Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium

Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production

Exploration of high-yield mechanism is important for further titer improvement of valuable antibiotics, but how to achieve this goal is challenging. Tiancimycins (TNMs) are anthraquinone-fused enediynes with promising drug development potentials, but their prospective applications are limited by low titers. This work aimed to explore the intrinsic high-yield mechanism in previously obtained TNMs high-producing strain Streptomyces sp. CB03234-S for the further titer amelioration of TNMs. First, the typical ribosomal RpsL(K43N) mutation in CB03234-S was validated to be merely responsible for the streptomycin resistance but not the titer improvement of TNMs. Subsequently, the combined transcriptomic, pan-genomic and KEGG analyses revealed that the significant changes in the carbon and amino acid metabolisms could reinforce the metabolic fluxes of key CoA precursors, and thus prompted the overproduction of TNMs in CB03234-S. Moreover, fatty acid metabolism was considered to exert adverse effects on the biosynthesis of TNMs by shunting and reducing the accumulation of CoA precursors. Therefore, different combinations of relevant genes were respectively overexpressed in CB03234-S to strengthen fatty acid degradation. The resulting mutants all showed the enhanced production of TNMs. Among them, the overexpression of fadD, a key gene responsible for the first step of fatty acid degradation, achieved the highest 21.7 ± 1.1 mg/L TNMs with a 63.2% titer improvement. Our studies suggested that comprehensive bioinformatic analyses are effective to explore metabolic changes and guide rational metabolic reconstitution for further titer improvement of target products. KEY POINTS: • Comprehensive bioinformatic analyses effectively reveal primary metabolic changes. • Primary metabolic changes cause precursor enrichment to enhance TNMs production. • Strengthening of fatty acid degradation further improves the titer of TNMs.

Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium

Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five-membered MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that V. beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally relevant hydration conditions. We find that methyl halide production can report on an MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC responds to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

Effects of perfluorooctanoic acid (PFOA) on activated sludge microbial community under aerobic and anaerobic conditions

Per- and polyfluoroalkyl substances (PFASs) have received increasing attention due to their widespread presence in diverse environments including wastewater treatment plants (WWTPs) and their potential adverse health effects. Perfluorooctanoic acid (PFOA) is one of the most detected forms of PFASs in WWTPs. However, there is still a paucity of knowledge about the effect of PFASs on microorganisms of the key component of WWTP, activated sludge. In this study, lab-scale microcosm experiments were established to evaluate the influences of PFOA on activated sludge microbes under aerobic and anaerobic conditions. The diversity, structure, and microbe-microbe interaction of microbial community were determined by 16S rRNA gene amplicon sequencing and co-occurrence network analysis. After 90 days of exposure to PFOA, activated sludge microbial richness decreased under both aerobic and anaerobic conditions. Specifically, under aerobic condition, Rhodopseudomonas (mean relative abundance 3.6%), Flavobacterium (2.4%), and Ignavibacterium (6.6%) were enriched in PFOA-spiked activated sludge compared with that in the unspiked sludge (2.6%, 0.1%, and 1.9%, respectively). By contrast, after 90 days of exposure to PFOA, Eubacterium (2.1%), Hyphomicrobium (1.8%), and Methyloversatilis (1.2%) were enriched under anaerobic condition, and more abundant than that in the control sludge (0.4%, 1.5%, and 0.6%, respectively). These genera were the potential PFOA-resistant members. In addition, Azospirillum and Sporomusa were the most connected taxa in PFOA-aerobic and PFOA-anaerobic networks, respectively. Prediction of the functional gene showed that PFOA inhibited some gene expression of sludge microbes, such as transcription, amino acid transport and metabolism, and energy production and conversion. In summary, continued exposure to PFOA induced substantial shifts of the sludge bacterial diversity and composition under both aerobic and anaerobic conditions.

The biogeochemical cycling of chlorine

Chlorine has important roles in the Earth's systems. In different forms, it helps balance the charge and osmotic potential of cells, provides energy for microorganisms, mobilizes metals in geologic fluids, alters the salinity of waters, and degrades atmospheric ozone. Despite this importance, there has not been a comprehensive summary of chlorine's geobiology. Here, we unite different areas of recent research to describe a biogeochemical cycle for chlorine. Chlorine enters the biosphere through volcanism and weathering of rocks and is sequestered by subduction and the formation of evaporite sediments from inland seas. In the biosphere, chlorine is converted between solid, dissolved, and gaseous states and in oxidation states ranging from -1 to +7, with the soluble, reduced chloride ion as its most common form. Living organisms and chemical reactions change chlorine's form through oxidation and reduction and the addition and removal of chlorine from organic molecules. Chlorine can be transported through the atmosphere, and the highest oxidation states of chlorine are produced by reactions between sunlight and trace chlorine gases. Partial oxidation of chlorine occurs across the biosphere and creates reactive chlorine species that contribute to the oxidative stress experienced by living cells. A unified view of this chlorine cycle demonstrates connections between chlorine biology, chemistry, and geology that affect life on the Earth.

Genome-Wide Transcription Start Sites Mapping in Methylorubrum Grown with Dichloromethane and Methanol

Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, Methylorubrum extorquens DM4 is a longstanding reference strain. Here, the primary 5′-ends of transcripts were obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM or methanol. In total, 7231 putative TSSs were annotated and classified with respect to their localization to coding sequences (CDSs). TSSs on the opposite strand of CDS (antisense TSS) account for 31% of all identified TSSs. One-third of the detected TSSs were located at a distance to the start codon inferior to 250 nt (average of 84 nt) with 7% of leaderless mRNA. Taken together, the global TSS map for bacterial growth using DCM or methanol will facilitate future studies in which transcriptional regulation is crucial, and efficient DCM removal at polluted sites is limited by regulatory processes.

A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics

BACKGROUND

Chloromethane (CH₃Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH₃Cl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CH₃Cl-degrading methylotrophs occurring in soils might be an important and overlooked sink.

RESULTS AND CONCLUSIONS

The objective of our study was to link the biotic CH₃Cl sink with the identity of active microorganisms and their biochemical pathways for CH₃Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH₃Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH₃Cl g^-1 dry weight h^-1, were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH₃Cl degradation compartments of forest ecosystems. The DNA of these [¹³C]-CH₃Cl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [¹³C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CH₃Cl degradation, via the methyltransferase system encoded by the CH₃Cl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CH₃Cl sink in this deciduous forest soil operates by a cmu-independent metabolism.

13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern

Chloromethane (CH₃ Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH₃ Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH₃ Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH₃ Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with ¹³ C-labelled CH₃ Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH₃ Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH₃ Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH₃ Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH₃ Cl degradation in the investigated tree ferns.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.

Enhanced removal of tetrachloroethylene from aqueous solutions by biodegradation coupled with nZVI modified by layered double hydroxide

Chlorinated volatile organic compounds, such as tetrachloroethylene (PCE), are the most commonly detected toxic contaminants in groundwater. In this study, the performance of PCE removal by a microbial consortium combined with nZVI modified by layered double hydroxide (nZVI-LDH) was evaluated. The enriched PCE-degrading consortium consisted of 44.49% Clostridium and other potential PCE degraders, and 0.5-2.5 mg/L PCE was completely biodegraded within 4 days. The characterization of nZVI-LDH indicated that LDH was coated on the surfaces of nZVI particles with an increased surface area. The PCE removal kinetics by nZVI-LDH was well described by a second-order model, and the removal rate constant of nZVI-LDH was 0.12 L h/mg, higher than that of native nZVI (0.02 L h/mg). Interestingly, the presence of Cu²⁺ improved the removal efficiency of PCE by nZVI-LDH, owing to its role as a catalyst or medium for charge transfer during reduction. Removal of PCE was enhanced by coupling the PCE-degrading consortium and nZVI-LDH. The initial removal of PCE was mainly dominated by the abiotic degradation and adsorption of nZVI-LDH, and biodegradation then played a major role in the exhaustion of nZVI-LDH. These results suggest that biodegradation coupled with nZVI-LDH has a great potential for applications in the remediation of chlorinated-solvent contaminated groundwater.

Chloromethane formation and degradation in the fern phyllosphere

Chloromethane (CH₃Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH₃Cl budget are approximate. The strength of the CH₃Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly ferns, have been identified as substantial emitters of CH₃Cl. Their ability to degrade CH₃Cl remains uncertain. In this study, we investigated the potential of leaves from 3 abundant ferns (Osmunda regalis, Cyathea cooperi, Dryopteris filix-mas) to produce and degrade CH₃Cl by measuring their production and consumption rates and their stable carbon and hydrogen isotope signatures. Investigated ferns are able to degrade CH₃Cl at rates from 2.1 to 17 and 0.3 to 0.9μgg_dw^-1day^-1 for C. cooperi and D. filix-mas respectively, depending on CH₃Cl supplementation and temperature. The stable carbon isotope enrichment factor of remaining CH₃Cl was -39±13‰, whereas negligible isotope fractionation was observed for hydrogen (-8±19‰). In contrast, O. regalis did not consume CH₃Cl, but produced it at rates ranging from 0.6 to 128μgg_dw^-1day^-1, with stable isotope values of -97±8‰ for carbon and -202±10‰ for hydrogen, respectively. Even though the 3 ferns showed clearly different formation and consumption patterns, their leaf-associated bacterial diversity was not notably different. Moreover, we did not detect genes associated with the only known chloromethane utilization pathway "cmu" in the microbial phyllosphere of the investigated ferns. Our study suggests that still unknown CH₃Cl biodegradation processes on plants play an important role in global cycling of atmospheric CH₃Cl.

Methanol consumption drives the bacterial chloromethane sink in a forest soil

Halogenated volatile organic compounds (VOCs) emitted by terrestrial ecosystems, such as chloromethane (CH₃Cl), have pronounced effects on troposphere and stratosphere chemistry and climate. The magnitude of the global CH₃Cl sink is uncertain since it involves a largely uncharacterized microbial sink. CH₃Cl represents a growth substrate for some specialized methylotrophs, while methanol (CH₃OH), formed in much larger amounts in terrestrial environments, may be more widely used by such microorganisms. Direct measurements of CH₃Cl degradation rates in two field campaigns and in microcosms allowed the identification of top soil horizons (i.e., organic plus mineral A horizon) as the major biotic sink in a deciduous forest. Metabolically active members of Alphaproteobacteria and Actinobacteria were identified by taxonomic and functional gene biomarkers following stable isotope labeling (SIP) of microcosms with CH₃Cl and CH₃OH, added alone or together as the [¹³C]-isotopologue. Well-studied reference CH₃Cl degraders, such as Methylobacterium extorquens CM4, were not involved in the sink activity of the studied soil. Nonetheless, only sequences of the cmuA chloromethane dehalogenase gene highly similar to those of known strains were detected, suggesting the relevance of horizontal gene transfer for CH₃Cl degradation in forest soil. Further, CH₃Cl consumption rate increased in the presence of CH₃OH. Members of Alphaproteobacteria and Actinobacteria were also ¹³C-labeled upon [¹³C]-CH₃OH amendment. These findings suggest that key bacterial CH₃Cl degraders in forest soil benefit from CH₃OH as an alternative substrate. For soil CH₃Cl-utilizing methylotrophs, utilization of several one-carbon compounds may represent a competitive advantage over heterotrophs that cannot utilize one-carbon compounds.