Magnetite-driven Bio-Fenton degradation of chloroacetanilide herbicides by a newly isolated hydrogen peroxide producing bacterium Desemzia sp. strain C1

The efficiency of the Fenton reaction is markedly contingent upon the operational pH related to iron solubility. Therefore, a heterogeneous Fenton reaction has been developed to function at neutral pH. In the present study, the Bio-Fenton reaction was carried out using magnetite (Fe(II)Fe(III)2O4) and H2O2 generated by a newly isolated H2O2-producing bacterium, Desemzia sp. strain C1 at pH 6.8 to degrade chloroacetanilide herbicides. The optimal conditions for an efficient Bio-Fenton reaction were 10 mM of lactate, 0.5% (w/v) of magnetite, and resting-cells (O.D.600 = 1) of strain C1. During the Bio-Fenton reaction, 1.8-2.0 mM of H2O2 was generated by strain C1 and promptly consumed by the Fenton reaction with magnetite, maintaining stable pH conditions. Approximately, 40-50% of the herbicides underwent oxidation through non-specific reactions of •OH, leading to dealkylation, dechlorination, and hydroxylation via hydrogen atom abstraction. These findings will contribute to advancing the Bio-Fenton system for non-specific oxidative degradation of diverse organic pollutants under in-situ environmental conditions with bacteria producing high amount of H2O2 and magnetite under a neutral pH condition.

Fungal biodegradation of poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based commercial bio-plastic film at ambient conditions

Microbial biodegradation of commercially available poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based bio-plastic has been pursued at high temperatures exceeding 55 °C. Herein, we first reported three newly isolated fungal strains from farmland soil samples of Republic of Korea namely, Pyrenochaetopsis sp. strain K2, Staphylotrichum sp. S2-1, and Humicola sp. strain S2-3 were capable of degrading a commercial bio-plastic film with degradation rates of 9.5, 8.6, and 12.2%, respectively after 3 months incubation at ambient conditions. Scanning electron microscopy (SEM) analyses showed that bio-plastic film was extensively fragmented with severe cracking on the surface structure after incubation with isolated fungal strains. X-ray diffraction (XRD) analysis also revealed that high crystallinity of the commercial bio-plastic film was significantly decreased after degradation by fungal strains. Liquid chromatography-mass spectrometry (LC-MS) analyses of the fungal culture supernatants containing the bio-plastic film showed the peaks for adipic acid, terephthalic acid (TPA), and terephthalate-butylene (TB) as major metabolites, suggesting cleavage of ester bonds and accumulation of TPA. Furthermore, a consortium of fungal strain K2 with TPA degrading bacterium Pigmentiphaga sp. strain P3-2 isolated from the same sampling site exhibited faster degradation rate of the bio-plastic film within 1 month of incubation with achieving complete biodegradation of accumulated TPA. We assume that the extracellular lipase activity presented in the fungal cultures could hydrolyze the ester bonds of PBAT component of bio-plastic film. Taken together, the fungal and bacterial consortium investigated herein could be beneficial for efficient biodegradation of the commercial bio-plastic film at ambient conditions.

Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants

Root-nodule nitrogen-fixing bacteria are known for being specific to particular legumes. This study isolated the endophytic root-nodule bacteria from the nodules of legumes and examined them to determine whether they could be used to promote the formation of nodules in other legumes. Forty-six isolates were collected from five leguminous plants and screened for housekeeping (16S rRNA), nitrogen fixation (nifH), and nodulation (nodC) genes. Based on the 16S rRNA gene sequencing and phylogenetic analysis, the bacterial isolates WC15, WC16, WC24, and GM5 were identified as Rhizobium, Sphingomonas, Methylobacterium, and Bradyrhizobium, respectively. The four isolates were found to have the nifH gene, and the study confirmed that one isolate (GM5) had both the nifH and nodC genes. The Salkowski method was used to measure the isolated bacteria for their capacity to produce phytohormone indole acetic acid (IAA). Additional experiments were performed to examine the effect of the isolated bacteria on root morphology and nodulation. Among the four tested isolates, both WC24 and GM5 induced nodulation in Glycine max. The gene expression studies revealed that GM5 had a higher expression of the nifH gene. The existence and expression of the nitrogen-fixing genes implied that the tested strain had the ability to fix the atmospheric nitrogen. These findings demonstrated that a nitrogen-fixing bacterium, Methylobacterium (WC24), isolated from a Trifolium repens, induced the formation of root nodules in non-host leguminous plants (Glycine max). This suggested the potential application of these rhizobia as biofertilizer. Further studies are required to verify the N2-fixing efficiency of the isolates.

Prevalence and Characterization of CRISPR Locus 2.1 Spacers in Escherichia coli Isolates Obtained from Feces of Animals and Humans

The clustered regularly interspaced short palindromic repeat (CRISPR) has been studied as an immune system in prokaryotes for the survival of bacteriophages. The CRISPR system in prokaryotes records the invasion of bacteriophages or other genetic materials in CRISPR loci. Accordingly, CRISPR loci can reveal a history of infection records of bacteriophages and other genetic materials. Therefore, identification of the CRISPR array may help trace the events that bacteria have undergone. In this study, we characterized and identified the spacers of the CRISPR loci in Escherichia coli isolates obtained from the feces of animals and humans. Most CRISPR spacers were found to stem from phages. Although we did not find any patterns in CRISPR spacers according to sources, our results showed that phage-derived spacers mainly originated from the families Inoviridae, Myoviridae, Podoviridae, and Siphoviridae and the order Caudovirales, whereas plasmid-derived CRISPR spacers were mainly from the Enterobacteriaceae family. In addition, it is worth noting that the isolates from each animal and human source harbored source-specific spacers. Considering that some of these taxa are likely found in the gut of mammalian animals, CRISPR spacers identified in these E. coli isolates were likely derived from the bacteriophageome and microbiome in closed gut environments. Although the bacteriophageome database limits the characterization of CRISPR arrays, the present study showed that some spacers were specifically found in both animal and human sources. Thus, this finding may suggest the possible use of E. coli CRISPR spacers as a microbial source tracking tool. IMPORTANCE We characterized spacers of CRISPR locus 2.1 in E. coli isolates obtained from the feces of various sources. Phage-derived CRISPR spacers are mainly acquired from the order Caudovirales, and plasmid-derived CRISPR spacers are mostly from the Enterobacteriaceae family. This is thought to reflect the microbiome and phageome of the gut environment of the sources. Hence, spacers may help track the encounter of bacterial cells with bacterial cells, viruses, or other genetic materials. Interestingly, source-specific spacers are also observed. The identification of source-specific spacers is thought to help develop the methodology of microbial source tracking and understanding the interactions between viruses and bacteria. However, very few spacers have been uncovered to track where they originate. The accumulation of genome sequences can help identify the hosts of spacers and can be applied for microbial source tracking.

Highly effective biosorption capacity of Cladosporium sp. strain F1 to lead phosphate mineral and perovskite solar cell PbI2

Fungus Cladosporium sp. strain F1 showed highly effective biosorption capacity to lead phosphate mineral and perovskite solar cells lead iodide compared to other fungi Aspergillus niger VKMF-1119 and Mucor ramannianus R-56. Scanning electron microscopy and transmission electron microscopy analyses shows that Cladosporium sp. strain F1, which previously showed high biosorption capacity to uranium phosphate nanorods and nanoplates, can accumulate lead phosphate mineral and lead iodide on the fungal hyphae surface in large amounts under a wide range of pH conditions, while A. niger VKMF-1119 and M. ramannianus R-56 adsorbed small amounts of minerals. After biosorption of lead iodide minerals on Cladosporium sp. strain F1, aqueous dimethyl sulfoxide (50%) at pH 2 (70 °C) released the mineral more than 99%. Based on the fungal surface analyses, hydrophobic properties on the surfaces of Cladosporium sp. strain F1 could affect the higher biosorption capacity of strain F1 to lead phosphate mineral and lead iodide as compared to other tested fungi. Cladosporium sp. strain F1 may be the novel biosorbents to remediate the phosphate rich environment and to recover lead from perovskite solar cells lead iodide.

Resistome Study in Aquatic Environments

Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs (e.g. strA, sul1, int1) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.

Dynamics of Genotypic and Phenotypic Antibiotic Resistance in a Conventional Wastewater Treatment Plant in 2 Years

Wastewater treatment plants (WWTPs) are considered a sink and a source of antibiotic resistance. In this study, we applied both culture-dependent and SmartChip-based culture-independent approaches for the investigation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) at Jungnang (JN), located in the Han River, Seoul, South Korea, for 2 years, i.e., 2017 and 2018. The JN WWTP reduced the diversity and abundance of ARB and ARGs but was not sufficient for removing them all. Interestingly, through the treatment process in the JN WWTP, the composition of diverse multidrug-resistant (MDR) bacteria was concentrated mainly into some genera of the Gammaproteobacteria class (Citrobacter, Escherichia-Shigella, and Stenotrophomonas), which could be key carriages to spread ARGs into the environments. In addition, SmartChip analyses showed that the relative abundance and the number of ARGs were significantly decreased from the influents to the effluents in both 2017 and 2018. SmartChip analyses for 2 years also allowed to notify the core ARGs in the influents and the effluents with the presence of clinically relevant core ARGs, such as vanC, bla_OXA, and bla_NDM, which persisted in the treatment process. Considering diverse bacterial mechanisms for exchanging and transferring ARGs, the occurrence of MDR bacteria and core ARGs could be a source for the blooming of the antibiotic resistome in the WWTP and nearby environments.

Non-specific degradation of chloroacetanilide herbicides by glucose oxidase supported Bio-Fenton reaction

Bio-Fenton reaction supported by glucose oxidase (GOx) for producing H₂O₂ was applied to degrade persistent chloroacetanilide herbicides in the presence of Fe (Ⅲ)-citrate at pH 5.5. There were pH decrease to 4.3, the production of 8 mM H₂O₂ and simultaneous consumption to produce •OH radicals which non-specifically degraded the herbicides. The degradation rates followed the order acetochlor ≈ alachlor ≈ metolachlor > propachlor ≈ butachlor with the degradation percent of 72.8%, 73.4%, 74.0%, 47.4%, and 43.8%, respectively. During the Bio-Fenton degradation, alachlor was dechlorinated and filtered into catechol via the production of intermediates formed through a series of hydrogen atom abstraction and hydrogen oxide radical addition reactions. The current Bio-Fenton reaction leading to the production of •OH radicals could be applied for non-specific oxidative degradation to various persistent organic pollutants under in-situ environmental conditions, considering diverse microbial metabolic systems able to continuously supply H₂O₂ with ubiquitous Fe(II) and Fe(III) and citrate.

Degradation of sulfonated polyethylene by a bio-photo-fenton approach using glucose oxidase immobilized on titanium dioxide

Polyethylene (PE) plastics are highly recalcitrant and resistant to photo-oxidative degradation due to its chemically inert backbone structure. We applied two novel reactions such as, Bio-Fenton reaction using glucose oxidase (GOx) enzyme alone and Bio-Photo-Fenton reaction using GOx immobilized on TiO₂ nanoparticles (TiO₂-GOx) under UV radiation, for (bio)degradation of pre-activated PE with sulfonation (SPE). From both the reactions, GC-MS analyses identified small organic acids such as, acetic acid and butanoic acid as a major metabolites released from SPE. In the presence of UV radiation, 21 fold and 17 fold higher amounts of acetic acid (4.78 mM) and butanoic acid (0.17 mM) were released from SPE after 6 h of reaction using TiO₂-GOx than free GOx, which released 0.22 mM and 0.01 mM of acetic acid and butanoic acid, respectively. Our results suggest that (bio)degradation and valorization of naturally weathered and oxidized PE using combined reactions of biochemistry, photochemistry and Fenton chemistry could be possible.

Antibacterial effect of copper nanoparticles produced in a Shewanella-supported non-external circuit bioelectrical system on bacterial plant pathogens

The inhibition of copper nanoparticles produced in a nec_BES to plant pathogens was investigated in this study.

Higher abundance of core antimicrobial resistant genes in effluent from wastewater treatment plants

Wastewater treatment plants (WWTPs) receive sewage water from a variety of sources, including livestock farms, hospitals, industries, and households, that contain antimicrobial resistant bacteria (ARB) and antimicrobial resistant genes (ARGs). Current treatment technologies are unable to completely remove ARB and ARGs, which are eventually released into the aquatic environment. This study focused on the core resistome of urban WWTPs that are persistent through wastewater treatment processes. We adopted the Hiseq-based metagenomic sequencing approach to identify the core resistome, their genetic context, and pathogenic potential of core ARGs in the influent (IN) and effluent (EF) samples of 12 urban WWTPs in South Korea. In this study, the abundance of ARGs ranged from 0.32 to 3.5 copies of ARGs per copy of the 16S rRNA gene, where the IN samples were relatively higher than the EF samples, especially for the macrolide-lincosamide-streptogramin (MLS)- and tetracycline- resistant genes. On the other hand, there were 43 core ARGs sharing up to 90% of the total, among which the relative abundance of sul1, APH(3'')-lb, and RbpA was higher in EF than in IN (p < 0.05). Moreover, tetracycline and sulfonamide-related core ARGs in both EF and IN were significantly more abundant on plasmids than on chromosomes (p < 0.05). We also found that the majority of core ARGs were carried by opportunistic pathogens such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa in both IN and EF. In addition, phages were the only mobile elements whose abundance correlated with that of core ARGs in EF, suggesting that transduction may play a major role in disseminating ARGs in the receiving water environment of the urban WWTP. The persistent release of core ARGs with pathogenic potential into environmental water is of immediate concern. The mobility of ARGs and ARBs in the environment is a major public health concern. These results should be taken into consideration when developing policy to mitigate environmental dissemination of ARG by WWTPs.

Direct and Indirect Reduction of Cr(VI) by Fermentative Fe(III)-Reducing Cellulomonas sp. Strain Cellu-2a

Hexavalent chromium (Cr(VI)) is recognized to be carcinogenic and toxic and registered as a contaminant in many drinking water regulations. It occurs naturally and is also produced by industrial processes. The reduction of Cr(VI) to Cr(III) has been a central topic for chromium remediation since Cr(III) is less toxic and less mobile. In this study, fermentative Fe(III)-reducing bacterial strains (Cellu-2a, Cellu-5a, and Cellu-5b) were isolated from a groundwater sample and were phylogenetically related to species of Cellulomonas by 16S rRNA gene analysis. One selected strain, Cellu-2a showed its capacity of reduction of both soluble iron (ferric citrate) and solid iron (hydrous ferric oxide, HFO), as well as aqueous Cr(VI). The strain Cellu-2a was able to reduce 15 μM Cr(VI) directly with glucose or sucrose as a sole carbon source under the anaerobic condition and indirectly with one of the substrates and HFO in the same incubations. The heterogeneous reduction of Cr(VI) by the surface-associated reduced iron from HFO by Cellu-2a likely assisted the Cr(VI) reduction. Fermentative features such as large-scale cell growth may impose advantages on the application of bacterial Cr(VI) reduction over anaerobic respiratory reduction.

Layers of Uranium Phosphate Nanorods and Nanoplates Encrusted on Fungus Cladosporium sp. Strain F1 Hyphae

The hyphae of Cladosporium sp. strain F1 (CFGR 2020-301-00084) were heavily encrusted with pre-synthesized uranium phosphate minerals under a wide range of pH conditions. SEM and TEM images showed that nanorods and nanoplates of uranium phosphate minerals at pH 4 and 5 and at pH 6, 7, and 8, respectively, were tightly adsorbed along the hyphae of Cladosporium sp. strain F1, while only a few uranium phosphate minerals were observed on the hyphae of Aspergillus niger VKMF 1119. Based on the physical mobility and chemical stability of uranium phosphate minerals under in situ oxidizing environmental conditions, the application of Cladosporium sp. strain F1 has potential as a novel strategy for the remediation of uranium contamination in sediments and aquifers under a wide range of pH conditions where larger amounts of phosphate are present in the environment.

Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water

Environmental dissemination of antimicrobial resistance is a global health problem. Antimicrobial-resistant bacteria and antibiotic-resistant genes (ARGs) are constantly released into the environment through effluents (EFs) from wastewater treatment plants (WWTPs). Thus, requiring a better understanding of the selection and fate of ARGs in wastewater treatment processes. Therefore, we investigated the impacts of urban WWTP EFs on receiving water in the context of their resistomes and mobilomes. We used a HiSeq-based short read metagenomic approach to address the dynamics and diversity of ARGs in WWTP EF as well as the upstream (UP) and downstream (DN) river waters, followed by an investigation of plasmid-mediated ARGs. The abundance of ARGs at each site varied from 7.2 × 10^-2 to 7.4 × 10^-1 ARG copies per 16S rRNA gene copy, and EF samples showed the highest abundance, followed by DN and UP water samples. ARG diversity ranged from 121 to 686 types per site, and EF had the most diverse ARGs. Commonly identified ARGs in the EF and DN samples were clinically important and were absent in UP samples. The abundance of ARGs, mobile genetic elements (MGEs), and plasmid contigs found only in EF and DN were positively correlated with each other, indicating the importance of mobilomes in the dissemination of ARGs in the environment. Moreover, the proportions of plasmid-mediated ARGs was highest in the EF samples, followed by the DN and UP samples. These findings suggest that WWTP EF may act as a driving factor shaping the resistomes and mobilomes of receiving waters. In particular, a higher abundance of plasmid-mediated ARGs in WWTP EF suggests higher transmissibility in the DN environment.

Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea

High level carbapenem and extensively drug resistant (XDR) Escherichia coli strain N7, which produces a variant of New Delhi metallo-β-lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han River, Seoul, South Korea. Phenotypic and genotypic resistances to carbapenem were tested using agar and broth dilution methods, and polymerase chain reaction. Whole-genome sequencing was performed to characterize the genetic structure of strain N7. E. coli strain N7, which harbors the bla NDM-5 gene, showed high level of carbapenem resistance at concentrations of doripenem (512 mg/L) and meropenem (256 mg/L), and XDR to 15 antibiotics. Based on the genomic sequence analysis, two plasmids, a hybrid IncHI2/N-type and an IncX3 type, were present. The former contains a cluster (bla NDM-5-ble MBL -trpF-dsbD) bracketed by multi-insertional sequences, IS3000, ISAba125, IS5, and IS26. The latter carries the following resistance genes: bla CTX-14, aac(3)-IV, aadA1, aadA2, aph(3')-Ia, aph(4)-Ia, sul1, sul2, sul3, dfrA12, fosA3, oqxA, oqxB, mph(A), and floR, and cmlA1. The chromosome, contig3, and contig5 also carry bla CTX-64 and mdf(A), tet(A), and erm(B), tet(M) and aadA22, respectively. Strain N7 also harbors virulence factors such as fimH, flu, ecpABCDE, sfmA, hlyE, and gadA. This study demonstrates the emergence of high level carbapenem resistant XDR E. coli strain N7 containing bla NDM-5 in aquatic environment, Seoul, South Korea. Due to the presence of mobile genetic elements, this strain could horizontally transfer resistance genes, including bla NDM-5 to environmental bacteria. Thus, it is necessary to conduct continuous surveillance for carbapenem resistance in various aquatic environments.

A novel pathway for initial biotransformation of dinitroaniline herbicide butralin from a newly isolated bacterium Sphingopyxis sp. strain HMH

Butralin (N-sec- Butyl-4-tert-butyl-2,6-dinitroaniline) is a highly persistent dinitroaniline herbicide frequently detected in the environment. In this study, butralin-degrading soil bacterium, Sphingopyxis sp. strain HMH was isolated from agricultural soil samples. Based on whole genome sequence analysis of the strain HMH, the gene encoding a nitroreductase NfnB was identified and expressed in Escherichia coli (E. coli), and protein was purified to homogeneity. NfnB is a flavin-nitroreductase, found to be a functional tetramer, composed of subunit molecular mass of 25 kDa. The metabolites from butralin degradation by strain HMH and purified NfnB were identified using ultra performance liquid chromatography high resolution mass spectrometry (UPLC-HRMS), and a novel mechanism of butralin degradation was proposed. NfnB selectively nitro-reduced butralin into N- (sec-Butyl)-4-(tert-butyl)-6-nitrobenzene- 1,2-diamine, followed by formation of 5-(tert-Butyl)-3 -nitrobenzene-1,2-diamine and butanone by N- dealkylation through possible hydroxylation reaction onto the carbon linked amine of the N-(sec-Butyl) moiety. In our study, we could not detect the hydroxylated product 2-(2-Amino-4-tert-butyl-6-nitro- phenylamino)-butan-2-ol) (carbinolamine), instead its Schiff base product (E)-2-(Butan-2-yildeneamino)-5- (tert-butyl)-3-nitroaniline was detected. The release of butanone was further confirmed by derivatization with 2,4- dinitrophenylhydrazine (DNPH) followed by MS analysis. In conclusion, this study explores a novel multi-functional flavin- nitroreductase family enzyme NfnB, catalyzing unique and sequential nitroreduction and N-dealkylation through oxidative hydroxylation of dinitroaniline herbicide butralin.

High genetic diversity of Vibrio parahaemolyticus isolated from tidal water and mud of southern coast of South Korea

A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-polymerase chain reaction (rep-PCR) DNA fingerprinting technique was adapted to examine the genotypic richness and source differentiation of Vibrio parahaemolyticus (n = 1749) isolated from tidal water and mud of southern coast of South Korea. The number of unique genotypes observed from June (163, 51.9%), September (307, 63.9%), December (205, 73.8%) and February (136, 74.7%), indicating a high degree of genetic diversity. Contrary, lower genetic diversity was detected in April (99, 46.8%), including predominant genotypes comprised >30 V. parahaemolyticus isolates. Jackknife analysis indicated that 65.1% tidal water isolates and 87.1% mud isolates were correctly assigned to their source groups. Sixty-nine isolates of pathogenic V. parahaemolyticus were clustered into two groups, separated by sampling month, source of isolation and serogroups. Serotypes O1, O4, O5, O10/O12 and O11 were the dominant serovariants, while serotypes O3/O13 were highly detected in April where there were no pathogenic V. parahaemolyticus isolates. Most of the V. parahaemolyticus isolates were resistant to ampicillin, ceftazidime and sulfamethoxazole. Interestingly, four V. parahaemolyticus isolates resistant to carbepenem did not contain the known carbapenemase-encoding gene, but possess an extended-spectrum β-lactamase blaTEM.

Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an Ecological Shift in Bacterial Assemblages Involved in Phytoplankton-Derived DMSP Degradation

The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.

Biogenic Hematite from Bacteria: Facile Synthesis of Secondary Nanoclusters for Lithium Storage Capacity

Ferrihydrite, or iron(III) (oxyhydr)oxide (Fe(OH)₃), a representative scavenger of environmentally relevant toxic elements, has been repurposed as a low-cost and scalable precursor of well-developed hematite (α-Fe₂O₃) secondary nanoclusters with a hierarchically structured morphology for lithium-ion anode materials. Here, we report that the bacteria Clostridium sp. C8, isolated from a methane-gas-producing consortium, can synthesize self-assembled secondary hematite nanoclusters (∼150 nm) composed of small nanoparticles (∼15 nm) through the molecular structural rearrangement of amorphous ferrihydrite under mild conditions. The biogenic hematite particles, wrapped with graphene oxide reduced in situ by the reducing bacteria Shewanella sp. HN-41 via one-pot synthesis, deliver an excellent reversible capacity of ∼1000 mA h g^-1 after 100 cycles at a current density of 1 A g^-1. Furthermore, the heat-treated hematite/rGO exhibits a capacity of 820 mA h g^-1 at a high current density of 5 A g^-1 and a reversible capacity of up to 1635 mA h g^-1 at a current density of 100 mA g^-1. This study provides an easy, eco-efficient, and scalable microbiological synthetic route to produce hierarchical hematite/rGO secondary nanoclusters with potential as high-performance Li-ion anode materials.

Characterization of a novel thermostable carboxylesterase from thermoalkaliphilic bacterium Bacillus thermocloaceae

A novel thermostable carboxylesterase (Est5250) of thermoalkaliphilic bacterium Bacillus thermocloaceae was heterologously expressed in Escherichia coli and its biochemical properties were investigated. Est5250 showed optimum esterase activity at 60 °C and pH 8.0. The enzyme was highly thermostable at 60 °C, interestingly, the thermostability was enhanced in the presence of Ca²⁺, retaining more than 60% of its original activity after 12 h of pre-incubation. Est5250 was active in the presence of 1% (v/v) of organic solvents and 0.1% (v/v) of non-ionic detergents. The enzyme activity was significantly enhanced up to 167% and 159% in the presence of 2-mercaptoethanol and dithiothreitol, respectively. Est5250 showed high substrate specificity for short-chain p-nitrophenyl-esters. Kinetic constants, K_m and k_cat, for p-nitrophenyl-acetate were 185.8 μM and 186.6 s^-1, respectively. Est5250 showed outstanding thermostability and tolerance to various organic solvents under thermoalkaliphilic conditions, suggesting that it would be a highly suitable biocatalyst for various biotechnological applications. Abbreviations: B. thermocloaceae sp.: Bacillus thermocloaceae; E. coli: Escherichia coli; NP: nitrophenyl; DMSO: dimethyl sulfoxide; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; DMF: dimethyl formamide; EGTA: ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid; CTAB: cetrimonium bromide; PMSF: phenylmethylsulfonyl fluoride; DEPC: diethyl pyrocarbonate; 2-ME: 2-mercaptoethanol; DTT: dithiothreitol.

Biosynthesis of Nanomaterials by Shewanella Species for Application in Lithium Ion Batteries

Nanomaterials exhibit extraordinary properties based on their size, shape, chemical composition, and crystal structure. Owing to their unique properties nanomaterials are preferred over their bulk counterparts for a number of applications. Although conventional physical and chemical routes were established for the massive production of nanomaterials, there are some drawbacks such as environmental burden and high cost that cannot be disregarded. Recently, there has been great interest toward the green synthesis of inorganic nanomaterials. It has been reported that dissimilatory metal reduction by microorganisms is a cost-effective process to remediate toxic organic and inorganic compounds under anaerobic conditions. Particularly, members of the Shewanella genus have been utilized to produce various biogenic nanomaterials with unique micro/nanostructured morphologies through redox transformations as well as to remove harmful metals and metalloids in eco-efficient and environment-friendly methods under ambient conditions. In the present mini-review, we specifically address the active utilization of microbial respiration processes for the synthesis of novel functional biogenic nanomaterials by the members of the Shewanella genus. This biosynthetic method may provide alternative approaches to produce electrode materials for sustainable energy storage applications.

Adsorption and Incorporation of Arsenic to Biogenic Lepidocrocite Formed in the Presence of Ferrous Iron during Denitrification by Paracoccus denitrificans

We demonstrate adsorption and partial incorporation of arsenic, in its soluble form, either as arsenite or arsenate into lepidocrocite (γ-FeOOH), which was formed through nitrite-driven Fe(II) oxidation by Paracoccus denitrificans under nitrate-reducing conditions. Fe and As K-edge XANES and radial distribution functions of Fourier-transformed EXAFS spectra showed that portions of As were found to be incorporated in the biogenic lepidocrocite, in addition to higher portions of adsorbed As. We suggest that denitrifying bacteria such as Paracoccus denitrificans, studied here, could facilitate decrease of aqueous arsenic As(III) and/or As(V) through indirect Fe(II) oxidation to solid phase iron minerals, here as lepidocrocite, by the denitrification product nitrite in the presence of nitrate, ferrous iron, and arsenic, under certain environmental conditions where these materials could be found, such as in As-contaminated paddy soils and wetlands.

Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing

In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

Inactivation efficiency of plasmid-encoded antibiotic resistance genes during water treatment with chlorine, UV, and UV/H2O2

This study assessed the inactivation efficiency of plasmid-encoded antibiotic resistance genes (ARGs) both in extracellular form (e-ARG) and present within Escherichia coli (intracellular form, i-ARG) during water treatment with chlorine, UV (254 nm), and UV/H₂O₂. A quantitative real-time PCR (qPCR) method was used to quantify the ARG damage to amp^R (850 bp) and kan^R (806 bp) amplicons, both of which are located in the pUC4K plasmid. The plate count and flow cytometry methods were also used to determine the bacterial inactivation parameters, such as culturability and membrane damage, respectively. In the first part of the study, the kinetics of E. coli inactivation and ARG damage were determined in phosphate buffered solutions. The ARG damage occurred much more slowly than E. coli inactivation in all cases. To achieve 4-log reduction of ARG concentration at pH 7, the required chlorine exposure and UV fluence were 33-72 (mg × min)/L for chlorine and 50-130 mJ/cm² for UV and UV/H₂O₂. After increasing pH from 7 to 8, the rates of ARG damage decreased for chlorine, while they did not vary for UV and UV/H₂O₂. The i-ARGs mostly showed lower rates of damage compared to the e-ARGs due to the protective roles of cellular components against oxidants and UV. The contribution of OH radicals to i-ARG damage was negligible in UV/H₂O₂ due to significant OH radical scavenging by cellular components. In all cases, the ARG damage rates were similar for amp^R versus kan^R, except for the chlorination of e-ARGs, in which the damage to amp^R occurred faster than that to kan^R. Chlorine and UV dose-dependent ARG inactivation levels determined in a wastewater effluent matrix could be reasonably explained by the kinetic data obtained from the phosphate buffered solutions and the expected oxidant (chlorine and OH radicals) demands by water matrix components. These results can be useful in optimizing chlorine and UV-based disinfection systems to achieve ARG inactivation.

Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea

Objectives

To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains.

Methods

Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river.

Results

Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess bla NDM-9 genes. Antimicrobial susceptibility testing indicated resistance of these strains to aminoglycosides, carbapenems, cephems, folate pathway inhibitors, fosfomycin and penicillins, but susceptibility to fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed that the 108 kb IncFII(Y)-like plasmids carry bla NDM-9 sandwiched between IS 15 for the GJ1 strain, IS 26 for the GJ2 strain, IS 15D1 for the GJ3 strain and IS Vsa3 , and further bracketed by IS 26 and Tn AS3 along with the mercury resistance operon upstream and the class 1 integron composed of gene cassettes of aadA2 , dfrA12 and sul1 downstream. An aph(3')-Ia gene conferring resistance to aminoglycosides is located after the integrons. Chromosomally encoded bla LEN-13 , fosA , aqxA and oqxB genes, as well as plasmid-mediated bla TEM-1B and bla CTX-M-65 encoding ESBL, ant(3')-Ia and mph (A) genes, were also identified.

Conclusions

The findings of the present study provide us with the information that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the environment has raised a health risk alarm as this variant of NDM carries MDR genes with highly transferable mobile genetic elements, increasing the possibility of resistance gene transfer among microorganisms in the environment.

Inference on Paleoclimate Change Using Microbial Habitat Preference in Arctic Holocene Sediments

The present study combines data of microbial assemblages with high-resolution paleoceanographic records from Core GC1 recovered in the Chukchi Sea. For the first time, we have demonstrated that microbial habitat preferences are closely linked to Holocene paleoclimate records, and found geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. In Core GC1, the layer of maximum crenarchaeol concentration was localized surrounding the SMTZ. The vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota (MG-II) were consistent with patterns of the known global SMTZs. MG-II was the most prominent archaeal group, even within the layer of elevated concentrations of crenarchaeol, an archaeal lipid biomarker most commonly used for Marine Group I Thaumarchaeota (MG-I). The distribution of MG-I and MG-II in Core GC1, as opposed to the potential contribution of MG-I to the marine tetraether lipid pool, suggests that the application of glycerol dibiphytanyl glycerol tetraethers (GDGT)-based proxies needs to be carefully considered in the subsurface sediments owing to the many unknowns of crenarchaeol. In conclusion, microbiological profiles integrated with geological records seem to be useful for tracking microbial habitat preference, which reflect climate-triggered changes from the paleodepositional environment.

Synthesis of gold structures by gold-binding peptide governed by concentration of gold ion and peptide

Although biological synthesis methods for the production of gold structures by microorganisms, plant extracts, proteins, and peptide have recently been introduced, there have been few reports pertaining to controlling their size and morphology. The gold ion and peptide concentrations affected on the size and uniformity of gold plates by a gold-binding peptide Midas-11. The higher concentration of gold ions produced a larger size of gold structures reached 125.5 μm, but an increased amount of Midas-11 produced a smaller size of gold platelets and increased the yield percentage of polygonal gold particles rather than platelets. The mechanisms governing factors controlling the production of gold structures were primarily related to nucleation and growth. These results indicate that the synthesis of gold architectures can be controlled by newly isolated and substituted peptides under different reaction conditions.

Bacterial biogeography influenced by shelf-basin exchange in the Arctic surface sediment at the Chukchi Borderland

It has been known that continental shelves around the Arctic Ocean play a major role in the ventilation of the deep basins as a consequence of shelf-basin exchange. In the present study, we found that bacterial assemblage of the surface sediment was different from that of seawater while seawater harboured local bacterial assemblages in response to the Arctic hydrography. This finding suggests that the Arctic seafloor sediments may have distinctive bacterial biogeography. Moreover, the distribution of bacterial assemblages and physicochemical properties in surface sediments changed gradually from the Arctic continental shelf to deep-sea basin. Based on the results, bacterial biogeography in the Arctic seafloor sediments may be influenced by winnowing and re-deposition of surface sediments through the sediment gravity flow. The present study offers a deeper understanding of shelf convection and its role for the construction of bacterial assemblages in the Arctic Ocean.

Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis

The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass.

Changes in human gut microbiota influenced by probiotic fermented milk ingestion

We investigated the effect of consuming probiotic fermented milk (PFM) on the microbial community structure in the human intestinal tract by using high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings of PFM daily for 3 wk, and their fecal microbiota were analyzed before and after 3 wk of PFM ingestion period and for another 3 wk following the termination of PFM ingestion (the noningestion period). Fecal microbial communities were characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA gene. All subjects showed a similar pattern of microbiota at the phylum level, where the relative abundance of Bacteriodetes species increased during the PFM ingestion period and decreased during the noningestion period. The increase in Bacteroidetes was found to be due to an increase in members of the families Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the phylum level, the taxonomic composition at the genus level showed a considerable alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis of operational taxonomic units (OTU), the numbers of shared OTU were low among the 3 different treatments (before, during, and after PFM ingestion), but the abundance of the shared OTU was relatively high, indicating that the majority (>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion and after its termination. Our results suggest that PFM consumption could alter microbial community structure in the gastrointestinal tract of adult humans while maintaining the stability of microbiota.

Improved antifouling performance of polyethersulfone (PES) membrane via surface modification by CNTs bound polyelectrolyte multilayers

This study investigated the improved anti-fouling properties of CNTs bound polyelectrolyte membrane and proposed the mechanisms for anti-fouling.

Biologically based method for the synthesis of Hg–Se nanostructures by Shewanella spp

Living organisms, especially microorganisms, have the potential to offer cheap and benign synthetic routes for the production of nanomaterials.

Accumulation of amorphous Cr(III)-Te(IV) nanoparticles on the surface of Shewanella oneidensis MR-1 through reduction of Cr(VI)

Industrial effluents constitute a major source of metal pollution of aquatic bodies. Moreover, due to their environmental persistence, toxic metal pollution is of special concern. Microbial reduction is considered a promising strategy for toxic metal removal among the several methods available for metal remediation. Here, we describe the coremediation of toxic Cr(VI) and Te(IV) by the dissimilatory metal reducing bacterium-Shewanella oneidensis MR-1. In the presence of both Cr(VI) and Te(IV), S. oneidensis MR-1 reduced Cr(VI) to the less toxic Cr(III) form, but not Te(IV) to Te(0). The reduced Cr(III) ions complexed rapidly with Te(IV) ions and were precipitated from the cell cultures. Electron microscopic analyses revealed that the Cr-Te complexed nanoparticles localized on the bacterial outer membranes. K-edge X-ray absorption spectrometric analyses demonstrated that Cr(III) produced by S. oneidensis MR-1 was rapidly complexed with Te(IV) ions, followed by formation of amorphous Cr(III)-Te(IV) nanoparticles on the cell surface. Our results could be applied for the simultaneous sequestration and detoxification of both Cr(VI) and Te(IV) as well as for the preparation of nanomaterials through environmental friendly processes.

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575^T under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575^T grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575^T are dominant under anoxic conditions. Furthermore, strain DSM 6575^T forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575^T, and could contribute to biogeochemical cycles of Fe and N in the environment.

Seasonal and genotypic changes in escherichia coli phylogenetic groups in the Yeongsan River basin of South Korea

With 3,480 E. coli strains isolated from the Yeongsan River basin, South Korea, correlations between phylogenetic groups and horizontal fluorophore enhanced rep-PCR (HFERP) genotypes were examined, and environmental factors affecting E. coli phylogenetic groups in the river water were determined. Interestingly, multidimentional scaling (MDS) analyses based on HFERP DNA fingerprint data indicated that E. coli in phylogenetic groups A and B1 were uniquely clustered. Results of self-organized maps (SOMs) analyses also indicated that E. coli phylogenetic groups were seasonally affected by water temperature, with greater occurrences of phylogenetic groups A and B1 in low and high temperature seasons, respectively. The presence of E. coli in phylogenetic groups A and B1 were inversely related. Furthermore, redundancy analysis (RDA) revealed that phylogenetic group B1 correlated positively with temperature, strain diversity, and biochemical oxygen demand (BOD) but negatively with phylogenetic group A. Results of this study indicated that while E. coli strains could be clustered based on their genotypes and environment conditions, their phylogenetic groups did not change in relation to the same conditions. The distributional differences of phylogenetic groups among E. coli populations in different environments may be caused by different genomic adaptability and plasticity of E. coli strains belonging to each phylogenetic group. Although several previous studies have reported different E. coli ecological structures depending on their origins, this study is a first description of the specific environmental factors affecting E. coli phylogenetic groups in river water.

Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting

From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.

Characterization of a self-sufficient trans-anethole oxygenase from Pseudomonas putida JYR-1

A novel flavoprotein monooxygenase, trans-anethole oxygenase (TAO), from Pseudomonas putida JYR-1, which is capable of catalyzing the oxidation of trans-anethole to p-anisaldehyde, was heterologously expressed in E. coli and purified. Enzymatic kinetics of diverse substrates and cofactors revealed that TAO is likely to be a novel self-sufficient flavoprotein monooxygenase. Enzyme assays of GST-TAO demonstrated that TAO catalyzed a trans-anethole oxidation reaction without auxiliary component enzyme-like electron-transfer flavin reductases. The single component TAO had the ability to reduce flavin cofactors and simultaneously oxidize trans-anthole to p-anisaldehyde. In the processes of reduction of flavin and oxidation of trans-anethole, TAO accepted various flavin and NAD(P)H cofactors. TAO also catalyzed oxidation of isoeugenol, O-methyl isoeugenol, and isosafrole, all of which contain the 2-propenyl functional group on the aromatic ring structure with different catalytic efficiency. TAO had the greatest catalytic efficiency (k_cat/K_m) with the original substrate, trans-anethole. Investigation about partially deleted mutants of TAO indicated that reductase active sites appeared to be located near the N terminal. Site directed mutagenesis studies also proved that the proposed flavin binding sites, Trp-38, Thr-43, Tyr-55, were critical for flavin reduction. However, disruption of any portion of TAO eliminated the oxygenase activity.

Methanogenesis facilitated by geobiochemical iron cycle in a novel syntrophic methanogenic microbial community

Production and emission of methane have been increasing concerns due to its significant effect on global climate change and the carbon cycle. Here we report facilitated methane production from acetate by a novel community of methanogens and acetate oxidizing bacteria in the presence of poorly crystalline akaganeite slurry. Comparative analyses showed that methanogenesis was significantly enhanced by added akaganeite and acetate was mostly stoichiometrically converted to methane. Electrons produced from anaerobic acetate oxidation are transferred to akaganeite nanorods that likely prompt the transformation into goethite nanofibers through a series of biogeochemical processes of soluble Fe(II) readsorption and Fe(III) reprecipitation. The methanogenic archaea likely harness the biotransformation of akaganeite to goethite by the Fe(III)-Fe(II) cycle to facilitate production of methane. These results provide new insights into biogeochemistry of iron minerals and methanogenesis in the environment, as well as the development of sustainable methods for microbial methane production.

Promoted reduction of tellurite and formation of extracellular tellurium nanorods by concerted reaction between iron and Shewanella oneidensis MR-1

The reduction of tellurite (Te(IV)) by dissimilatory metal reducing bacterium, Shewanella oneidensis MR-1, was promoted in the presence of Fe(III) in comparison with Te(IV) bioreduction in the absence of Fe(III). Electron microscopic analyses revealed that iron promoted Te(IV) reduction led to form exclusively extracellular crystalline Te(0) nanorods, as compared to the mostly intracellular formation of Te(0) nanorods in the absence of Fe(III). The Te K-edge X-ray absorption spectrometric analyses demonstrated that S. oneidensis MR-1 in the presence of Fe(III) reduced Te(IV) to less harmful metallic Te(0) nanorods through the precipitation of tellurite (Te(IV)Ox) complex by the bacterial respiration of Fe(III) to Fe(II) under anaerobic conditions. However, Fe(II) ion itself was only able to precipitate the solid tellurite (Te(IV)Ox) complex from the Te(IV) solution, which was not further reduced to Te(0). The results clearly indicated that bacterial S. oneidensis MR-1 plays important roles in the reduction and crystallization of Te(0) nanorods by as yet undetermined biochemical mechanisms. As compared to the slow bacterial Te(IV) reduction in the absence of Fe(III), the rapid reduction of Te(IV) to Te(0) by the concerted biogeochemical reaction between Fe(II) and S. oneidensis MR-1 could be applied for the sequestration and detoxification of Te(IV) in the environments as well as for the preparation of extracellular Te(0) nanorod structures.

Differential arsenic mobilization from As-bearing ferrihydrite by iron-respiring Shewanella strains with different arsenic-reducing activities

Arsenic immobilization and release in the environment is significantly influenced by bacterial oxidation and reduction of arsenic and arsenic-bearing minerals. In this study, we tested three iron-reducing bacteria, Shewanella oneidensis MR-1, Shewanella sp. HN-41, and Shewanella putrefaciens 200, which have diverse arsenate-reducing activities with regard to reduction of an As-bearing ferrihydrite slurry. In the cultures of S. oneidensis MR-1 and Shewanella sp. HN-41, which are not capable of respiratory reduction of As(V) to As(III), arsenic was maintained predominantly in its pentavalent form, existing in particulate poorly crystalline As-bearing ferrihydrite and formed small quantities of a stable ferrous arsenate [Fe3(AsO4)2] precipitate. However, in the culture of the As(V) reducer, S. putrefaciens 200, As(V) was reduced to As(III) and a small fraction of As-bearing ferrihydrite was transformed into ribbon-shaped siderite that subsequently re-released arsenic into the liquid phase. Our results indicated that release of arsenic and formation of diverse secondary nanoscale Fe-As minerals are specifically closely related to the arsenic-reducing abilities of different bacteria. Therefore, bacterial arsenic reduction appears to significantly influence As mobilization in soils, minerals, and other Fe-rich environments.

Effects of the anaerobic respiration of Shewanella oneidensis MR-1 on the stability of extracellular U(VI) nanofibers

Uranium (VI) is considered to be one of the most widely dispersed and problematic environmental contaminants, due in large part to its high solubility and great mobility in natural aquatic systems. We previously reported that under anaerobic conditions, Shewanella oneidensis MR-1 grown in medium containing uranyl acetate rapidly accumulated long, extracellular, ultrafine U(VI) nanofibers composed of polycrystalline chains of discrete meta-schoepite (UO³·2H₂O) nanocrystallites. Wild-type MR-1 finally transformed the uranium (VI) nanofibers to uranium (IV) nanoparticles via further reduction. In order to investigate the influence of the respiratory chain in the uranium transformation process, a series of mutant strains lacking a periplasmic cytochrome MtrA, outer membrane (OM) cytochrome MtrC and OmcA, a tetraheme cytochrome CymA anchored to the cytoplasmic membrane, and a trans-OM protein MtrB, were tested in this study. Although all the mutants produced U(VI) nanofibers like the wild type, the transformation rates from U(VI) nanofibers to U(IV) nanoparticles varied; in particular, the mutant with deletion in tetraheme cytochrome CymA stably maintained the uranium (VI) nanofibers, suggesting that the respiratory chain of S. oneidensis MR-1 is probably involved in the stability of extracellular U(VI) nanofibers, which might be easily treated via the physical processes of filtration or flocculation for the remediation of uranium contamination in sediments and aquifers, as well as the recovery of uranium in manufacturing processes.

Pathogenic Escherichia coli strains producing extended-spectrum β-lactamases in the Yeongsan River basin of South Korea

A total of 3564 E. coli isolates obtained from Yeongsan River basin of South Korea were investigated for their production of extended-spectrum β-lactamases (ESBLs) and potential pathogenicity to better understand the linkage between antibiotic-resistant pathogens in the environment and their public health risks. Interestingly, 60% (53 of 89) of the screen-positive ESBL producers were determined to be potentially one or both of the diarrheagenic and extraintestinal pathogenic (ExPEC) pathotypes, suggesting that trade-off between resistance and virulence of E. coli may not apply to this study. In addition, 67% (60 of 89) of the screen-positive ESBL producers possessed more than one β-lactamase gene, and most (59 of 63) of the ESBL producers had the CTX-M-14 enzyme, which is the most dominant ESBL and seems to be related to urban anthropogenic activities. About 68% (36 of 53) of the potential pathogenic strains were resistant to more than 2 non-β-lactam antibiotics. Results from this study indicate that the Yeongsan River basin has been contaminated with antibiotic-resistant and potential pathogenic E. coli strains. While few studies have examined pathogenecity of ESBL-producing bacteria, this study reports the possible public health risk which could be caused by the fecal indicator bacterium itself containing both ESBL genes and virulence factors. This will likely impact the dissemination of potential pathogenic E. coli producing ESBLs in the environment and suggests the need for further investigations of antibiotic-resistant pathogens to prevent public health impacts in the Yeongsan River basin.

Production of natural fragrance aromatic acids by coexpression of trans-anethole oxygenase and p-anisaldehyde dehydrogenase genes of Pseudomonas putida JYR-1 in Escherichia coli

A gene encoding p-anisaldehyde dehydrogenase (PAADH), which catalyzes the oxidation of p-anisaldehyde to p-anisic acid, was identified to be clustered with the trans-anethole oxygenase (tao) gene in Pseudomonas putida JYR-1. Heterologously expressed PAADH in Escherichia coli catalyzed the oxidation of vanillin, veratraldehyde, and piperonal to the corresponding aromatic acids vanillic acid, veratric acid, and piperonylic acid, respectively. Coexpression of trans-anethole oxygenase (TAO) and PAADH in E. coli also resulted in the successful transformation of trans-anethole, isoeugenol, O-methyl isoeugenol, and isosafrole to p-anisic acid, vanillic acid, veratric acid, and piperonylic acid, respectively, which are compounds found in plants as secondary metabolites. Because of the relaxed substrate specificity and high transformation rates by coexpressed TAO and PAADH in E. coli , the engineered strain has potential to be applied in the fragrance industry.

Biological accumulation of tellurium nanorod structures via reduction of tellurite by Shewanella oneidensis MR-1

The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, reduced tellurite (Te(IV), TeO(3)(2-)) to elemental tellurium under anaerobic conditions resulting in the intracellular accumulation of needle shaped crystalline Te(0) nanorods. Fatty acid analyses showed that toxic Te(IV) increased the unsaturated fatty acid composition of the lipid components of the cell membrane, implying a deconstruction of the integrity of the cellular membrane structure. The current results suggest that dissimilatory metal reducing bacteria such as S. oneidensis MR-1 may play an important role in recycling toxic tellurium elements, and may be applied as a novel selective biological filter via the accumulation of industry-applicable rare materials, Te(0) nanorods, in the cell.