging from 0.49 to 1.61 log CFU/mL. For kosher processing, the water-soaking step did not reduce pathogenic and other bacteria on the surface of fresh beef. Salting and rinsing steps reduced non-O157 STEC, E. coli O157:H7, and Salmonella ranging from 0.83 to 1.42 log CFU/cm2, and reduced Enterobacteriaceae, coliforms, and aerobic bacteria by 1.04, 0.95, and 0.70 log CFU/cm2, respectively. The salting process for kosher beef resulted in reducing pathogens on the surface of fresh beef, color changes, increased salt residues, and increased lipid oxidation on the final products.

Potential of Indigenous Strains Isolated from the Wastewater Treatment Plant of a Crude Oil Refinery

Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures' and a strain mixture's ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants.

Effects of Cashew Nut Shell Liquid on Hindgut Fermentation and Microbiota of Chickens

Cashew nut shell liquid (CNSL), a feed additive for chickens, was evaluated for its influence on the hindgut environment by determining fermentation and bacterial profiles using cecal contents, fecal slurry and pure cultures. A farm-scale study showed that CNSL feeding to broiler chickens from 0 to 42 days of age improved body weight gain and lowered mortality. Cecal levels of short chain fatty acids increased with CNSL feeding, while ammonia and indole levels decreased. Feeding CNSL decreased the relative abundance of cecal bacteria belonging to some clostridial groups and Ruminococcaceae. In particular, Clostridium perfringens was undetectable following CNSL feeding. A pure culture study showed that CNSL (≥ 6.25 μg/ml) inhibited C. perfringens growth, accompanied by cell surface disruption based on electron microscopic observation. Fermentation profiles of slurry cultures prepared from feces of chickens were altered by CNSL supplementation toward less ammonia production. The lowered ammonia was correlated positively with the abundance of unclassified Lachnospiraceae and unclassified Ruminococcaceae, and negatively with unclassified Enterobacteriaceae and Sutterella. These results suggest that CNSL could exert its beneficial influence on the hindgut health of chickens through impacting the microbiota.

METAGENOMICS: DNA SEQUENCING OF UNCULTURED MICROORGANISMS

Microbiology has completely transformed in the last 25 years and the realization that most microorganisms cannot be grown in a pure culture resulted in new methods of analyzing genomic diversity. One such method, Metagenomics, refers to the study of microorganisms on the basis of their genomic diversity, acquired directly from environmental samples. It facilitates the study of physiology and ecology of environmental microorganisms through a vast array of sequencing and functional techniques. Over the years, many sequencing techniques like Sangers Sequencing, Shotgun Sequencing, Whole Metagenomic Sequencing and 16s rRNA gene sequencing were used, which revolutionized the portrait of the microbial world. Microbiome profiles of these samples can be generated and analysed through various statistical tools like functional annotations, marker data profiling and biomarker detection which can give a description of community membership, and provide insight into the genetics and biochemistry of the members. The application of metagenomic sequence information will result in better culturing strategies and help link genomic analysis with pure culture studies.

Nanomaterials and environmental antimicrobial resistance: Propagation and inhibition of antibiotic resistance gene flow in the soil-plant system

<p indent="0mm">The propagation of antibiotic resistance genes (ARGs), one of the emerging contaminants threatening global sanitation and health, has called for the necessity to overcome the spread of antimicrobial resistance (AMR). ARGs derived from manure is the main source of AMR in agricultural soil that can be propagated rapidly in soil-plant system and finally into food chain via horizontal gene transfer (HGT), which mainly includes three pathways mediated by mobile genetic elements (MGEs), namely, plasmid-mediated conjugation, extracellular DNA-mediated transformation, and phage- mediated transduction. The massive production and wide application of engineered nanomaterials (ENMs) and micro(nano) plastics have resulted in increasing concentrations of ENMs and micro(nano) plastics in the environment, which will eventually enter the soil and lead to migration and propagation of ARGs in soil-plant system. Bacterial pure culture studies reported that ENMs can exacerbate the dissemination of ARGs via changing intracellular reactive oxygen species (ROS), cell membrane permeability, and expression of genes related to conjugation. Moreover, ENMs and micro(nano) plastics in soil can change the soil antibiotic resistome and plant root morphology, structure and root exudates, which may affect the migration of ARB and ARGs from the rhizosphere to plants. The interactions between ENMs/micro(nano) plastics and ARGs might drive the development of multidrug resistance in soil-plant system. Although research targeting the effects of ENMs/micro(nano) plastics on the fate of ARGs is growing, an overview of biological impact and related mechanism is somehow lacking. In this review article, we systematically reviewed the interaction between ENMs/micro(nano) plastics and ARGs, especially in soil-plant system and attempted to explore the possibilities of nanotechnology to inhibit the transfer of antibiotic resistance gene flow. This review mainly covers: (1) Molecular mechanisms of ENMs and micro(nano) plastics regulating ARGs propagation. ENMs (i.e., Ag ENMs, CuO ENMs, TiO₂/Ag/GO ENMs and nano-graphene oxide) can promote ARGs propagation by accumulating intracellular reactive oxygen species (ROS), increasing cell membrane permeability and up-regulating of conjugation-related gene expression. However, CeO₂ ENMs and Fe₂O₃@MoS₂ ENMs have the potential to inhibit the propagation of ARGs via ROS elimination and down-regulating expression of HGT-related genes. (2) Influence of ENMs/micro(nano) plastics on ARGs in soil-plant system. ENMs/micro(nano) plastics can alter soil bacterial community and affect plant growth which will likely reduce the horizontal transfer of ARGs in soil by inhibiting the growth of soil microorganisms, reducing the abundance and diversity of ARB in soil, or changing the amount and composition of root exudates. (3) Application of nanotechnology on inhibiting antibiotic resistance gene flow. The regulatory mechanisms of nanotechnology on ARGs can be classified as: Inhibition of HGT, change of bacterial community composition, adsorption/degradation on ARGs and antimicrobial performance. Nanotechnology is promising for eliminating ARGs with high accuracy while its high cost and instability remain to be solved. For future study, more attention should be paid on the management of antibiotics, ARB and ARGs and the establishment of AMR risk assessment system to comprehensively assess the potential risk of AMR propagation via soil-plant-human pathways. Besides, the propagation of ARGs regulated by ENMs might be a challenge to distinguish and balance the advantages and disadvantages of ENMs in soil-plant system. Thus, it is urgent to comprehensively and systematically assess the environmental behavior and ecological risks of ENMs and micro(nano) plastics, contributing to the safe and efficient nano-based reduction of AMR.

Copper availability governs nitrous oxide accumulation in wetland soils and stream sediments

Denitrification is microbially-mediated through enzymes containing metal cofactors. Laboratory studies of pure cultures have highlighted that the availability of Cu, required for the multicopper enzyme nitrous oxide reductase, can limit N2O reduction. However, in natural aquatic systems, such as wetlands and hyporheic zones in stream beds, the role of Cu in controlling denitrification remains incompletely understood. In this study, we collected soils and sediments from three natural environments -- riparian wetlands, marsh wetlands, and a stream -- to investigate their nitrogen species transformation activity at background Cu levels and different supplemented Cu loadings. All of the systems contained solid-phase associated Cu below or around geological levels (40–280 nmol g−1) and exhibited low dissolved Cu (3–50 nM), which made them appropriate sites for evaluating the effect of limited Cu availability on denitrification. In laboratory incubation experiments, high concentrations of N2O accumulated in all microcosms lacking Cu amendment except for one stream sediment sample. With Cu added to provide dissolved concentrations at trace levels (10–300 nM), the reduction rate of N2O to N2 in the wetland soils and stream sediments was enhanced. A kinetic model could account for the trends in nitrogen species by combining the reactions for microbial reduction of NO3− to NO2−/N2O/N2 and abiotic reduction of NO2− to N2. The model revealed that the rate of N2O to N2 conversion increased significantly in the presence of Cu. For riparian wetland soils and stream sediments, the kinetic model also suggested that overall denitrification is driven by abiotic reduction of NO2− in the presence of inorganic electron donors. This study demonstrated that natural aquatic systems containing Cu at concentrations less than or equal to crustal abundances may display incomplete reduction of N2O to N2 that would cause N2O accumulation and release to the atmosphere.

Sensitivity of vaginal and mammary bacterial microflora of sows from patients with postpartum dysgalactic syndrome to antibacterial drugs

Purpose: Investigation of the sensitivity of conditionally pathogenic and pathogenic causative agents of postpartum disgalacting syndrome isolated from the pathological discharge of the vagina and the secretion of the mammary glands of patients with sorts to the most common antibacterial drugs.Materials and methods. The fence of the biological material was carried out within 2-3 days after supporting in sows of different ages and parity with the clinical manifestation of postpartum disgalacting syndrome from June to August 2021. In sows, the purse was taken in a mosper, milk, discharge from the vagina for the purpose of bacteriological research.Samples of vaginal wasches were sent in a special transportation environment of Ames. Samples of colostrum and milk (3-5 ml) were gained in sterile test tubes in compliance with the rules of antiseptics (the mammary glands were laid with warm water and 70% ethyl alcohol were treated). For the allocation and study of pure cultures of microorganisms from the above biomaterials produced crops on various nutrient media.The material brought to the laboratory was studied as follows: from the transport medium was carried out primary sowing on triptica-soybean agar, tryptichase-soybean broth, triptichase-soy agar with the addition of 5% of the defibrous blood of the ram; Samples were incubated in aerobic conditions at 37; The growth was taken into account after 24 hours. Then, pure cultures were isolated for the study of the cultural and morphological properties of the microorganisms obtained.The primary identification of the strains of microorganisms was carried out using the Microflex® LRF Bruker Maldi Biotyper system. The accuracy of the results obtained was confirmed by classical microbiological methods based on morphological, cultural and biochemical signs of microorganisms.The resistance of the isolated and identified pure crops to antibiotics was determined by diffusion in agar. In the study, the "advanced set of disks to estimate the antibiotic sensitivity of enterobacteria was used.Results. Inflammatory processes in the reproductive path of sows with postpartum diskalactic syndrome are caused by predominant gram-negative microorganisms, in lactic glands - associations of gram-positive and gram-negative microflora. The main conditionally pathogenic and pathogenic pathogens of endometritis and / or mastitis associated with postpartum diskalactic syndrome are the microorganisms of Escherichia, Enterobacter, Klebsiella, Actinobacillus, Rothia, Weisella, Pseudomonas, Proteus, Enterococcus, Streptococcus and Staphylococcus. It has been established that the overwhelming majority of microorganisms are sensitive to cephalosporine antibiotics: cefepim, zefisim, cefotaxim, ceftazidim, ceftriaxone, ceftinibuthen, cefuroxime.Conclusion. With respect to a large number of the most frequently used antibacterial drugs on this pig-breeding enterprise, high resistance is observed in microorganisms. Treatment of postpartum diskalactic syndrome sowers using antibacterial drugs is recommended to be carried out taking into account sensitivity to them allocated conditional and pathogenic microorganisms.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH4) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NOx) on methanogenic activity are known from pure culture studies, the role of NOx in the methane cycling of peatlands remains unexplored. Here, we investigated the CH4 content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NOx and nitrous oxide (N2O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and 13C enrichment in dissolved inorganic carbon and CH4 pools, which are primarily contingent on H2-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NOx cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NOx. Experiments testing the interaction of NOx species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N2O (complete inhibition), which would act as an unaccounted CH4 control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH4 fluxes.

Biofouling control: the impact of biofilm dispersal and membrane flushing

Pure culture studies have shown that biofilm dispersal can be triggered if the nutrient supply is discontinued by stopping the flow. Stimulating biofilm dispersal in this manner would provide a sustainable manner to control unwanted biofilm growth in industrial settings, for instance on synthetic membranes used to purify water. The response of multispecies biofilms to nutrient limitation has not been thoroughly studied. To assess biomass dispersal during nutrient limitation it is common practise to flush the biofilm after a stop-period. Hence, flow-stop-induced biomass removal could occur as a response to nutrient limitation followed by mechanical removal due to biofilm flushing (e.g. biofilm detachment). Here, we investigated the feasibility to reduce membrane biofouling by stopping the flow and flushing the membrane. Using a membrane fouling simulator, biomass removal from synthetic membranes after different stop-periods was determined, as well as biomass removal at different cross flow velocities. Biomass removal from membrane surfaces depended on the nutrient limiting period and on the flow velocity during the biofilm flush. When flushed at a low flow velocity (0.1 m.s−1), the duration of the stop-period had a large effect on the biomass removal rate, but when the flow velocity was increased to 0.2 m.s−1, the length of the stop period became less considerable. The flow velocity during membrane flushing has an effect on the bacterial community that colonized the membranes afterwards. Repetition of the stop-period and biofilm flushing after three repetitive biofouling cycles led to a stable bacterial community. The increase in bacterial community stability coincided with a decrease in cleaning effectivity to restore membrane performance. This shows that membrane cleaning comes at the costs of a more stable bacterial community that is increasingly difficult to remove.

Interaction of Soil Microbes with Organoclays and their Impact on the Immobilization of Hg under Aerobic Conditions

Immobilization of mercury (Hg) leaching from bank soils of East Fork Poplar Creek (EFPC) is considered part of remediation strategies to mitigate the amount of Hg entering the creek. Different approaches are currently being evaluated, such as utilizing engineered sorbents to immobilize Hg species in EFPC bank soils. However, the influence of environmental microbes on the immobilization of Hg by sorbents is unknown. Organocation-modified phyllosilicate clay minerals (organoclays) are widely used as sorbents for the immobilization of contaminants. This study evaluates the interactions of Serratia marcescens and Burkholderia thailandensis with the sorbent Organoclay PM-199 and their impact on the immobilization of Hg under aerobic conditions. We evaluated the competitive binding of Hg between sorbents and selected microorganisms in a series of pure culture studies using bacterial strains identified in EFPC bank soil samples. Our results suggest that Hg sorption by Organoclay PM-199 is not significantly impacted by common soil bacteria present in EFPC, specifically Serratia marcescens and Burkholderia thailandensis, which are known to form biofilms. These findings suggest that sorbent amendments are an effective strategy for the remediation of Hg contamination in natural ecosystems.

Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics.

Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.

Biogeochemistry and microbiology of high Arctic marine sediment ecosystems—Case study of Svalbard fjords

AbstractFjord ecosystems of the high Arctic are distinct from fjords of temperate latitudes due to the influence of glaciers, icebergs, sea ice, and the permanently low temperatures. The sediment microbiology and biogeochemical processes were analyzed during an international research program with multiple field studies in Svalbard, situated between the Barents Sea and the Arctic Ocean. We here describe the physical and geochemical setting and the predominant microbiological processes in several fjords. Physiological studies of sediments and pure cultures show how the predominantly psychrophilic bacteria are adapted to the near‐zero temperature. The microbial communities include bacteria responsible for organic matter hydrolytic degradation, fermentation, and terminal oxidation to CO2. These processes drive the cycling of carbon, sulfur, iron, and manganese. The balance between the dominant sediment microbial processes changes along transects out through the fjords, reflecting the varying impact of the glacier‐derived rock flour, rich in metal oxides at the head, and the plankton‐derived, labile, marine organic matter at the mouth. Due to accelerated warming of Arctic ecosystems, glaciers are retreating with impacts on the physical, chemical, and biological functioning of the fjord sediment ecosystems.

Utilization of xylan-type polysaccharides in co-culture fermentations of Bifidobacterium and Bacteroides species

Although most members of the genus Bifidobacterium are unable to utilize xylan as a carbon source, the growth of these species can be induced by this polysaccharide in the gut environment. This indicates a requirement for an association between Bifidobacterium species and some other members of gut microbiota. In this study, the role of cross-feeding between Bifidobacterium and Bacteroides species in the bifidogenic effect of xylan was investigated using in-vitro pure and co-culture fermentations. The pure culture studies showed that among the Bifidobacterium species tested, only Bifidobacterium animalis subsp. lactis was able to utilize xylooligosaccharides. The co-culture of this strain with Bacteroides species enabled it to grow in the presence of xylan. These results suggest that the ability of Bacteroides species to hydrolyze xylan could allow the proliferation of specific Bifidobacterium species in the gut through substrate cross-feeding.

Medium-Chain Fatty Acid Synthesis by "Candidatus Weimeria bifida" gen. nov., sp. nov., and "Candidatus Pseudoramibacter fermentans" sp. nov.

Chain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse β-oxidation pathway has been identified as a key metabolic function to elongate the intermediate products of fermentation to MCFA. Here, we describe two uncultured chain-elongating microorganisms that were enriched in an anaerobic microbiome transforming the residues from a lignocellulosic biorefining process. Based on a multi-omic analysis, we describe "Candidatus Weimeria bifida" gen. nov., sp. nov., and "Candidatus Pseudoramibacter fermentans" sp. nov., both predicted to produce MCFA but using different substrates. The analysis of a time series metatranscriptomic data set suggests that "Ca Weimeria bifida" is an effective xylose utilizer since both the pentose phosphate pathway and the bifid shunt are active. Furthermore, the metatranscriptomic data suggest that energy conservation during MCFA production in this organism is essential and occurs via the creation of an ion motive force using both the RNF complex and an energy-conserving hydrogenase. For "Ca Pseudoramibacter fermentans," predicted to produce MCFA from lactate, the metatranscriptomic analysis reveals the activity of an electron-confurcating lactate dehydrogenase, energy conservation via the RNF complex, H2 production for redox balance, and glycerol utilization. A thermodynamic analysis also suggests the possibility of glycerol being a substrate for MCFA production by "Ca Pseudoramibacter fermentans." In total, this work reveals unknown characteristics of MCFA production in two novel organisms.IMPORTANCE Chain elongation by medium-chain fatty acid (MCFA)-producing microbiomes offers an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation are only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure-culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms.