The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea

Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.

Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture

Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L-1), potassium (37-78 mg L-1), and zinc (8-17 mg L-1), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml-1). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm-1. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.

Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria

Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism to changing environmental conditions. Typically, these systems recognize signals through dedicated ligand binding domains (LBDs) to ultimately trigger a diversity of physiological responses. Nonetheless, an increasing number of reports reveal that signal transduction receptors also bind antagonists to inhibit responses mediated by agonists. The mechanisms by which antagonists block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used the LysR-type transcriptional regulator AdmX as a model. AdmX activates the expression of an antibiotic biosynthetic cluster in the rhizobacterium Serratia plymuthica. AdmX specifically recognizes the auxin phytohormone indole-3-acetic acid (IAA) and its biosynthetic intermediate indole-3-pyruvic acid (IPA) as signals. However, only IAA, but not IPA, was shown to regulate antibiotic production in S. plymuthica. Here, we report the high-resolution structures of the LBD of AdmX in complex with IAA and IPA. We found that IAA and IPA compete for binding to AdmX. Although IAA and IPA binding does not alter the oligomeric state of AdmX, IPA binding causes a higher degree of compactness in the protein structure. Molecular dynamics simulations revealed significant differences in the binding modes of IAA and IPA by AdmX, and the inspection of the three-dimensional structures evidenced differential agonist- and antagonist-mediated structural changes. Key residues for auxin binding were identified and an auxin recognition motif defined. Phylogenetic clustering supports the recent evolutionary emergence of this motif specifically in plant-associated enterobacteria. IMPORTANCE Although antagonists were found to bind different bacterial signal transduction receptors, we are still at the early stages of understanding the molecular details by which these molecules exert their inhibitory effects. Here, we provide insight into the structural changes resulting from the binding of an agonist and an antagonist to a sensor protein. Our data indicate that agonist and antagonist recognition is characterized by small conformational differences in the LBDs that can be efficiently transmitted to the output domain to modulate the final response. LBDs are subject to strong selective pressures and are rapidly evolving domains. An increasing number of reports support the idea that environmental factors drive the evolution of sensor domains. Given the recent evolutionary history of AdmX homologs, as well as their narrow phyletic distribution within plant-associated bacteria, our results are in accordance with a plant-mediated evolutionary process that resulted in the emergence of receptor proteins that specifically sense auxin phytohormones.

The Medium Cut-Off Membrane Does Not Lower Protein-Bound Uremic Toxins

The accumulation of protein-bound uremic toxins (PBUT) is associated with increased cardiovascular outcomes in patients on dialysis. However, the efficacy of PBUT removal for a medium-cutoff (MCO) membrane has not been clarified. This study was designed to assess the efficacy of PBUT clearance according to dialysis modalities. In this prospective and cross-over study, we enrolled 22 patients who received maintenance hemodiafiltration (HDF) thrice weekly from three dialysis centers. The dialysis removal of uremic toxins, including urea, beta 2-microglobulin (B2MG), lambda free light chain (λ-FLC), indoxyl sulfate (IS), and p-cresyl sulfate (pCS), was measured in the 22 patients on high-flux HD (HF-HD), post-dilution online HDF (post-OL-HDF), and MCO-HD over 3 weeks. The average convection volume in post-OL-HDF was 21.4 ± 1.8 L per session. The reduction rate (RR) of B2MG was higher in post-OL-HDF than in MCO-HD and HF-HD. The RR of λ-FLC was the highest in MCO-HD, followed by post-OL-HDF and HF-HD. The dialysate albumin was highest in MCO-HD, followed by post-OL-HDF and HF-HD. Post-dialysis plasma levels of IS and pCS were not statistically different across dialysis modalities. The total solute removal and dialytic clearance of IS and pCS were not significantly different. The clearance of IS and pCS did not differ between the HF-HD, post-OL-HDF, and MCO-HD groups.

Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance

Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.

Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants

Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.

A bacterial chemoreceptor that mediates chemotaxis to two different plant hormones

Indole-3-acetic acid (IAA) is the main naturally occurring auxin and is produced by organisms of all kingdoms of life. In addition to the regulation of plant growth and development, IAA plays an important role in the interaction between plants and growth-promoting and phytopathogenic bacteria by regulating bacterial gene expression and physiology. We show here that a IAA metabolizing plant-associated Pseudomonas putida isolate exhibits chemotaxis to IAA that is independent of auxin metabolism. We found that IAA chemotaxis is based on the activity of the PcpI chemoreceptor and heterologous expression of pcpI conferred IAA taxis to different environmental and human pathogenic isolates of the Pseudomonas genus. Using ligand screening, microcalorimetry and quantitative chemotaxis assays, we found that PcpI failed to bind IAA directly, but recognized and mediated chemoattractions to various aromatic compounds, including the phytohormone salicylic acid. The expression of pcpI and its role in the interactions with plants was also investigated. PcpI extends the range of central signal molecules recognized by chemoreceptors. To our knowledge, this is the first report on a bacterial receptor that responds to two different phytohormones. Our study reinforces the multifunctional role of IAA and salicylic acid as intra- and inter-kingdom signal molecules. This article is protected by copyright. All rights reserved.

Insight into the effects of regulating denitrification on composting: Strategies to simultaneously reduce environmental pollution risk and promote aromatic humic substance formation

Denitrification during composting is a hidden danger that causes environmental pollution risk and aromatic humic substance damage, which needs to be better regulate urgently. In this study, two denitrification regulation methods, moisture and biochar amendment, were conducted during chicken manure composting. Denitrification performance data showed two regulation methods obviously reduced NO₃^--N, NO₂^--N and N₂ contents. Humic substance increased by 25.3 % and 29.1 % under two regulations. Microbiological analysis indicated that two regulation methods could decreasing denitrifying functional microbes with aroma degradation capability. Subsequently, denitrification gene narG, nirS, nosZ were significantly inhibited (p < 0.05) and the aromatic degradation metabolism pathways were down-regulated. Correlation analysis further revealed the important influence of interspecific interactions and non-biological characteristics on functional microbes. These results provided important scientific basis to denitrification regulation in the practice of composting, which achieved the purpose of simultaneously controlling environmental pollution risk and conducing end-product formation.

Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?

The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.

Environmental aspects of hormones estriol, 17β-estradiol and 17α-ethinylestradiol: Electrochemical processes as next-generation technologies for their removal in water matrices

Hormones as a group of emerging contaminants have been increasingly used worldwide, which has increased their concern at the environmental level in various matrices, as they reach the water bodies through effluents due to the ineffectiveness of conventional treatments. Here we review the environmental scenario of hormones estriol (E3), 17β-estradiol (E2), and 17α-ethinylestradiol (EE2), explicitly their origins, their characteristics, interactions, how they reach the environment, and, above all, the severe pathological and toxicological damage to animals and humans they produce. Furthermore, studies for the treatment of these endocrine disruptors (EDCs) are deepened using electrochemical processes as the remediation methods of the respective hormones. In the reported studies, these micropollutants were detected in samples of surface water, underground, soil, and sediment at concentrations that varied from ng L^-1 to μg L^-1 and are capable of causing changes in the endocrine system of various organisms. However, although there are studies on the ecotoxicological effects concerning E3, E2, and EE2 hormones, little is known about their environmental dispersion and damage in quantitative terms. Moreover, biodegradation becomes the primary mechanism of removal of steroid estrogens removal by sewage treatment plants, but it is still inefficient, which shows the importance of studying electrochemically-driven processes such as the Electrochemical Advanced Oxidation Processes (EAOP) and electrocoagulation for the removal of emerging micropollutants. Thus, this review covers information on the occurrence of these hormones in various environmental matrices, their respective treatment, and effects on exposed organisms for ecotoxicology purposes.

Field Tracer Tests to Evaluate Transport Properties of Tryptophan and Humic Acid in Karst

The monitoring of water quality, especially of karst springs, requires methods for rapidly estimating and quantifying parameters that indicate contamination. In the last few years, fluorescence-based measurements of tryptophan and humic acid have become a promising tool to assess water quality in near real-time. In this study, we conducted comparative tracer tests in a karst experimental site to investigate the transport properties and behavior of tryptophan and humic acid in a natural karst aquifer. These two tracers were compared with the conservative tracer uranine. Fluorescence measurements were conducted with an online field fluorometer and in the laboratory. The obtained breakthrough curves (BTCs) and the modeling results demonstrate that (1) the online field fluorometer is suitable for real-time fluorescence measurements of all three tracers; (2) the transport parameters obtained for uranine, tryptophan, and humic acid are comparable in the fast flow areas of the karst system; (3) the transport velocities of humic acid are slower and the resulting residence times are accordingly higher, compared to uranine and tryptophan, in the slower and longer flow paths; (4) the obtained BTCs reveal additional information about the investigated karst system. As a conclusion, the experiments show that the transport properties of tryptophan are similar to those of uranine while humic acid is partly transported slower and with retardation. These findings allow a better and quantitative interpretation of the results when these substances are used as natural fecal and contamination indicators.

Bacterial catabolism of indole-3-acetic acid

Indole-3-acetic acid (IAA) is a molecule with the chemical formula C₁₀H₉NO₂, with a demonstrated presence in various environments and organisms, and with a biological function in several of these organisms, most notably in plants where it acts as a growth hormone. The existence of microorganisms with the ability to catabolize or assimilate IAA has long been recognized. To date, two sets of gene clusters underlying this property in bacteria have been identified and characterized: one (iac) is responsible for the aerobic degradation of IAA into catechol, and another (iaa) for the anaerobic conversion of IAA to 2-aminobenzoyl-CoA. Here, we summarize the literature on the products, reactions, and pathways that these gene clusters encode. We explore two hypotheses about the benefit that iac/iaa gene clusters confer upon their bacterial hosts: (1) exploitation of IAA as a source of carbon, nitrogen, and energy; and (2) interference with IAA-dependent processes and functions in other organisms, including plants. The evidence for both hypotheses will be reviewed for iac/iaa-carrying model strains of Pseudomonas putida, Enterobacter soli, Acinetobacter baumannii, Paraburkholderia phytofirmans, Caballeronia glathei, Aromatoleum evansii, and Aromatoleum aromaticum, more specifically in the context of access to IAA in the environments from which these bacteria were originally isolated, which include not only plants, but also soils and sediment, as well as patients in hospital environments. We end the mini-review with an outlook for iac/iaa-inspired research that addresses current gaps in knowledge, biotechnological applications of iac/iaa-encoded enzymology, and the use of IAA-destroying bacteria to treat pathologies related to IAA excess in plants and humans. KEY POINTS: • The iac/iaa gene clusters encode bacterial catabolism of the plant growth hormone IAA. • Plants are not the only environment where IAA or IAA-degrading bacteria can be found. • The iac/iaa genes allow growth at the expense of IAA; other benefits remain unknown.

Gut-Derived Protein-Bound Uremic Toxins

Chronic kidney disease (CKD) afflicts more than 500 million people worldwide and is one of the fastest growing global causes of mortality. When glomerular filtration rate begins to fall, uremic toxins accumulate in the serum and significantly increase the risk of death from cardiovascular disease and other causes. Several of the most harmful uremic toxins are produced by the gut microbiota. Furthermore, many such toxins are protein-bound and are therefore recalcitrant to removal by dialysis. We review the derivation and pathological mechanisms of gut-derived, protein-bound uremic toxins (PBUTs). We further outline the emerging relationship between kidney disease and gut dysbiosis, including the bacterial taxa altered, the regulation of microbial uremic toxin-producing genes, and their downstream physiological and neurological consequences. Finally, we discuss gut-targeted therapeutic strategies employed to reduce PBUTs. We conclude that targeting the gut microbiota is a promising approach for the treatment of CKD by blocking the serum accumulation of PBUTs that cannot be eliminated by dialysis.

Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions

Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.

Microbial community dynamics in mesophilic and thermophilic batch reactors under methanogenic, phenyl acid-forming conditions

BACKGROUND

Proteinaceous wastes exhibit high theoretical methane yields and their residues are considered valuable fertilisers. The routine anaerobic degradation of proteins often raises problems like high aromatic compound concentrations caused by the entry of aromatic amino acids into the system. A profound investigation of the consequences of aromatic compound exposure on various microorganisms, which cascade-like and interdependently degrade complex molecules to biogas, is still pending.

RESULTS

In mesophilic samples, methane was predominantly produced via acetoclastic methanogenesis. The highest positive correlation was observed between phenylacetate (PAA) and Psychrobacter spp. and between phenylpropionate (PPA) and Haloimpatiens spp. Moreover, Syntrophus spp. negatively correlated with PAA (Spearman's rank correlations coefficient (rs) = - 0.46, p < 0.05) and PPA concentrations (rs = - 0.44, p < 0.05) and was also associated with anaerobic benzene ring cleavage. In thermophilic samples, acetate was predominantly oxidised by Tepidanaerobacter spp. or Syntrophaceticus spp. in syntrophic association with a hydrogenotrophic methanogen. The genera Sedimentibacter and Syntrophaceticus correlated positively with both PAA and PPA concentrations. Moreover, Sedimentibacter spp., Tepidanaerobacter spp., Acetomicrobium spp., and Sporanaerobacter spp. were significant LEfSe (linear discriminant analysis effect size) biomarkers for high meso- as well as thermophilic phenyl acid concentrations. Direct negative effects of phenyl acids on methanogenic properties could not be proven.

CONCLUSIONS

Anaerobic phenyl acid formation is not restricted to specific microbial taxa, but rather done by various meso- and thermophilic bacteria. The cleavage of the highly inert benzene ring is possible in methanogenic batch reactors-at least in mesophilic fermentation processes. The results indicated that phenyl acids rather affect microorganisms engaged in preceding degradation steps than the ones involved in methanogenesis.

Evidences of aromatic degradation dominantly via the phenylacetic acid pathway in marine benthic Thermoprofundales

Thermoprofundales (Marine Benthic Group D archaea, MBG-D) is a newly proposed archaeal order and widely distributed in global marine sediment, and the members in the order may play a vital role in carbon cycling. However, the lack of pure cultures of these oeganisms has hampered the recognition of their catabolic roles. Here, by constructing high-quality metagenome-assembled genomes (MAGs) of two new subgroups of Thermoprofundales from hydrothermal sediment and predicting their catabolic pathways, we here provide genomic evidences that Thermoprofundales are capable of degrading aromatics via the phenylacetic acid (PAA) pathway. Then, the gene sequences of phenylacetyl-CoA ligase (PCL), a key enzyme for the PAA pathway, were searched in reference genomes. The widespread distribution of PCL genes among 14.9% of archaea and 75.9% of Thermoprofundales further supports the importance of the PAA pathway in archaea, particularly in Thermoprofundales where no ring-cleavage dioxygenases were found. Two PCLs from Thermoprofundales MAGs, PCL_M8-3 and PCL_M10-15 , were able to convert PAA to phenylacetyl-CoA (PA-CoA) in vitro, demonstrating the involvement of Thermoprofundales in aromatics degradation through PAA via CoA activation. Their acid tolerance (pH 5-7), high-optimum temperatures (60°C and 80°C), thermostability (stable at 60°C and 50°C for 48 h) and broad substrate spectra imply that Thermoprofundales are capable of transforming aromatics under extreme conditions. Together with the evidence of in situ transcriptional activities for most genes related to the aromatics pathway in Thermoprofundales, these genomic, and biochemical evidences highlight the essential role of this ubiquitous and abundant archaeal order in the carbon cycle of marine sediments.

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota

The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.IMPORTANCE Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them.

Small RNA NcS27 co-regulates utilization of carbon sources in Burkholderia cenocepacia J2315

Small non-coding sRNAs have versatile roles in regulating bacterial metabolism. Four short homologous Burkholderia cenocepacia sRNAs strongly expressed under conditions of growth arrest were recently identified. Here we report the detailed investigation of one of these, NcS27. sRNA NcS27 contains a short putative target recognition sequence, which is conserved throughout the order Burkholderiales. This sequence is the reverse complement of the Shine-Dalgarno sequence of a large number of genes involved in transport and metabolism of amino acids and carbohydrates. Overexpression of NcS27 sRNA had a distinct impact on growth, attenuating growth on a variety of substrates such as phenylalanine, tyrosine, glycerol and galactose, while having no effect on growth on other substrates. Transcriptomics and proteomics of NcS27 overexpression and silencing mutants revealed numerous predicted targets changing expression, notably of genes involved in degradation of aromatic amino acids phenylalanine and tyrosine, and in transport of carbohydrates. The conserved target recognition sequence was essential for growth phenotypes and gene expression changes. Cumulatively, our data point to a role of NcS27 in regulating the shutdown of metabolism upon nutrient deprivation in B. cenocepacia. We propose Burkholderiadouble-hairpin sRNA regulator bdhR1 as designation for ncS27.

An auxin controls bacterial antibiotics production

The majority of clinically used antibiotics originate from bacteria. As the need for new antibiotics grows, large-scale genome sequencing and mining approaches are being used to identify novel antibiotics. However, this task is hampered by the fact that many antibiotic biosynthetic clusters are not expressed under laboratory conditions. One strategy to overcome this limitation is the identification of signals that activate the expression of silent biosynthetic pathways. Here, we report the use of high-throughput screening to identify signals that control the biosynthesis of the acetyl-CoA carboxylase inhibitor antibiotic andrimid in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153. We reveal that the pathway-specific transcriptional activator AdmX recognizes the auxin indole-3-acetic acid (IAA). IAA binding causes conformational changes in AdmX that result in the inhibition of the expression of the andrimid cluster and the suppression of antibiotic production. We also show that IAA synthesis by pathogenic and beneficial plant-associated bacteria inhibits andrimid production in A153. Because IAA is a signalling molecule that is present across all domains of life, this study highlights the importance of intra- and inter-kingdom signalling in the regulation of antibiotic synthesis. Our discovery unravels, for the first time, an IAA-dependent molecular mechanism for the regulation of antibiotic synthesis.

Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity

The gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effect on the gut microbiota. The microbiota was isolated from mouse cecum and was exposed to tempol for 4 h under strict anaerobic conditions. The flow cytometry data suggested that short-term tempol exposure to the microbiota is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short-chain fatty acids, branched-chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating that the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology, and metabolism and a comparison of in vitro and in vivo exposures with tempol, suggest that physiologic and metabolic phenotyping can provide unique insight into gut microbiota toxicity. IMPORTANCE The gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global metabolomics with flow cytometry to evaluate the direct effect of tempol on the microbiota. This approach may be useful in deciphering how other xenobiotics directly influence the microbiota.

Adaptations to a Loss-of-Function Mutation in the Betaproteobacterium Aromatoleum aromaticum: Recruitment of Alternative Enzymes for Anaerobic Phenylalanine Degradation

Anaerobic phenylalanine (Phe) degradation in the betaproteobacterium Aromatoleum aromaticum involves transamination and decarboxylation to phenylacetaldehyde, followed by oxidation to phenylacetate. The latter reaction is catalyzed simultaneously by two enzymes, a highly specific phenylacetaldehyde dehydrogenase (PDH) and a rather unspecific tungsten-dependent aldehyde oxidoreductase (AOR). Attempting to establish increased synthesis of AOR, we constructed a mutant lacking the gene for PDH. This mutant still grew on phenylalanine, exhibiting increased AOR activities on medium containing tungstate. In the absence of tungstate, the mutant showed initially severe growth deficiency, but it resumed growth on Phe after longer incubation times. Moreover, the growth rates of the mutant increased during several reinoculation cycles on either tungstate-proficient or -deficient media, reaching the same values as recorded in wild-type strains. We confirmed AOR as the major alternative enzyme serving Phe degradation under tungstate-supplied conditions and identified and characterized the alternative NAD-dependent aldehyde dehydrogenase AldB taking over the function under tungstate-deficient conditions. Sequence analysis of the respective genes from adapted cultures under either growth condition revealed a mutation in the upstream region of the aor operon and a mutation within the coding region of aldB, which are likely involved in the observed adaptation of the deletion mutant to regain fast growth on Phe.IMPORTANCE The betaproteobacterium Aromatoleum aromaticum degrades many aromatic compounds under denitrifying conditions. One of the steps of phenylalanine degradation is catalyzed by two simultaneously induced enzymes, a NAD(P)-dependent phenylacetaldehyde dehydrogenase and a W-containing aldehyde oxidoreductase. We report here that the latter fully complements a constructed deletion mutant lacking the gene for phenylacetaldehyde dehydrogenase and is overproduced after several reinoculations. Moreover, an alternative NAD-dependent dehydrogenase is recruited to resume growth in tungstate-free medium, which does not allow the production of aldehyde oxidoreductase. This alternative enzyme is overproduced and seems to have acquired a point mutation in the active center. Our research illustrates the flexibility of environmentally important bacteria in adapting their metabolic pathways to new challenges within only a few generations.

Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari

Few microorganisms have been examined for current generation under thermophilic (40-65°C) or hyperthermophilic temperatures (≥80°C) in microbial electrochemical systems. Two iron-reducing archaea from the family Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A current density (j) of 0.68±0.11A/m² was attained in F. placidus MECs at 85°C, and 0.57±0.10A/m² in G. ahangari MECs at 80°C, with an applied voltage of 0.7V. Cyclic voltammetry (CV) showed that both strains produced a sigmoidal catalytic wave, with a mid-point potential of -0.39V (vs. Ag/AgCl) for F. placidus and -0.37V for G. ahangari. The comparison of CVs using spent medium and turnover CVs, coupled with the detection of peaks at the same potentials in both turnover and non-turnover conditions, suggested that mediators were not used for electron transfer and that both archaea produced current through direct contact with the electrode. These two archaeal species, and other hyperthermophilic exoelectrogens, have the potential to broaden the applications of microbial electrochemical technologies for producing biofuels and other bioelectrochemical products under extreme environmental conditions.

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs.

Enzymes of the benzoyl-coenzyme A degradation pathway in the hyperthermophilic archaeon Ferroglobus placidus

The Fe(III)-respiring Ferroglobus placidus is the only known archaeon and hyperthermophile for which a complete degradation of aromatic substrates to CO2 has been reported. Recent genome and transcriptome analyses proposed a benzoyl-coenzyme A (CoA) degradation pathway similar to that found in the phototrophic Rhodopseudomonas palustris, which involves a cyclohex-1-ene-1-carboxyl-CoA (1-enoyl-CoA) forming, ATP-dependent key enzyme benzoyl-CoA reductase (BCR). In this work, we demonstrate, by first in vitro studies, that benzoyl-CoA is ATP-dependently reduced by two electrons to cyclohexa-1,5-dienoyl-CoA (1,5-dienoyl-CoA), which is further degraded by hydration to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA (6-OH-1-enoyl-CoA); upon addition of NAD(+) , the latter was subsequently converted to β-oxidation intermediates. The four candidate genes of BCR were heterologously expressed, and the enriched, oxygen-sensitive enzyme catalysed the two-electron reduction of benzoyl-CoA to 1,5-dienoyl-CoA. A gene previously assigned to a 2,3-didehydropimeloyl-CoA hydratase was heterologously expressed and shown to act as a typical 1,5-dienoyl-CoA hydratase that does not accept 1-enoyl-CoA. A gene previously assigned to a 1-enoyl-CoA hydratase was heterologously expressed and identified to code for a bifunctional crotonase/3-OH-butyryl-CoA dehydrogenase. In summary, the results consistently provide biochemical evidence that F. placidus and probably other archaea predominantly degrade aromatics via the Thauera/Azoarcus type and not or only to a minor extent via the predicted R. palustris-type benzoyl-CoA degradation pathway.

Mechanisms involved in Fe(III) respiration by the hyperthermophilic archaeon Ferroglobus placidus

The hyperthermophilic archaeon Ferroglobus placidus can utilize a wide variety of electron donors, including hydrocarbons and aromatic compounds, with Fe(III) serving as an electron acceptor. In Fe(III)-reducing bacteria that have been studied to date, this process is mediated by c-type cytochromes and type IV pili. However, there currently is little information available about how this process is accomplished in archaea. In silico analysis of the F. placidus genome revealed the presence of 30 genes coding for putative c-type cytochrome proteins (more than any other archaeon that has been sequenced to date), five of which contained 10 or more heme-binding motifs. When cell extracts were analyzed by SDS-PAGE followed by heme staining, multiple bands corresponding to c-type cytochromes were detected. Different protein expression patterns were observed in F. placidus cells grown on soluble and insoluble iron forms. In order to explore this result further, transcriptomic studies were performed. Eight genes corresponding to multiheme c-type cytochromes were upregulated when F. placidus was grown with insoluble Fe(III) oxide compared to soluble Fe(III) citrate as an electron acceptor. Numerous archaella (archaeal flagella) also were observed on Fe(III)-grown cells, and genes coding for two type IV pilin-like domain proteins were differentially expressed in Fe(III) oxide-grown cells. This study provides insight into the mechanisms for dissimilatory Fe(III) respiration by hyperthermophilic archaea.