Plastisphere and microorganisms involved in polyurethane biodegradation.

Rapid accumulation of end-of-life polyurethanes (PUR) in the environment is a global crisis. While biodegradation of PUR has been reported, the process is slow, and the microbiology involved in PUR biodegradation is poorly understood. This study reported the microbial community involved in PUR biodegradation (designed as PUR-plastisphere) in estuary sediments, and isolation and characterization of two PUR-utilizing isolates. PUR foams were pretreated with oxygen plasma (referred as p-PUR foams) to mimic weathered conditions before embedded in microcosms containing estuary sediments. After 6 months of incubation, a substantial loss of ester/urethane bonds on the embedded p-PUR foams was observed, according to Fourier transform infrared (FTIR) spectroscopy. Analysis of PUR-plastisphere showed two dominant genera, Pseudomonas (2.7 %) and Hyphomicrobium (3.0 %), along with many unknown genera in Sphingomonadaceae (9.2 %), and predicted hydrolytic enzymes such as esterases and proteases. Purpureocillium sp., and Pseudomonas strain PHC1 (designated as strain PHC1 hereafter), isolated from the PUR plastisphere, can grow on Impranil (a commercial water-borne PUR) as a sole nitrogen or carbon source. High esterase activities were detected in the spent Impranil-containing media, and a significant loss of ester bonds of the spent Impranil was also observed. After 42 days of incubation, the strain PHC1-inoculated p-PUR foam showed a noticeable development of biofilm as observed via scanning electron microscopy (SEM), and disappearance of ester and urethane bonds of the PUR as detected by FTIR, supporting the role of strain PHC1 in biodegradation of the p-PUR foam. Also, the FTIR spectra observed for the sediment-embedded p-PUR foams was similar to those for the strain PHC1-inoculated p-PUR foams, suggesting the potential role of the dominant species of Pseudomonas in PUR-plastisphere. The results of this study showed the promise of rapid biodegradation of PUR foam through inoculating with a PUR-utilizing isolate, Pseudomonas strain PHC1.

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications.

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Draft genome of methanol-oxidizing Methylobacterium fujisawaense strain LAC1.

We report the draft genome of Methylobacterium fujisawaense LAC1 isolated from an acidic aquifer in Indian Head, MD, USA. The genome contains 5,883,000 bp and has a GC content of 70% with 5,434 protein-encoding genes with functional assignments. This strain can grow on methanol with lanthanum, a rare earth element.

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation.

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

Visualization of Productivity Zones Based on Nitrogen Mass Balance Model in Narragansett Bay, Rhode Island.

Primary productivity in the coastal regions, linked to eutrophication and hypoxia, provides a critical understanding of ecosystem function. Although primary productivity largely depends on riverine nutrient inputs, estimation of the extent of riverine nutrient influences in the coastal regions is challenging. A nitrogen mass balance model is a practical tool to evaluate coastal ocean productivity to understand biological mechanisms beyond data observations. This study visualizes the biological production zones in Narragansett Bay, Rhode Island, USA, where hypoxia frequently occurs, by applying a nitrogen mass balance model. The Bay is divided into three zones - brown, green, and blue zones - based on primary productivity, which are defined by the mass balance model results. Brown, green, and blue zones represent a high physical process, a high biological process, and a low biological process zone, depending on river flow, nutrient concentrations, and mixing rates. The results of this study can better inform nutrient management in the coastal ocean in response to hypoxia and eutrophication.

Dual-function oleaginous biocatalysts for non-sterile cultivation and solvent-free biolipid bioextraction to reduce biolipid-based biofuel production costs.

Triacylglycerols (TAGs) are starting materials for the production of biolipid-based fuels such as biodiesel and biojet fuel. While various microorganisms can produce TAGs from renewable resources, the cultivation of TAG-producing microorganisms under sterilization conditions to avoid microbial contamination and application of solvent to extract TAGs from the TAG-filled microorganisms are costly. To overcome these challenges, this study reports the feasibility of a non-sterile cultivation of an oleaginous bacterium Rhodococcus opacus PD631SpAHB under saline conditions, followed by the use of a solvent-free, phage-lysis-protein-based bioextraction approach for TAGs release. The engineered strain PD631SpAHB was developed by introducing a recombinant plasmid carrying a phage lytic gene cassette (pAHB) into Rhodococcus opacus PD631 via transformation, followed by adaptive evolution under saline conditions. This newly developed strain is a salt-tolerant strain with the inducible plasmid pAHB to enable TAGs release into the supernatant upon induction. Cell lysis of PD631SpAHB was confirmed by the decrease of the optical density of cell suspension, by the loss of cell membrane integrity, and by the detection of TAGs in the culture medium. Up to 38% of the total TAGs accumulated in PD631SpAHB was released into supernatant after the expression of the lytic genes. PD631SpAHB strain is a promising candidate to produce TAGs from non-sterile growth medium and release of its TAGs without solvent extraction - a new approach to reduce the overall cost of biolipid-based biofuel production.

Recent advances in production and extraction of bacterial lipids for biofuel production.

Lipid-based biofuel is a clean and renewable energy that has been recognized as a promising replacement for petroleum-based fuels. Lipid-based biofuel can be made from three different types of intracellular biolipids; triacylglycerols (TAGs), wax esters (WEs), and polyhydroxybutyrate (PHB). Among many lipid-producing prokaryotes and eukaryotes, biolipids from prokaryotes have been recently highlighted due to simple cultivation of lipid-producing prokaryotes and their ability to accumulate high biolipid contents. However, the cost of lipid-based biofuel production remains high, in part, because of high cost of lipid extraction processes. This review summarizes the production mechanisms of these different types of biolipids from prokaryotes and extraction methods for these biolipids. Traditional and improved physical/chemical approaches for biolipid extraction remain costly, and these methods are summarized and compared in this review. Recent advances in biological lipid extraction including phage-based cell lysis or secretion of biolipids are also discussed. These new techniques are promising for bacterial biolipids extraction. Challenges and future research needs for cost-effective lipid extraction are identified in this review.

From Organic Wastes to Bioplastics: Feasibility of Nonsterile Poly(3-hydroxybutyrate) Production by Zobellella denitrificans ZD1.

Poly(3-hydroxybutyrate) (PHB)-a renewable and biodegradable polymer-is a promising alternative to nonbiodegradable synthetic plastics that are derived from petrochemicals. The methods currently employed for PHB production are costly, in part, due to the expensive cultivation feedstocks and the need to sterilize the culture medium, which is energy-intensive. This study investigates the feasibility of nonsterile PHB production from several saline organic wastes using a salt-tolerant strain, Zobellella denitrificans ZD1 (referred to as strain ZD1). Factors such as the pH, salinity, carbon/nitrogen (C/N) ratio, nitrogen source, and electron acceptor that might affect the growth of strain ZD1 and its PHB production were determined. Our results showed successful nonsterile PHB production by growing the strain ZD1 on nonsterile synthetic crude glycerol, high-strength saline wastewater, and real municipal wastewater-activated sludge under saline conditions. The PHB production was significantly enhanced when the levels of salts and nitrate-nitrogen in the culture medium were increased. This study suggested a promising low-cost nonsterile PHB production strategy from organic wastes using strain ZD1.

Complete Genome Sequence of Escherichia coli Podophage Penshu1.

Escherichia coli 4s is a Gram-negative bacterium found in the equine intestinal ecosystem alongside diverse other coliform bacteria and bacteriophages. This announcement describes the complete genome of the T7-like E. coli 4s podophage Penshu1. From its 39,263-bp genome, 54 protein-encoding genes and a 179-bp terminal repeat were predicted.

Effective one-step saccharification of lignocellulosic biomass using magnetite-biocatalysts containing saccharifying enzymes.

Lignocellulosic biomass, packed with sugars, is one of the most available renewable resources for biofuels and bioproducts production. To release the sugars for the production, enzymatic hydrolysis (saccharification) of pretreated lignocellulosic biomass are required. However, the saccharification process is costly, inefficient, and requires multi-step operations. This is in part due to the high cost and the limited selection of commercial enzymes which commonly have different optimal pH and temperatures. Here we reported a one-step saccharification of pretreated lignocellulosic biomass using immobilized biocatalysts containing five different saccharifying enzymes (SEs) with a similar optimum pH and temperature. The five SEs - endo-1,4-ß-d-glucanase (an endoglucanase, eglS), cellobiohydrolase (an exoglucanase, cbhA), and ß-glucosidase (bglH), endo-1,4-ß-xylanase (an endoxylanase, xynC) and ß-xylosidase (bxlB) - were successfully expressed and produced by E. coli BL21. Better saccharification of pretreated corn husks was observed when using the five crude SE enzymes than those using two commonly used SEs, endo-1,4-ß-d-glucanase and ß-glucosidase. The five SEs were cross-linked in the absence or the presence of magnetic nanoparticles (hereafter referred as SE-CLEAs and M-SE-CLEAs, respectively). By using SE-CLEAs, the highest amount of reduced sugar (250 mg/g biomass) was measured. The activity of immobilized SEs is better than free crude SEs. The M-SE-CLEAs can be reused at least 3 times for effective saccharification of pretreated lignocellulosic biomass.

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system.

Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.

Effectiveness of zinc oxide-assisted photocatalysis for concerned constituents in reclaimed wastewater: 1,4-Dioxane, trihalomethanes, antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs).

Microbial and emerging chemical contaminants are unwanted constituents in reclaimed wastewater, due to the health concerns of using the water for agricultural irrigation, aquifer recharges, and potable water. Removal of these contaminants is required but it is currently challenging, given that there is no simple treatment technology to effectively remove the mixture of these contaminants. This study examined the effectiveness of ZnO-assisted photocatalytic degradation of several constituents, including 1,4-dioxane, trihalomethanes (THMs), triclosan (TCS), triclocarban (TCC), antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), under low intensity of UV exposure. E. coli with an ARGs-carrying circular plasmid (pUC19) was used as a model antibiotic resistant bacterium. Our results show that commercial zinc oxide (C-ZnO) assisted photodegradation of 1,4-dioxane, and dehalogenation of THMs, TCS, and TCC, while tetrapodal zinc oxide (T-ZnO) enhanced the dehalogenation of TCS and TCC. Additionally, T-ZnO assisted the photocatalytic inactivation of the E. coli within 6 h and caused structural changes in the plasmid DNA (pUC19) with additional UV exposure, resulting in non-functional AGR-containing plasmids. These results also suggest that higher UV dose is required not only to inactivate ARB but also to damage ARGs in the ARB in order to decrease risks in promoting ARB population in the environment. Overall, our results implicated that, under low UV intensity, ZnO-assisted photocatalysis is a promising alternative to simultaneously remove biological and emerging chemical contaminants in treated wastewater for safe reuse.

Reusable Functionalized Hydrogel Sorbents for Removing Long- and Short-Chain Perfluoroalkyl Acids (PFAAs) and GenX from Aqueous Solution.

Per- and poly-fluoroalkyl substances (PFASs) are man-made chemicals that are toxic and widely detected in the environment, including drinking water sources. A cost-effective treatment process for PFASs is currently not available. We developed reusable hydrogel sorbents to remove long- and short-chain perfluoroalkyl acids and 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid (GenX), which is are emerging PFAS. Through fluoridation and amination of poly(ethylene glycol) diacrylate (PEGDA), the newly synthesized sorbents can sorb the five targeted PFASs (perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorobutanesulfonic acid (PFBS), and perfluorobutanoic acid (PFBA) and GenX) to different degrees from aqueous solution. Aminated PEGDA showed the highest sorption capacity for all five PFASs, particularly for PFBA and PFBS. The bifunctionalized PEGDA showed higher capacities for PFOA and PFOS, suggesting that both hydrophobic interactions and charges contribute to the sorption. Both aminated and bifunctionalized sorbents can remove GenX from water, with the highest sorption capacity of 98.7 µmol g aminated PEGDA-1 within 6 h. The absorbed PFASs on the sorbents were observed and characterized by Fourier-transform infrared spectroscopy. The spent sorbents were reusable after readily regenerated with 70% methanol contained 1% NaCl.