Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate

Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation

In this study, a long-term operation of 2,747 days was conducted to evaluate the performance of the upflow anaerobic sludge blanket (UASB) reactor and investigated the degradation mechanisms of high-organic loading phenol wastewater. During the reactor operation, the maximum chemical oxygen demand (COD) removal rate of 6.1 ± 0.6 kg/m3/day under 1,680 mg/L phenol concentration was achieved in the mesophilic UASB reactor. After a significant change in the operating temperature from 24.0 ± 4.1 °C to 35.9 ± 0.6 °C, frequent observations of floating and washout of the bloated granular sludge (novel types of the bulking phenomenon) were made in the UASB reactor, suggesting that the change in operating temperature could be a trigger for the bulking phenomenon. Through the metagenomic analysis, phenol degradation mechanisms were predicted that phenol was converted to 4-hydroxybenzoate via two possible routes by Syntrophorhabdaceae and Pelotomaculaceae bacteria. Furthermore, the degradation of 4-hydroxybenzoate to benzoyl-CoA was carried out by members of Syntrophorhabdaceae and Smithellaceae. In the bulking sludge, a predominant presence of Nanobdellota, belonging to DPANN archaea, was detected. The metagenome-assembled genome of the Nanobdellota lacks many biosynthetic pathways and has several genes for the symbiotic lifestyle such as trimeric autotransporter adhesin-related protein. Furthermore, the Nanobdellota have significant correlations with several methanogenic archaea that are predominantly present in the UASB reactor. Considering the results of this study, the predominant Nanobdellota may negatively affect the growth of the methanogens through the parasitic lifestyle and change the balance of microbial interactions in the granular sludge ecosystem.

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance. Understanding how it affects microbial communities development and the degradation progress is a key operational issue to propose more stable processes. Thirty batch digesters were set-up with different levels of ammonia. Microbial community structure and metabolomic profiles were monitored with 16 S-metabarcoding and GCMS (gas-chromatography-mass-spectrometry). Digesters were first grouped according to similar degradation performances. Within each group, time profiles of OTUs and metabolites were modelled, then clustered into similar time trajectories, evidencing for example a syntrophic interaction between Syntrophomonas and Methanoculleus that was maintained up to 387 mg FAN/L. Metabolites resulting from organic matter fermentation, such as dehydroabietic or phytanic acid, decreased with increasing ammonia levels. Our analytical framework enabled to fully account for time variability and integrate this parameter in data analysis.

2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D's high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0-40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.

Microbial analysis and enrichment of anaerobic phenol and p-cresol degrading consortia with addition of AQDS

Quinones and humus are ubiquitous in the biosphere and play an important role in the anaerobic biodegradation and biotransformation of organic acids, poisonous compounds as well as inorganic compounds. The impact of humic model compound, anthraquinone-2, 6-disulfonate (AQDS) on anaerobic phenol and p-cresol degradation were studied. Four methanogenic AQDS-free phenol and p-cresol enrichments and two phenol-AQDS enrichments were obtained using two sludges with potential biodegradability of phenol and cresol isomers as inoculum. 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that syntrophic aromatic compound degrading bacterium Syntrophorhabdus aromaticivorans was dominant in four AQDS-free enrichments, whereas phenol degrading Cryptanaerobacter phenolicus was dominant in two phenol-AQDS enrichments. Neither co-culture of S. aromaticivorans with Methanospirillum hungatei nor two phenol-AQDS enrichments could metabolize phenol using AQDS as the terminal electron acceptor. Further degradation experiments suggested that C. phenolicus related microbes in two phenol-AQDS enrichments were responsible for the conversion of phenol to benzoate, and benzoate was further degraded by benzoate degraders of Syntrophus aciditrophicus or Sporotomaculum syntrophicum to acetate.

Towards Understanding COVID-19: Molecular Insights, Co-infections, Associated Disorders, and Aging

BACKGROUND

COVID-19 can be related to any diseases caused by microbial infection(s) because 1) co-infection with COVID-19-related virus and other microorganism(s) and 2) because metabolites produced by microorganisms such as bacteria, fungi, and protozoan can be involved in necrotizing pneumonia and other necrotizing medical conditions observed in COVID-19.

OBJECTIVE

By way of illustration, the microbial metabolite of aromatic amino acid tryptophan, a biogenic amine tryptamine inducing neurodegeneration in cell and animal models, also induces necrosis.

METHODS

This report includes analysis of COVID-19 positivity by zip codes in Florida and relation of the positivity to population density, possible effect of ecological and social factors on spread of COVID-19, autopsy analysis of COVID-19 cases from around the world, serum metabolomics analysis, and evaluation of autoantigenome related to COVID-19.

RESULTS

In the present estimations, COVID-19 positivity percent per zip code population varied in Florida from 4.65% to 44.3% (February 2021 data). COVID-19 analysis is partially included in my book Microbial Metabolism and Disease (2021). The autoantigenome related to COVID-19 is characterized by alterations in protein biosynthesis proteins including aminoacyl-tRNA synthetases. Protein biosynthesis alteration is a feature of Alzheimer's disease. Serum metabolomics of COVID-19 positive patients show alteration in shikimate pathway metabolism, which is associated with the presence of Alzheimer's disease-associated human gut bacteria.

CONCLUSION

Such alterations in microbial metabolism and protein biosynthesis can lead to toxicity and neurodegeneration as described earlier in my book Protein Biosynthesis Interference in Disease (2020).

Net release and uptake of xenometabolites across intestinal, hepatic, muscle, and renal tissue beds in healthy conscious pigs

Xenometabolites from microbial and plant sources are thought to confer beneficial as well as deleterious effects on host physiology. Studies determining absorption and tissue uptake of xenometabolites are limited. We utilized a conscious catheterized pig model to evaluate interorgan flux of annotated known and suspected xenometabolites, derivatives, and bile acids. Female pigs (n = 12, 2-3 mo old, 25.6 ± 2.2 kg) had surgically implanted catheters across portal-drained viscera (PDV), splanchnic compartment (SPL), liver, kidney, and hindquarter muscle. Overnight-fasted arterial and venous plasma was collected simultaneously in a conscious state and stored at -80°C. Thawed samples were analyzed by liquid chromatography-mass spectrometry. Plasma flow was determined with para-aminohippuric acid dilution technology and used to calculate net organ balance for each metabolite. Significant organ uptake or release was determined if net balance differed from zero. A total of 48 metabolites were identified in plasma, and 31 of these had at least one tissue with a significant net release or uptake. All bile acids, indole-3-acetic acid, indole-3-arylic acid, and hydrocinnamic acid were released from the intestine and taken up by the liver. Indole-3-carboxaldehyde, p-cresol glucuronide, 4-hydroxyphenyllactic acid, dodecanendioic acid, and phenylacetylglycine were also released from the intestines. Liver or kidney uptake was noted for indole-3-acetylglycine, p-cresol glucuronide, atrolactic acid, and dodecanedioic acid. Indole-3-carboxaldehyde, atrolactic acid, and dodecanedioic acids showed net release from skeletal muscle. The results confirm gastrointestinal origins for several known xenometabolites in an in vivo overnight-fasted conscious pig model, whereas nongut net release of other putative xenometabolites suggests a more complex metabolism.NEW & NOTEWORTHY Xenometabolites from microbe origins influence host health and disease, but absorption and tissue uptake of these metabolites remain speculative. Results herein are the first to demonstrate in vivo organ uptake and release of these metabolites. We used a conscious catheterized pig model to confirm gastrointestinal origins for several xenometabolites (e.g., indolic compounds, 4-hydroxyphenyllactic acid, dodecanendioic acid, and phenylacetylgycine). Liver and kidney were major sites for xenometabolite uptake, likely highlighting liver conjugation metabolism and renal excretion.

Rapid granulation using calcium sulfate and polymers for refractory wastewater treatment in up-flow anaerobic sludge blanket reactor

Long start-up period and slow granulation are major restraints in up-flow anaerobic sludge blanket (UASB) reactors for the treatment of refractory wastewater. In this study, Calcium sulfate (CaSO4), CaSO4/guar gum (GG), and CaSO4/cationic polyacrylamide (CPAM) were used to enhance granulation during the treatment of phenolic wastewaters in UASB reactors. Use of CaSO4, CaSO4/GG, and CaSO4/CPAM increased formation of granules (>0.25 mm) by 7%, 21% and 40%, respectively, after 90 days in comparison with the control. Use of CaSO4/GG and CaSO4/CPAM at an organic loading rate of 2.89 kg chemical oxygen demand (COD) m-3 d-1 increased the COD removal efficiency by 9% and 3%, respectively, in comparison with the control (75%). The CaSO4 enhanced the granulation rate as nuclei and the subsequent dissolution of CaSO4 improves the activity of methanogens. Polymers facilitated bacteria adhesion and improved the diversity of phenols-degrading bacteria. This study describes a new method for rapid granulation in UASB reactors when treating toxic and refractory wastewaters.

Propionate Converting Anaerobic Microbial Communities Enriched from Distinct Biogeochemical Zones of Aarhus Bay, Denmark under Sulfidogenic and Methanogenic Conditions

The relationship between predominant physiological types of prokaryotes in marine sediments and propionate degradation through sulfate reduction, fermentation, and methanogenesis was studied in marine sediments. Propionate conversion was assessed in slurries containing sediment from three different biogeochemical zones of Aarhus Bay, Denmark. Sediment slurries were amended with 0, 3, or 20 mM sulfate and incubated at 25 °C and 10 °C for 514-571 days. Methanogenesis in the sulfate zone and sulfate reduction in the methane zone slurries was observed. Both processes occurred simultaneously in enrichments originating from samples along the whole sediment. Bacterial community analysis revealed the dominance of Desulfobacteraceae and Desulfobulbaceae members in sulfate-amended slurries incubated at 25°C and 10°C. Cryptanaerobacter belonging to the Peptococcaceae family dominated sulfate-free methanogenic slurries at 25°C, whereas bacteria related to Desulfobacteraceae were dominant at 10°C. Archaeal community analysis revealed the prevalence of different genera belonging to Methanomicrobiales in slurries incubated at different temperatures and amended with different sulfate concentrations. Methanosarcinaceae were only detected in the absence of sulfate. In summary, Aarhus Bay sediment zones contain sulfate reducers, syntrophs, and methanogens interacting with each other in the conversion of propionate. Our results indicate that in Aarhus Bay sediments, Cryptanaerobacter degraded propionate in syntrophic association with methanogens.

Palladium/iron nanoparticles stimulate tetrabromobisphenol a microbial reductive debromination and further mineralization in sediment

Tetrabromobisphenol A (TBBPA) has aroused serious pollution in surface sediment. To date, whether and how iron-based nanoparticles could stimulate TBBPA in situ anaerobic biodegradation in sediment remains poorly understood. In this study, the distinctly enhanced TBBPA degradation activity with the rate constant k improved 4.7 times by fed with Pd/Fe nanoparticles (0.412 g L^-1 dosage, 0.5 wt% Pd loading) was observed. TBBPA degradation first went through reductive dehalogenation with bisphenol A (BPA) as the metabolites, and after the addition of Pd/Fe nanoparticles, BPA was further degraded to 4-(allene)phenol and 2,2-bis(4-hydroxyphenyl) propanoic acid via UPLC-QTOF-MS analysis, suggesting the complete detoxification potential. By the addition of Pd/Fe nanoparticles, the large amount of H₂ production (560 times higher) and the significant inhibition of methane generation facilitated the metabolism of potential reductive dehalogenators (Desulfovibrio, Clostridium, etc.), demonstrated by their increased ecological abundance and the tighter cooperative interrelations between each other. Meanwhile, the addition of Pd/Fe nanoparticles largely promoted the ecological abundance of Fe(III) reducing and aromatics degrading bacteria (Bacillus, Cryptanaerobacter, etc.), resulting in BPA further degradation. The bacterial ecological network further revealed that the potential BPA degrading bacteria shared the more positive interactions with the potential dehalogenators in the presence of Pd/Fe nanoparticles. The study firstly revealed the addition of Pd/Fe nanoparticles obviously enhanced the respiratory metabolic activities and cooperative interrelations of reductive dehalogenators and BPA degraders, which gives suggestions for in situ remediation and detoxification of BFRs in contaminated sediment.

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using ¹⁵N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.

Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats

Propionate is one of the most important intermediates of anaerobic fermentation. Its oxidation performed by syntrophic propionate-oxidizing bacteria coupled with hydrogenotrophic methanogens is considered to be a rate-limiting step for methane production. However, the current understanding of SPOB is limited due to the difficulty of pure culture isolation. In the present study, two anaerobic chemostats fed with propionate as the sole carbon source were operated at different dilution rates (0.05 d^-1 and 0.15 d^-1). The propionate- and acetate-oxidizing bacteria in the two methanogenic chemostats were investigated combining DNA-stable isotope probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results of DNA-SIP with ¹³C-propionate/acetate suggested that, Smithella, Syntrophobacter, Cryptanaerobacter, and unclassified Rhodospirillaceae may be putative propionate-oxidizing bacteria; unclassified Spirochaetaceae, unclassified Synergistaceae, unclassified Elusimicrobia, Mesotoga, and Gracilibacter may contribute to acetate oxidation; unclassified Syntrophaceae and Syntrophomonas may be butyrate oxidizers. By DNA-SIP, unclassified OTUs with 16S rRNA gene abundance higher than 62% of total Bacteria in the PL chemostat and 38% in the PH chemostat were revealed to be related to the degradation of propionate. These results suggest that a variety of uncultured bacteria contribute to propionate degradation during anaerobic digestion. The functions and metabolic characteristics of these bacteria require further investigation.

Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin

Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 - 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15 : 0, C15 : 0, C16 : 0 and C14 : 0. The percentage of the straight-chain fatty acid C15 : 0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).

Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives

The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.

Formation of phenylacetic acid and phenylpropionic acid under different overload conditions during mesophilic and thermophilic anaerobic digestion

BACKGROUND

Substrate spectra for anaerobic digestion have been broadened in the past decade, inter alia, due to the application of different pretreatment strategies and now include materials rich in lignocellulose, protein, and/or fat. The application of these substrates, however, also entails risks regarding the formation of undesired by-products, among which phenolic compounds are known to accumulate under unfavorable digestion conditions.

METHODS

Different states of overload were simulated in batch experiments while reviewing the generation of phenyl acids out of different lab-use substrates in order to evaluate the impact on biogas and methane production as well as some additional process performance parameters under defined laboratory conditions. Investigations were conducted under both mesophilic and thermophilic conditions.

RESULTS

It could be shown that the tested input materials led to the formation of phenyl acids in a substrate-dependent manner with the formation itself being less temperature driven. Once formed, the formation of phenyl acids turned out to be a reversible process.

CONCLUSIONS

Although a mandatory negative impact of phenyl acids per se on the anaerobic digestion process in general and the methanogenesis process in particular could not be proven, phenyl acids, however, seem to play an important role in the microbial response to overloaded biogas systems.

Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects

A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate. In this framework, the impact of 10  g/L of different types of zeolites and activated carbons (AC) on microbial community dynamics during anaerobic digestion of biowaste in the presence of 1.3 g/L of phenol was evaluated with 16 S rRNA gene sequencing. In the presence of AC, methanogenesis inhibition was rapidly removed due to a decrease of phenol concentration. This abiotic effect related to the physico-chemical properties of AC led to increased final CH4 and CO2 productions by 29-31% compared to digesters incubated without support. Interestingly, although zeolite did not adsorb phenol, final CH4 and CO2 production reached comparable levels as with AC. Nevertheless, compared to digesters incubated without support, methanogenesis lag phase duration was less reduced in the presence of zeolites (5 ± 1 days) than in the presence of activated carbons (12 ± 2 days). Both types of support induced biotic effects. AC and zeolite both allowed the preservation of the major representative archaeal genus of the non-inhibited ecosystem, Methanosarcina. By contrast, they distinctly shaped bacterial populations. OTUs belonging to class W5 became dominant at the expense of OTUs assigned to orders Clostridiales, Bacteroidales and Anaerolinales in the presence of AC. Zeolite enhanced the implantation of OTUs assigned to bacterial phylum Cloacimonetes. This study highlighted that supports can induce biotic and abiotic effects within digesters inhibited with phenol, showing potentialities to enhance anaerobic digestion stability under disrupting conditions.

Review of Desulfotomaculum species and proposal of the genera Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov

The genus Desulfotomaculumis a heterogeneous group of spore-forming sulfate-reducing bacteria. The type species of the genus is Desulfotomaculum nigrificans (Approved Lists 1980) emend. Visser et al. 2014. The results of phylogenetic analysis demonstrated that the genus Desulfotomaculum already has lost the clustering monophyly and was segregated into some distinct groups with low sequence similarity. Major features of the type strains in these groups were compared, and four novel genera, Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. were proposed to accommodate species transferred from the genus Desulfotomaculum.

Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model

Clostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of C. difficile colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that C. difficile gene expression is consistent with their utilization by the bacterium in vivo. We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for C. difficile colonization and disease.

Antibiotics alter the gut microbiota and decrease resistance to Clostridium difficile colonization; however, the mechanisms driving colonization resistance are not well understood. Loss of resistance to C. difficile colonization due to antibiotic treatment is associated with alterations in the gut metabolome, specifically, with increases in levels of nutrients that C. difficile can utilize for growth in vitro. To define the nutrients that C. difficile requires for colonization and pathogenesis in vivo, we used a combination of mass spectrometry and RNA sequencing (RNA Seq) to model the gut metabolome and C. difficile transcriptome throughout an acute infection in a mouse model at the following time points: 0, 12, 24, and 30 h. We also performed multivariate-based integration of the omics data to define the signatures that were most important throughout colonization and infection. Here we show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time in the mouse cecum and that C. difficile gene expression is consistent with their utilization in vivo. This was also reinforced by the multivariate-based integration of the omics data where we were able to discriminate the metabolites and transcripts that support C. difficile physiology between the different time points throughout colonization and infection. This report illustrates how important the availability of amino acids and other nutrients is for the initial stages of C. difficile colonization and progression of disease. Future studies identifying the source of the nutrients and engineering bacteria capable of outcompeting C. difficile in the gut will be important for developing new targeted bacterial therapeutics.

IMPORTANCEClostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of C. difficile colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that C. difficile gene expression is consistent with their utilization by the bacterium in vivo. We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for C. difficile colonization and disease.

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics

BACKGROUND

Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information.

RESULTS

Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured ε-Proteobacterium G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a Sulfurovum-like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a Chloroflexi T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a Cryptanaerobacter bacterium.

CONCLUSION

Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.

Peptococcus simiae sp. nov., isolated from rhesus macaque faeces and emended description of the genus Peptococcus

A study of the faecal microbiome in three healthy female rhesus macaques revealed the presence of a novel obligately anaerobic, chemoorganoheterotrophic, non-sporing, coccoid, non-motile, Gram-stain-positive bacterial species. Three strains of this species, designated as M108T, M916-1/1, and M919-2/1, were non-haemolytic, H2S-positive, catalase-positive, bile- and NaCl-sensitive and required peptone for growth. Strains also were asaccharolytic, able to utilize sulfite, thiosulfate and elemental sulfur as electron acceptors, and produced acetic and butyric acids as metabolic end-products. Strain M108T is characterized by the prevalence of C14 : 0, C16 : 0 and C18 : 1ω9cis dimethyl acetal among the cellular fatty acids, and the presence of MK-10 menaquinone. The DNA G+C content was found to be 51 mol%. Phylogenetic analysis of partial 16S rRNA gene sequences of strains M108T, M916-1/1 and M919-2/1 placed these strains into the genus Peptococcus (family Peptococcaceae). On the basis of phenotypic and genotypic properties we conclude that these strains represent a novel bacterial species for which the name Peptococcus simiae sp. nov. is proposed. The type strain is M108T (=DSM 100347T=VKM B-2932T).

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil

Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions.

Construction of a novel phenol synthetic pathway in Escherichia coli through 4-hydroxybenzoate decarboxylation

Phenol is a bulk chemical with lots of applications in the chemical industry. Fermentative production of phenol had been realized in both Pseudomonas putida and Escherichia coli by recruiting tyrosine phenol-lyase (TPL). The TPL pathway needs tyrosine as the direct precursor for phenol production. In this work, a novel phenol synthetic pathway was created in E. coli by recruiting 4-hydroxybenzoate decarboxylase, which can convert 4-hydroxybenzoate to phenol and carbon dioxide. Activating 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase and chorismate pyruvate lyase (UbiC) through plasmid overexpression led to 7- and 69-fold increase of phenol production, respectively, demonstrating that these two enzymes were the rate-limiting steps for phenol production. Genetically stable strains were then obtained by gene integration and gene modulation directly in chromosome. Phenol titer increased 147-fold (from 1.7 to 250 mg/L) after modulating the DAHP synthase, UbiC, and 4-hydroxybenzoate decarboxylase genes in chromosome. Five solvents were tested for two-phase extractive fermentation to eliminate phenol toxicity to E. coli cells. Tributyrin and dibutyl phthalate were the best two solvents for improving phenol production, leading to 23 and 30 % increase of total phenol production, respectively. Two-phase fed-batch fermentation of the best strain Phe009 was performed in a 7 L fermentor, which produced 9.51 g/L phenol with a yield of 0.061 g/g glucose.

Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds

Aromatic compounds are a major component of the global carbon pool and include a diverse range of compounds such as humic acid, lignin, amino acids, and industrial contaminants. Due to the prevalence of aromatic compounds in the environment, aerobic and anaerobic microorganisms have evolved mechanisms by which to metabolize that available carbon. Less well understood are the anaerobic pathways. We now know that anaerobic metabolism of a variety of monoaromatic compounds can be initiated in a number of different ways, and a key metabolite for these pathways is benzoyl-CoA. Chemicals can have different upstream anaerobic degradation pathways yet can still be assessed by targeting the downstream benzoyl-CoA pathway. In this pathway, we propose that the ring opening hydrolase, encoded by the bamA gene, is especially useful because, in contrast to the benzoyl-CoA reductase, it is detected under a number of respiratory settings, including denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions, and has a wide distribution in the environment. This review examines the bamA gene in enrichment cultures and environmental DNA extracts to consider whether it can be used as a biomarker for anaerobic aromatic degradation. Given the number of potential upstream inputs from natural and man-made monoaromatic compounds, the benzoyl-CoA pathway and the bamA gene in particular may play an important role in the global carbon cycle that has thus far been overlooked.

Molecular characterization of bacterial and archaeal communities in a full-scale anaerobic reactor treating corn straw

A 16S rRNA gene-based method was used to characterize the structure of bacterial and archaeal communities in a full-scale, anaerobic reactor treating corn straw. Degradability experiment indicated biogas slurry had high microbial activity, the TS removal rate was 53% and the specific methanogenic activity was 86 mL CH4 g VSS(-1) d(-1). During anaerobic degradation of corn straw, volatile acids and aromatic compounds (p-cresol, phenylpropionate, phenol and benzoate) were detected as transient intermediates. Phylogenetic analysis revealed bacterial community exhibited high diversity, 69 bacterial phylotypes in 13 phyla were identified. Firmicutes (48.3%), Chloroflexi (20.1%), Actinobacteria (9.1%), Bacteroidetes (7.7%), and Proteobacteria (7.2%) represented the most abundant bacterial phyla. Hydrolytic and fermentative bacteria were major bacterial populations. Moreover, a relatively high proportion of syntrophic propionate and aromatic compounds degrading bacteria were detected. In the archaeal clone library, 11 archaeal phylotypes affiliated with two phyla of Crenarchaeota (10%) and Euryarchaeota (90%) were identified.

Persistent organic pollutants induced protein expression and immunocrossreactivity by Stenotrophomonas maltophilia PM102: a prospective bioremediating candidate

A novel bacterium capable of growth on trichloroethylene as the sole carbon source was identified as Stenotrophomonas maltophilia PM102 by 16S rDNA sequencing (accession number of NCBI GenBank: JQ797560). In this paper, we report the growth pattern, TCE degradation, and total proteome of this bacterium in presence of various other carbon sources: toluene, phenol, glucose, chloroform, and benzene. TCE degradation was comparatively enhanced in presence of benzene. Densitometric analysis of the intracellular protein profile revealed four proteins of 78.6, 35.14, 26.2, and 20.47 kDa while the extracellular protein profile revealed two distinct bands at 14 kDa and 11 kDa that were induced by TCE, benzene, toluene, and chloroform but absent in the glucose lane. A rabbit was immunised with the total protein extracted from the bacteria grown in 0.2% TCE + 0.2% peptone. Antibody preadsorbed on proteins from peptone grown PM102 cells reacted with a single protein of 35.14 kDa (analysed by MALDI-TOF-mass-spectrometry) from TCE, benzene, toluene, or chloroform grown cells. No reaction was seen for proteins of PM102 grown with glucose. The PM102 strain was immobilised in calcium alginate beads, and TCE degradation by immobilised cells was almost double of that by free cells. The beads could be reused 8 times.

Long-term anaerobic mineralization of pentachlorophenol in a continuous-flow system using only lactate as an external nutrient

A simple anaerobic upflow column system (15 cm long, 5 cm inner diameter) for complete pentachlorophenol (PCP) mineralization has been established using a microbial consortium requiring only lactate as the external nutrient. With lactate as an electron donor, PCP was dechlorinated to 3-chlorophenol (3-CP) and phenol. The degradation of 3-CP and phenol proceeded without an external electron acceptor, indicating fermentative or syntrophic characteristics. A tracer experiment using (14)C-U-ring-labeled PCP confirmed the conversion of PCP into CO(2) (54.1%), CH(4) (48.1%), and biomass (0.6%). The nitrogen required for degradation was supplied by N(2)-fixation, evidenced from the nitrogen balance and an acetylene reduction assay. A 16S rRNA gene library analysis showed that bottom of the upflow column harbored the potential dechlorinators, Dehalobacter and Desulfitobacterium, and the phenol/3-CP fermentative or syntrophic degraders, Cryptanaerobacter and Syntrophus. The nitrogen-fixing facultative anaerobes, Rhizobiales, were detected in the top of the upflow column, with other possible nitrogen-fixers at both bottom and top of the upflow column. The mineralization rate reached 1.96 μmoles L(-1) d(-1) for 50 μM of the initial PCP concentration: one of the highest efficiencies reported. This compact anaerobic mineralization system requiring no external supply of an electron acceptor would be useful for the remediation of chlorinated aromatic compounds under anaerobic conditions.

Conversion of phenols during anaerobic digestion of organic solid waste--a review of important microorganisms and impact of temperature

During anaerobic digestion of organic waste, both energy-rich biogas and a nutrient-rich digestate are produced. The digestate can be used as a fertiliser in agricultural soils if the levels of hazardous compounds and pathogens are low. This article reviews the main findings about phenols in anaerobic digestion processes degrading organic solid wastes, and examines the effect of process temperature on the anaerobic degradation of phenols, the microbial community and the quality of the digestate. The degradation efficiency of a number of different phenols has been shown to be correlated to the process temperature. Higher degradation efficiency is observed at mesophilic process temperature than at thermophilic temperature. Possible explanations for this variation in the degradation of phenols include differences in diversity, particularly of the phenol-degrading bacteria, and/or the presence of temperature-sensitive enzymes. Chemical analysis of digestate from bioreactors operating at thermophilic temperature detected a higher content of phenols compared to mesophilic bioreactors, verifying the degradation results. Digestate with the highest phenol content has the greatest negative impact on soil microbial activity.

Reductive dechlorination of chlorophenols in estuarine sediments of Lake Shinji and Lake Nakaumi

Dechlorination of all mono- and dichlorophenol isomers in anaerobic sediment samples of estuarine Lake Shinji and Lake Nakaumi was examined to characterize the chlorophenol-dechlorinating microbial communities in the environments with different salinity levels. Dechlorination was observed only in 2-chlorophenol (2-CP), 3-chlorophenol (3-CP) and 2,6-dichlorophenol (2,6-DCP), and in 2-CP and 2,6-DCP in the Lake Shinji and Nakaumi sediment, respectively. In the sediment of Lake Shinji, the highest activity was observed without adding sodium chloride and sulfate, whereas in the Lake Nakaumi sediment, the highest activity was at 0.7 % of sodium chloride and 6.0 mM of sodium sulfate. The chlorophenols were degraded to benzoate via phenol in both sediments under methanogenic conditions. Benzoate then disappeared from the cultures. All microbial consortia enriched with each monochlorophenol dechlorinated 2-CP, but showed different substrate specificities for dichlorophenols as follows: 2-CP-enriched consortium dechlorinated 2,3-dichlorophenol and 2,6-DCP, 3-CP-enriched consortium dechlorinated all dichlorophenol isomers, and 4-chlorophenol-enriched consortium dechlorinated 2,4-dichlorophenol and 2,6-DCP. Maintenance of the population by halorespiration was suggested in the dechlorination of 2-CP.

Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing

The flow of carbon under sulfate-reducing conditions within a benzene-mineralizing enrichment culture was analysed using fully labelled [13C6]-benzene. Over 180 days of incubation, 95% of added 13C-benzene was released as 13C-carbon dioxide. DNA extracted from cultures that had degraded different amounts of unlabelled or 13C-labelled benzene was centrifuged in CsCl density gradients to identify 13C-benzene-assimilating organisms by density-resolved terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA gene fragments. Two phylotypes showed significantly increased relative abundance of their terminal restriction fragments in 'heavy' fractions of 13C-benzene-incubated microcosms compared with a 12C-benzene-incubated control: a member of the Cryptanaerobacter/Pelotomaculum group within the Peptococcaceae, and a phylotype belonging to the Epsilonproteobacteria. The Cryptanaerobacter/Pelotomaculum phylotype was the most frequent sequence type. A small amount of 13C-methane was aceticlastically produced, as concluded from the linear relationship between methane production and benzene degradation and the detection of Methanosaetaceae as the only methanogens present. Other phylotypes detected but not 13C-labelled belong to several genera of sulfate-reducing bacteria, that may act as hydrogen scavengers for benzene oxidation. Our results strongly support the hypothesis that benzene is mineralized by a consortium consisting of syntrophs, hydrogenotrophic sulfate reducers and to a minor extent of aceticlastic methanogens.

Degradation of phenol via phenylphosphate and carboxylation to 4-hydroxybenzoate by a newly isolated strain of the sulfate-reducing bacterium Desulfobacterium anilini

A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660(T)). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminobenzoate, 2-fluorophenol, and 2-fluorobenzoate, but it does not degrade aniline, 3-hydroxybenzoate, 4-cyanophenol, 2,4-dihydroxybenzoate, monohalogenated phenols, or monohalogenated benzoates. Growth with sulfate as an electron acceptor occurred with acetate and pyruvate but not with citrate, propionate, butyrate, lactate, glucose, or succinate. Strain AK1 is able to use sulfate, sulfite, and thiosulfate as electron acceptors. A putative phenylphosphate synthase gene responsible for anaerobic phenol degradation was identified in strain AK1. In phenol-grown cultures inducible expression of the ppsA gene was verified by reverse transcriptase PCR, and 4-hydroxybenzoate was detected as an intermediate. These results suggest that the pathway for anaerobic degradation of phenol in D. anilini strain AK1 proceeds via phosphorylation of phenol to phenylphosphate, followed by carboxylation to 4-hydroxybenzoate. The details concerning such reaction pathways in sulfidogenic bacteria have not been characterized previously.

Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions

The microbial communities of in situ reactor columns degrading benzene with sulfate as an electron acceptor were analyzed based on clone libraries and terminal restriction fragment length polymorphism fingerprinting of PCR-amplified 16S rRNA genes. The columns were filled with either lava granules or sand particles and percolated with groundwater from a benzene-contaminated aquifer. The predominant organisms colonizing the lava granules were related to Magnetobacterium sp., followed by a phylotype affiliated to the genera Cryptanaerobacter/Pelotomaculum and several Deltaproteobacteria. From the sand-filled columns, a stable benzene-degrading consortium was established in sand-filled laboratory microcosms under sulfate-reducing conditions. It was composed of Delta- and Epsilonproteobacteria, Clostridia, Chloroflexi, Actinobacteria and Bacteroidetes. The most prominent phylotype of the consortium was related to the genus Sulfurovum, followed by Desulfovibrio sp. and the Cryptanaerobacter/Pelotomaculum phylotype. The proportion of the latter was similar in both communities and significantly increased after repeated benzene-spiking. During cultivation on aromatic substrates other than benzene, the Cryptanaerobacter/Pelotomaculum phylotype was outcompeted by other community members. Hence, this organism appears to be specific for benzene as a growth substrate and might play a key role in benzene degradation in both communities. Based on the possible functions of the community members and thermodynamic calculations, a functional model for syntrophic benzene degradation under sulfate-reducing conditions is proposed.

Identification of important microbial populations in the mesophilic and thermophilic phenol-degrading methanogenic consortia

Active mesophilic and thermophilic phenol-degrading methanogenic consortia were obtained after an 18-month acclimation and enriching process in the serum bottles, and characterized using the rRNA-based molecular approach. As revealed by cloning, fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP), these two enrichments differed greatly in the community structures. The results for the first time suggest that group TA in the Deltaproteobacteria (88.0% of EUBmix FISH-detectable bacterial cell area) and Pelotomaculum spp. in the Desulfotomaculum family (81.2%) were the predominant fermentative bacteria under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions, respectively. These populations closely associated with mesophilic and thermophilic members of Methanosaetaceae, Methanobacteriaceae and Methanomicrobiales to mineralize phenol as the sole carbon substrate to carbon dioxide and methane. Moreover, these two enrichments could mineralize terephthalate and benzoate. During benzoate degradation in the mesophilic enrichment, a shift in the predominant bacterial population from Deltaproteobacteria group TA to Syntrophus spp. was observed, suggesting Syntrophus-related spp. could have a higher substrate affinity for benzoate. FISH further revealed that member of the Deltaproteobacteria group TA represented more than 68.3% of EUBmix FISH-detectable bacterial cell area in a full-scale mesophilic bioreactor treating phenol-containing wastewaters.

Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen

Phenol degradation under methanogenic conditions has long been studied, but the anaerobes responsible for the degradation reaction are still largely unknown. An anaerobe, designated strain UI(T), was isolated in a pure syntrophic culture. This isolate is the first tangible, obligately anaerobic, syntrophic substrate-degrading organism capable of oxidizing phenol in association with an H(2)-scavenging methanogen partner. Besides phenol, it could metabolize p-cresol, 4-hydroxybenzoate, isophthalate, and benzoate. During the degradation of phenol, a small amount of 4-hydroxybenzoate (a maximum of 4 microM) and benzoate (a maximum of 11 microM) were formed as transient intermediates. When 4-hydroxybenzoate was used as the substrate, phenol (maximum, 20 microM) and benzoate (maximum, 92 microM) were detected as intermediates, which were then further degraded to acetate and methane by the coculture. No substrates were found to support the fermentative growth of strain UI(T) in pure culture, although 88 different substrates were tested for growth. 16S rRNA gene sequence analysis indicated that strain UI(T) belongs to an uncultured clone cluster (group TA) at the family (or order) level in the class Deltaproteobacteria. Syntrophorhabdus aromaticivorans gen. nov., sp. nov., is proposed for strain UI(T), and the novel family Syntrophorhabdaceae fam. nov. is described. Peripheral 16S rRNA gene sequences in the databases indicated that the proposed new family Syntrophorhabdaceae is largely represented by abundant bacteria within anaerobic ecosystems mainly decomposing aromatic compounds.

Properties of the reversible nonoxidative vanillate / 4-hydroxybenzoate decarboxylase fromBacillus subtilis

Bacillus subtilis (ATCC 6051) reversibly decarboxylates vanillate and 4-hydroxybenzoate under both aerobic and anoxic conditions. Thus, we have identified on the basis of gene sequence homology with Sedimentibacter hydroxybenzoicus and Streptomyces sp. strain D7, a putative B. subtilis hydroxybenzoate decarboxylase. The native form of this enzyme is encoded by 3 genes yclBCD (GI Sequence Identification Nos.: 2632649, 2632650, 2632651) that we have renamed during this research as bsdBCD to align with existing nomenclature. The bsdD gene is reported in the database to be 690 bp; however, our sequence analysis revealed that the size of this gene is in fact 228 bp, an observation that results in a shortening of YclD (i.e., BsdD) from 229 to 75 aa. The corresponding bsdBCD genes were cloned into Escherichia coli , and the heterologously expressed enzyme was assayed for activity. The decarboxylase exhibited a narrow substrate range, with only 2 of the tested substrates, vanillate (Kmapp = 4 mmol·L–1) and 4-hydroxybenzoate (Kmapp = ~1 mmol·L–1), being decarboxylated. The recombinant enzyme had properties similar to that of the native enzyme in respect to specific activity, kinetic properties, bidirectional decarboxylase–carboxylase activity, oxygen insensitivity, and substrate specificity.

Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium

An anaerobic, mesophilic, syntrophic, propionate-oxidizing bacterium, strain MGP(T), was isolated as a defined co-culture with Methanospirillum hungatei from the methanogenic sludge of a mesophilic upflow anaerobic sludge blanket (UASB) reactor. The strain grew in the presence of propionate, but only in co-culture with methanogens, suggesting that it is an obligately syntrophic bacterium. The optimum temperature for growth was 37 degrees C, and the optimum pH was between 6.5 and 7.2. Based on comparative 16S rRNA gene sequence analysis, strain MGP(T) was affiliated with subcluster Ih of 'Desulfotomaculum cluster I', in which it was found to be moderately related to known species of the genera Pelotomaculum and Cryptanaerobacter. Similar to known species of the genus Pelotomaculum, strain MGP(T) could degrade propionate in syntrophy, but had no ability to reduce sulfate, sulfite and thiosulfate. Further phenotypic and genetic studies supported the affiliation of the strain as a novel species in this genus, for which the name Pelotomaculum propionicicum sp. nov. is proposed. The type strain is MGP(T) (=DSM 15578(T)=JCM 11929(T)). The strain has been deposited in the DSM and JCM culture collections as a defined co-culture with Methanospirillum hungatei.

Desulfurispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming sulfate-reducer isolated from a sulfidogenic fluidized-bed reactor

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a sulfidogenic fluidized-bed reactor treating acidic metal- and sulfate-containing water. The strain, designated RA50E1T, was rod-shaped and motile. The strain grew at 40–67 °C (optimum growth at 59–61 °C) and pH 6.4–7.9 (optimum growth at pH 7.0–7.3). The strain tolerated up to 1 % NaCl. Sulfate, sulfite, thiosulfate and elemental sulfur were used as electron acceptors, but not nitrate, nitrite or iron(III). Electron donors utilized were H2/CO2 (80 : 20, v/v), alcohols, various carboxylic acids and some sugars. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 0. Strain RA50E1T was distantly related to representatives of the genera Desulfotomaculum, Pelotomaculum, Sporotomaculum and Cryptanaerobacter. On the basis of 16S rRNA gene sequence data, the strain cannot be assigned to any known genus. Based on the phenotypic and phylogenetic features of strain RA50E1T, it is proposed that the strain represents a novel species in a new genus, for which the name Desulfurispora thermophila gen. nov., sp. nov. is proposed. The type strain of Desulfurispora thermophila is RA50E1T (=DSM 16022T=JCM 14018T).

Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments

The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.

Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens

An anaerobic phthalate isomer-degrading strain (JT(T)) that we previously isolated was characterized. In addition, a strictly anaerobic, mesophilic, syntrophic phthalate isomer-degrading bacterium, designated strain JI(T), was isolated and characterized in this study. Both were non-motile rods that formed spores. In both strains, the optimal growth was observed at temperatures around 37 degrees C and neutral pH. In syntrophic co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei, both strains could utilize two or three phthalate isomers for growth, and produce acetate and methane as end products. Strain JT(T) was able to grow on isophthalate, terephthalate, and a number of low-molecular weight aromatic compounds, such as benzoate, hydroquinone, 2-hydroxybenzoate, 3-hydroxybenzoate, 2,5-dihydroxybenzoate, 3-phenylpropionate in co-culture with M. hungatei. It could also grow on crotonate, hydroquinone and 2,5-dihydroxybenzoate in pure culture. Strain JI(T) utilized all of the three phthalate isomers as well as benzoate and 3-hydroxybenzoate for growth in co-culture with M. hungatei. No substrates were, however, found to support the axenic growth of strain JI(T). Neither strain JT(T) nor strain JI(T) could utilize sulfate, sulfite, thiosulfate, nitrate, fumarate, Fe (III) or 4-hydroxybenzoate as electron acceptor. Phylogenetically, strains JT(T) and JI(T) were relatively close to the members of the genera Pelotomaculum and Cryptanaerobacter in 'Desulfotomaculum lineage I'. Physiological and chemotaxonomic characteristics indicated that the two isolates should be classified into the genus Pelotomaculum, creating two novel species for them. Here, we propose Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov. for strain JT(T) and strain JI(T), respectively. The type strains are strains JT(T) (= DSM 16121(T )= JCM 11824(T )= NBRC 100523(T)) and JI(T) (= JCM 12282(T) = BAA-1053(T)) for P. terephthalicum and P. isophthalicum, respectively.

The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum

A Gram-positive, spore-forming, syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov. strain HHT, was isolated as a co-culture with Methanospirillum hungatei JF-1T from anaerobic, freeze-dried granular sludge obtained from an upflow anaerobic sludge bed reactor treating sugar beet wastewater. The bacterium converted propionate to acetate in co-culture with Methanospirillum hungatei JF-1T or Methanobacterium formicicum MFNT, but not in co-culture with Methanobrevibacter arboriphilus AZ. The organism could not be cultured axenically with any of the substrates tested and therefore can be considered as a (the first) true anaerobic syntrophic bacterium. The bacterium contained two distinct 16S rRNA gene sequences, with 96·8 % sequence similarity, which were both expressed during syntrophic growth on propionate as revealed by fluorescent in situ hybridization. The most closely related organisms are Cryptanaerobacter phenolicus LR7.2T, a bacterium that transforms phenol into benzoate, and Pelotomaculum thermopropionicum SIT, a thermophilic, syntrophic propionate-oxidizing bacterium. Other related species belong to the Gram-positive, sulfate-reducing genus Desulfotomaculum. The type strain of Pelotomaculum schinkii is strain HHT (=ATCC BAA-615T=DSM 15200T).