Polyvinyl Chloride Biodegradation Fuels Survival of Invasive Insect Larva and Intestinal Degrading Strain of Klebsiella

Microbial degradation of polyvinyl chloride (PVC) is eco-friendly and economically attractive, but extremely challenging due to the lack of mechanistic understanding on the degrading strains and enzymes. Motivated by an accidental discovery that the larva of an agricultural invasive pest, Spodoptera frugiperda, effectively survived solely on PVC film, we profiled the intestinal microbiota of S. frugiperda and screened for PVC-degrading strains. The results showed PVC film feeding significantly changed the larvae intestinal microbiota through selective enrichment of Enterococcus, Ochrobactrum and Klebsiella. From the larva intestines, we isolated and named a biofilm-forming strain EMBL-1, and experimentally verified it as the first Klebsiella bacterium that can actively degrade and utilize PVC based on various classic physicochemical and morphological analyses. We further used multi-omics analyses that complementarily integrate whole genomic, transcriptomic, proteomic, and metabolic insights to identify enzyme-coding genes responsible for PVC degradation and proposed a putative biodegradation pathway by the bacterial strain. All in all, both S. frugiperda and its intestinal strain EMBL-1 are discovered to effectively survive on PVC film by exploiting its polymer as a sole energy source. Moreover, this work exemplifying PVC biodegradation provides reference for discovering more degrading microbes and enzymatic resources of other recalcitrant plastics.

Limited accessibility of nitrogen supplied as amino acids, amides, and amines as energy sources for marine Thaumarchaeota

Genomic and physiological evidence from some strains of ammonia-oxidizing Thaumarchaeota demonstrate their additional ability to oxidize nitrogen (N) supplied as urea or cyanate, fueling conjecture about their ability to conserve energy by directly oxidizing reduced N from other dissolved organic nitrogen (DON) compounds. Similarly, field studies have shown rapid oxidation of polyamine-N in the ocean, but it is unclear whether Thaumarchaeota oxidize polyamine-N directly or whether heterotrophic DON remineralization is required. We tested growth of two marine Nitrosopumilus isolates on DON compounds including polyamines, amino acids, primary amines, and amides as their sole energy source. Though axenic cultures only consumed N supplied as ammonium or urea, there was rapid but inconsistent oxidation of N from the polyamine putrescine when cultures included a heterotrophic bacterium. Surprisingly, axenic cultures oxidized 15N-putrescine during growth on ammonia, suggesting co-metabolism or accelerated breakdown of putrescine by reactive metabolic byproducts. Nitric oxide, hydrogen peroxide, or peroxynitrite did not oxidize putrescine in sterile seawater. These data suggest that the N in common DON molecules is not directly accessible to marine Thaumarchaeota, with thaumarchaeal oxidation (and presumably assimilation) of DON-N requiring initial heterotrophic remineralization. However, reactive byproducts or enzymatic co-metabolism may facilitate limited thaumarchaeal DON-N oxidation.

Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone

Short-chain alkanes (SCA; C2-C4) emitted from geological sources contribute to photochemical pollution and ozone production in the atmosphere. Microorganisms that oxidize SCA and thereby mitigate their release from geothermal environments have rarely been studied. In this study, propane-oxidizing cultures could not be grown from acidic geothermal samples by enrichment on propane alone, but instead required methane addition, indicating that propane was co-oxidized by methanotrophs. “Methylacidiphilum” isolates from these enrichments did not grow on propane as a sole energy source but unexpectedly did grow on C3 compounds such as 2-propanol, acetone, and acetol. A gene cluster encoding the pathway of 2-propanol oxidation to pyruvate via acetol was upregulated during growth on 2-propanol. Surprisingly, this cluster included one of three genomic operons (pmoCAB3) encoding particulate methane monooxygenase (PMO), and several physiological tests indicated that the encoded PMO3 enzyme mediates the oxidation of acetone to acetol. Acetone-grown resting cells oxidized acetone and butanone but not methane or propane, implicating a strict substrate specificity of PMO3 to ketones instead of alkanes. Another PMO-encoding operon, pmoCAB2, was induced only in methane-grown cells, and the encoded PMO2 could be responsible for co-metabolic oxidation of propane to 2-propanol. In nature, propane probably serves primarily as a supplemental growth substrate for these bacteria when growing on methane.

Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

ABSTRACT Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes. IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.

Opportunistic interactions on Fe0 between methanogens and acetogens from a climate lake

Microbial-induced corrosion has been extensively studied in pure cultures. However, Fe0 corrosion by complex environmental communities, and especially the interplay between microbial physiological groups, is still poorly understood. In this study, we combined experimental physiology and metagenomics to explore Fe0-dependent microbial interactions between physiological groups enriched from anoxic climate lake sediments. Then, we investigated how each physiological group interacts with Fe0. We offer evidence for a new interspecies interaction during Fe0 corrosion. We showed that acetogens enhanced methanogenesis but were negatively impacted by methanogens (opportunistic microbial interaction). Methanogens were positively impacted by acetogens. In the metagenome of the corrosive community, the acetogens were mostly represented by Clostridium and Eubacterium, the methanogens by Methanosarcinales, Methanothermobacter and Methanobrevibacter. Within the corrosive community, acetogens and methanogens produced acetate and methane concurrently, however at rates that cannot be explained by abiotic H2-buildup at the Fe0 surface. Thus, microbial-induced corrosion might have occurred via a direct or enzymatically mediated electron uptake from Fe0. The shotgun metagenome of Clostridium within the corrosive community contained several H2-releasing enzymes including [FeFe]-hydrogenases, which could boost Fe0-dependent H2-formation as previously shown for pure culture acetogens. Outside the cell, acetogenic hydrogenases could become a common good for any H2/CO2-consuming member in the microbial community including methanogens that rely on Fe0 as a sole energy source. However, the exact electron uptake mechanism from Fe0 remains to be unraveled.

Metal-Free Blue-Light-Mediated Cyclopropanation of Indoles by Aryl(diazo)acetates

Blue-light-mediated cyclopropanation of indoles with aryl(diazo)acetates has been developed. The salient features of this strategy are that it is metal-free, operationally simple and atom-efficient, and that it uses an environmentally friendly energy source. In this protocol, blue light was employed as the sole energy source for the transformation. A variety of cyclopropane-fused indoline compounds was obtained in moderate to excellent yields and high diastereoselectivities under mild conditions.

Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium

ABSTRACT Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined anoxic bicarbonate-buffered mineral salt medium. The products are formate, acetate, inorganic chloride, and biomass. The bacterium’s genome was sequenced using PacBio, assembled, and annotated. The complete genome consists of one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.

IDENTIFICATION OF NOVEL BACTERIAL SPECIES CAPABLE OF DEGRADING DALAPON USING 16S RRNA SEQUENCING

2,2-dichloropropionic acid (2,2DCP) is used as herbicide in agricultural industry and it is one of the halogenated organic compounds distributed widely in the world causing contamination. In this study, a bacterial strain isolated from contaminated soil where halogenated pesticides applied in Universiti Teknologi Malaysia and it was named “JHA1”. Bacterium JHA1 was able to utilize 2,2 dichloropropionate 2,2-DCP or (Dalapon) as a source of carbon and energy. Based on 16S rRNA analysis, the isolate showed 87% identity to Terrabacter terrae strain PPLB. The identity score was lower than 98% so that it was suggested to be new organisms that worth for further investigations if it will be proven that this is novel. Therefore, current isolate was designated as Terrabacter terrae JHA1. The isolate grew in the minimal media containing 10 mM, 15 mM, 20 mM and 25 mM of 2,2- DCP as the sole energy and carbon source and the best growth rate was in 20 mM as the optimum concentration of 2,2-DCP while bacterial growth was inhibited in medium with 30 mM 2,2-DCP.