Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor

Bacterial response to the combined pollution of benzo[a]pyrene and decabromodiphenyl ether in soil under flooding anaerobic condition

This study investigated the interaction between the co-pollutants of Benzo[a]pyrene (BaP) and decabromodiphenyl ether (BDE-209) and the bacterial community in soil under flooding anaerobic condition. Three levels of combined pollution (at nominal concentrations of 1, 5, and 25 mg/kg, respectively, for each pollutant), their corresponding sterilized controls, and a blank control (CK) were set up. During the incubation time of 270 days, BaP attenuated more easily than BDE-209. The second-order rate constant of BaP attenuation was negatively correlated with the Ln value of initial BaP concentration. Maximal difference in bacterial community occurred between the CK soil and the highly polluted soil. Desulfomonilaceae, Parcubacteria and Rhodanobacter were probably involved in BaP and BDE-209 degradation, while Nitrosomonadaceae, Phenylobacterium and Mitochondria were significantly suppressed by BaP and BDE-209 or their degrading products. Genes narI, bcrC, fadJ, had, dmpC, narG and CfrA were involved in the degradation of BaP and BDE-209. Impacts of BaP and BDE-209 on metabolisms of carbon, nitrogen and sulfur were not significant. The results provide guidance for the management and remediation of the contaminated soil.

Self-forming electroactive dynamic membrane for enhancing the decolorization of methyl orange by weak electrical stimulation

An electroactive dynamic membrane (EADM), which enabled simultaneous solid-liquid separation and contaminants removal, has been developed by electrostimulation using domestic wastewater as inoculum. Results showed that both the control dynamic membrane (CDM), without electrical stimulation, and the EADM systems exhibited stable removal performance with chemical oxygen demand (COD), and a robustness in responding to a fluctuating organic load. With the introduction of a weak electrical field, the EADM transmembrane pressure (TMP) was significantly reduced (0.02 kPa/d) compared with the control (0.20 kPa/d). In the treatment of methyl orange (MO), the EADM system achieved a decolorization efficiency of 85.87 %, much higher than the control dynamic membrane (CDM) system (58.84 %), which can be attributed to electrical stimulation and H₂ production on cathode. Microbial analysis has established that electrostimulation enriched the electroactive bacteria in the dynamic biofilm, and shaped the microbial structure, with improved contaminant removal. The results of this study highlight the potential of regulating the microbial community and creating a beneficial biofilm as a dynamic layer to facilitate contaminant removal.

Desulfoluna limicola sp. nov., a sulfate-reducing bacterium isolated from sediment of a brackish lake

A novel sulfate-reducing bacterium, strain ASN36^T, was isolated from sediment of a brackish lake in Japan. Cells of strain ASN36^T were not motile and rod-shaped, with length of 2.0-4.9 μm and width of 0.6-0.9 μm. Growth was observed at 5-35 °C with an optimum growth temperature of 25-30 °C. The pH range for growth was 6.6-8.8 with an optimum pH of 7.3. Major fatty acids were C_16:1 ω7c and C_16:0. Under sulfate-reducing conditions, strain ASN36^T utilized lactate, malate, pyruvate, butyrate, ethanol, butanol, glycerol, yeast extract and H₂/CO₂ as growth substrate. Fermentative growth occurred on malate and pyruvate. The novel isolate used sulfate, sulfite and thiosulfate as electron acceptors. The genome of strain ASN36^T is composed of a chromosome with length of 6.3 Mbp and G + C content of 55.1 mol%. Analyses of the 16S rRNA gene indicated that strain ASN36^T is related to Desulfoluna species. Overall genome relatedness indices indicated that strain ASN36^T does not belong to any existing species. In contrast to the closest relatives, strain ASN36^T lacks genes for reductive dehalogenase required for organohalide respiration and does not use halogenated aromatics as electron acceptors. On the basis of its genomic and phenotypic properties, strain ASN36^T (= DSM 111985 ^T = JCM 39257 ^T) is proposed as the type strain of a new species, Desulfoluna limicola sp. nov.

Organohalide respiration potential in marine sediments from Aarhus Bay

Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.

Desulfoluna spp. form a cosmopolitan group of anaerobic dehalogenating bacteria widely distributed in marine sponges

Host-specific microbial communities thrive within sponge tissues and this association between sponge and associated microbiota may be driven by the organohalogen chemistry of the sponge animal. Several sponge species produce diverse organobromine secondary metabolites (e.g. brominated phenolics, indoles, and pyrroles) that may function as a chemical defense against microbial fouling, infection or predation. In this study, anaerobic cultures prepared from marine sponges were amended with 2,6-dibromophenol as the electron acceptor and short chain organic acids as electron donors. We observed reductive dehalogenation from diverse sponge species collected at disparate temperate and tropical waters suggesting that biogenic organohalides appear to enrich for populations of dehalogenating microorganisms in the sponge animal. Further enrichment by successive transfers with 2,6-dibromophenol as the sole electron acceptor demonstrated the presence of dehalogenating bacteria in over 20 sponge species collected from temperate and tropical ecoregions in the Atlantic and Pacific Oceans and the Mediterranean Sea. The enriched dehalogenating strains were closely related to Desulfoluna spongiiphila and Desulfoluna butyratoxydans, suggesting a cosmopolitan association between Desulfoluna spp. and various marine sponges. In vivo reductive dehalogenation in intact sponges was also demonstrated. Organobromide-rich sponges may thus provide a specialized habitat for organohalide-respiring microbes and D. spongiiphila and/or its close relatives are responsible for reductive dehalogenation in geographically widely distributed sponge species.

In situ fabrication of gold nanoparticles into biocathodes enhance chloramphenicol removal

The development of highly conductive biofilms is a key strategy to enhance antibiotic removal in bioelectrochemical systems (BESs) with biocathodes. In this study, Au nanoparticles (Au-NPs) were in situ fabricated in a biocathode (Au biocathode) to enhance the removal of chloramphenicol (CAP) in BESs. The concentration of Au(III) was determined to be 5 mg/L. CAP was effectively removed in the BES containing a Au biocathode with a removal percentage of 94.0% within 48 h; this result was 1.8-fold greater than that obtained using a biocathode without Au-NPs (51.7%). The Au-NPs significantly reduced the charge transfer resistance and promoted the electrochemical activity of the biocathode. In addition, the Au biocathode showed a specifical enrichment of Dokdonella, Bosea, Achromobacter, Bacteroides and Petrimonas, all of which are associated with electron transfer and contaminant degradation. This study provides a new strategy for enhancing CAP removal in BESs through a simple and eco-friendly electrode design.

Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT

Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA₂B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.

The influence of external resistance on the performance of microbial fuel cell and the removal of sulfamethoxazole wastewater

Microbial fuel cells (MFCs) are promising equipment for simultaneous treatment of sewage and power generation. External resistance (R_ext) plays a crucial impact in the performance of MFCs in antibiotic wastewater treatment and antibiotic resistance genes (ARGs) reduction. In this study, R_ext and whether to add 20 mg/L sulfamethoxazole (SMX) as variables, it was observed that the performance of several chemical properties of MFCs was optimal when R_ext was 1000 Ω. The power density before and after addition of SMX was 1220.5 ± 24.5 mW/m² and 1186.2 ± 9.2 mW/m², respectively; Furthermore, the degradation rate of SMX was as high as 87.52 ± 1.97% within 48 h. High-throughput sequencing results showed that both R_ext and SMX affected the microbial community and relative abundance of the phylum and genera. Meanwhile, the MFCs with 1000 Ω R_ext generated less the targeted ARGs. Experimental results showed that 1000 Ω was the most suitable R_ext for MFCs in the treatment of antibiotic wastewater.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Harnessing the sponge microbiome for industrial biocatalysts

Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.