Domain Archaea Research Articles

Description of microbial diversity associated with ticks Hyalomma dromedarii (Acari: Ixodidae) isolated from camels in Hail region (Saudi Arabia) using massive sequencing of 16S rDNA.

Ticks are blood feeder able to transmit a wide diversity of microbes including pathogens. Therefore, it is of our interest to detect the diversity of microorganisms residing within ticks using massive sequencing of 16S rDNA. In this study, 200 adult ticks were collected from healthy camels in two localities from Hail province (Saudi Arabia). The analysis showed high microbial diversity dominated by the two domains (Archaea and Bacteria) associated with Hyalomma dromedarii from both regions. Proteobacteria (61.3%) and Firmicutes (31.2%) dominated the ticks from the Al Khotha region. While, the microbiome of ticks from the Al Gayed region was dominated by Proteobacteria (81.2%) and Firmicutes (9.2%). Twenty-three families were identified in the DNA-pool from the Al Gayed region, and was dominated by Pseudomonadaceae (45.37%), and Marinobacteraceae (14.39%) families. Francisellaceae (46%), Staphylococcaceae (24.26%) dominated the microbiome of the ticks collected from Al Gayed region. Thus, the genera Pseudomonas, Francisella, Proteus, Marinobacter, Glutamicibacter, Pedobacter, and Staphylococcus are largely distributed in the two identified microbiomes. This study concluded that ticks collected from the studied localities contained a wide range of microbial communities. These data have a great veterinary and medical importance in near future.

Temporal and vertical variability of bacterioplankton composition in Chipana bay (21º20’S) in a coastal upwelling system of northern Chile: A fluorescence in situ hybridization approach

The bacterioplankton in the upwelling systems associated with oceanographic condition of the oxygen minimum zone (OMZ) of the Eastern tropical South Pacific was studied through visualization and enumeration with fluorescent in situ hybridization (FISH). Six different taxonomic groups were studied (Alpha, Beta, Gamma-proteobacteria, Cytophaga-flavobacterium and the domains Archaea and Bacteria). The analysis showed a greater predominance of the Bacteria domain (20 to 68% of hybridized cells) over Archaea (2 to 18% of hybridized cells). The specific groups showed that Cytophaga-flavobacterium, Alpha-proteobacteria and Gamma-proteobacteria are more abundant in the surface layer. Gamma-proteobacteria is also most abundant in the deep oxycline and, Beta-proteobacteria is the group with the lowest registered abundances. Changes in the vertical distribution of the bacterial community in the water column between OMZ and on oxycline were observed through NMDS. This change is a product of a shift in the abundances of the specific groups Cytophaga-flavobacterium and Gamma-proteobacteria in the surface layers, due to low concentration of chlorophyll-a caused by periods of relaxation in the upwelling.

Archeal Di-O-geranylgeranyl Glyceryl Phosphate Synthase of a UbiA Superfamily Member Provides Insight into the Multiple Human Diseases.

One of the unique characteristic features of the domain archaea, are the lipids that form the hydrophobic core of their cell membrane. These membrane lipids are characterized by distinctive isoprenoid biochemistry and the building blocks are two core lipid structures, sn-2,3- diphytanyl glycerol diether (archaeol) and sn-2,3-dibiphytanyl diglycerol tetraether (caldarchaeol). Archaeol has two phytanyl chains (C20) in a bilayer structure connected to the glycerol moiety by an ether bond. The enzyme involved in this bilayer formation is Di-O-Geranylgeranyl Glyceryl Phosphate Synthase (DGGGPS), which is a member of a very versatile superfamily of enzymes known as UbiA superfamily. Multiple sequence analysis of the typical members of the UbiA superfamily indicates that the majority of conserved residues are located around the central cavity of these enzymes. Interestingly few of these conserved residues in the human homologs are centrally implicated in several human diseases, on basis of the major mutations reported against these diseases in the earlier clinical studies. It remains to be investigated about the role of these conserved residues in the biochemistry of these enzymes. The binding and active site of these enzymes found to be similar architecture but have different substrate affinities ranging from aromatic to linear compounds. So further investigation of UbiA superfamily may be translated to novel therapeutic and diagnostic application of these proteins in human disease management.

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.

Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remained elusive.

Fluorescent Labeling of Helminth Extracellular Vesicles Using an In Vivo Whole Organism Approach

In the last two decades, extracellular vesicles (EVs) from the three domains of life, Archaea, Bacteria and Eukaryotes, have gained increasing scientific attention. As such, the role of EVs in host-pathogen communication and immune modulation are being intensely investigated. Pivotal to EV research is the determination of how and where EVs are taken up by recipient cells and organs in vivo, which requires suitable tracking strategies including labelling. Labelling of EVs is often performed post-isolation which increases risks of non-specific labelling and the introduction of labelling artefacts. Here we exploited the inability of helminths to de novo synthesise fatty acids to enable labelling of EVs by whole organism uptake of fluorescent lipid analogues and the subsequent incorporation in EVs. We showed uptake of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (DOPE-Rho) in Anisakis spp. and Trichuris suis larvae. EVs isolated from the supernatant of Anisakis spp. labelled with DOPE-Rho were characterised to assess the effects of labelling on size, structure and fluorescence of EVs. Fluorescent EVs were successfully taken up by the human macrophage cell line THP-1. This study, therefore, presents a novel staining method that can be utilized by the EV field in parasitology and potentially across multiple species.

The LUCA and its complex virome.

The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis

In this work, a total of 72 samples of non-thermally treated commercial table olives were obtained from different markets of the world. Then, prokaryotic diversity in olive biofilms was investigated by metataxonomic analysis. A total of 660 different OTUs were obtained, belonging to Archaea (2.12%) and Bacteria domains (97.88%). From these, 41 OTUs with a proportion of sequences ≥ 0.01% were studied by compositional data analysis. Only two genera were found in all samples, Lactobacillus, which was the predominant bacteria in the biofilm consortium (median 54.99%), and Pediococcus (26.09%). Celerinatantimonas, Leuconostoc, Alkalibacterium, Pseudomonas, Marinilactibacillus, Weissella, and the family Enterobacteriaceae were also present in at least 80% of samples. Regarding foodborne pathogens, only Enterobacteriaceae, Vibrio, and Staphylococcus were detected in at least 91.66%, 75.00%, and 54.10% of samples, respectively, but their median values were always below 0.15%. Compositional data analysis allowed discriminating between lye treated and natural olive samples, as well as between olives packaged in glass, PET and plastic bags. Leuconostoc, Celerinatantimonas, and Alkalibacterium were the bacteria genera with a higher discriminant power among samples. These results expand our knowledge of the bacteria diversity in olive biofilms, providing information about the sanitary and hygienic status of this ready-to-eat fermented vegetable.

Methane, arsenic, selenium and the origins of the DMSO reductase family

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.

Methanogenic potential of diclofenac and ibuprofen in sanitary sewage using metabolic cosubstrates

Diclofenac (DCF) and ibuprofen (IBU) are widely used anti-inflammatory drugs and are frequently detected in wastewater from Wastewater Treatment Plants and in aquatic environments. In this study, the methanogenic potential (P) of anaerobic sludge subjected to DCF (7.11 ± 0.02 to 44.41 ± 0.05 mg L−1) and IBU (6.11 ± 0.01 to 42.61 ± 0.05 mg L−1), in sanitary sewage, was investigated in batch reactors. Cosubstrates (200 mg L−1 of organic matter) in the form of ethanol, methanol:ethanol and fumarate were tested separately for the removal of drugs. In the DCF assays, P was 6943 ± 121 μmolCH4, 9379 ± 259 μmolCH4, 9897 ± 212 μmolCH4 and 11,530 ± 368 μmolCH4 for control, fumarate, methanol:ethanol and ethanol conditions, respectively. In the IBU assays, under the same conditions, P was 6145 ± 101 μmolCH4, 6947 ± 66 μmolCH4, 8141 ± 191 μmolCH4and 10,583 ± 512 μmolCH4, respectively. Without cosubstrates, drug removal was below 18% for 43.10 ± 0.01 mgDCF L−1 and 43.12 ± 0.03 mgIBU L−1, respectively. Higher P and removal of DCF (28.24 ± 1.10%) and IBU (18.72 ± 1.60%) with ethanol was observed for 43.20 ± 0.01 mgDCF L−1 and 43.42 ± 0.03 mgIBU L−1, respectively. This aspect was better evidenced with DCF due to its molecular structure, a condition that resulted in a higher diversity of bacterial populations. Through the 16S rRNA sequencing, bacteria genera capable of performing aromatic ring cleavage, β-oxidation and oxidation of ethanol and fatty acids were identified. Higher relative abundance (>0.6%) was observed for Smithella, Sulfuricurvum and Synthophus for the Bacteria Domain and Methanosaeta (>79%) for the Archaea Domain. The use of ethanol favored greater mineralization of organic matter and greater methane production, which can directly assist in the metabolic pathways of microorganisms.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments.

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

Anti-CRISPR Proteins in Archaea.

Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.

Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes.

Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS’s condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.

Characterization of Halophilic Isolates Producing Bioactive Metabolites Against Pathogens

Halophiles are salt loving microorganisms that are able to survive in high salt conditions. Halophiles are highly diverse group belongs to all three domains of life, Archaea, bacteria and Eucarya. Halophiles adapted themselves through various strategies to maintain their osmotic balance in order to survive in high salt concentrations. Likewise halophiles are also able to produce bioactive molecules such as carotenoids, polyhydroxy-alkanoates, ectoine, bioplastics, and enzymes that have commercial importance. In current study halophiles were isolated at 1M NaCl concentration and characterized, and check its antibacterial activity against pathogenic E.coli, Pseudomonas aeruginosa and Klebsiella pneumonae. Two halophilic strains showed activity against pathogenic E.coli and Klebsiella pneumonae only. Antimicrobial activity was further analyzed through disc diffusion method and by using extracted filtrate. The activity only observed against E.coli after 48 hours old cultures that were served as filtrate extracts and discs against. Furthermore optimization as well as detailed characterization of the secondary metabolites will be needed to find the source of antibacterial metabolites against specific pathogens.

A Possible Primordial Acetyleno/Carboxydotrophic Core Metabolism.

Carbon fixation, in addition to the evolution of metabolism, is a main requirement for the evolution of life. Here, we report a one-pot carbon fixation of acetylene (C2H2) and carbon monoxide (CO) by aqueous nickel sulfide (NiS) under hydrothermal (>100 °C) conditions. A slurry of precipitated NiS converts acetylene and carbon monoxide into a set of C2–4-products that are surprisingly representative for C2–4-segments of all four central CO2-fixation cycles of the domains Bacteria and Archaea, whereby some of the products engage in the same interconversions, as seen in the central CO2-fixation cycles. The results suggest a primordial, chemically predetermined, non-cyclic acetyleno/carboxydotrophic core metabolism. This metabolism is based on aqueous organo–metal chemistry, from which the extant central CO2-fixation cycles based on thioester chemistry would have evolved by piecemeal modifications.

Functionalized Membrane Domains: An Ancestral Feature of Archaea?

Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.

Prokaryotic sigma factors and their transcriptional counterparts in Archaea and Eukarya.

RNA polymerases (RNAPs) carry out transcription in the three domains of life, Bacteria, Archaea, and Eukarya. Transcription initiation is highly regulated by a variety of transcription factors, whose number and subunit complexity increase during evolution. This process is regulated in Bacteria by the σ factor, while the three eukaryotic RNAPs require a complex set of transcription factors (TFs) and a TATA-binding protein (TBP). The archaeal transcription system appears to be an ancestral version of the eukaryotic RNAPII, requiring transcription factor B (TFB), TBP, and transcription factor E (TFE). The function of the bacterial sigma (σ) factor has been correlated to the roles played by the eukaryotic RNAP II and the archaeal RNAP. In addition, σ factors, TFB, and TFIIB all contain multiple DNA binding helix-turn-helix (HTH) structural motifs; although TFIIB and TFB display two HTH domains, while the bacterial σ factor spans 4 HTH motifs. The sequence similarities and structure alignments of the bacterial σ factor, eukaryotic TFIIB, and archaeal TFB evidence that these three proteins are homologs.Key Points• Transcription initiation is highly regulated by TFs.• Transcription is finely regulated in all domains of life by different sets of TFs.• Specific TFs in Bacteria, Eukarya and Archaea are homologs.

Molecular identification and evaluation of the impact of red heat damage causing halophilic microbes on salted hide and skin

Salt is widely used as preservative to protect animal skin from microbial attack. However, addition of salt creates a favorable condition for halophilic microorganisms associated with biodeterioration termed red heat damage. Knowledge about microbial diversity associated with red heat damage is expected to help develop appropriate control strategies. The objectives of this study were to isolate and characterize halophiles from salted sheepskin and evaluate their ability to degrade sheepskin. A total of 85 halophiles were isolated from salted sheepskins after enrichment in a medium containing 10%, 20% and 25% (w/v) NaCl and chopped sheepskin. In all the enrichment cultures the sheepskin was completely dissolved by the microbial consortia. Pure culture isolates belonging to the genera Halomonas, Bacillus, Salimicrobium, Nesterenkonia, and Marinococcus within Domain Bacteria and genus Halococcus from Domain Archaea were isolated. When tested independently, the isolates showed variation in their efficiency to hydrolyze sheepskin collagen. Isolate Halococcus sp. s2535 was the fastest in hydrolyzing the skin followed by Nesterenkonia sp. s2011, Marinococcus sp. s2526 and Halococcus sp. s2528. The results of this study demonstrate that halophilic microbes associated with red heat damage of salted sheepskin are highly diverse and preventive measures should target a diverse group of halophilic microbes.

Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.

Deciphering Pathways for Carotenogenesis in Haloarchaea.

Bacterioruberin and its derivatives have been described as the major carotenoids produced by haloarchaea (halophilic microbes belonging to the Archaea domain). Recently, different works have revealed that some haloarchaea synthetize other carotenoids at very low concentrations, like lycopene, lycopersene, cis- and trans-phytoene, cis- and trans-phytofluene, neo-β-carotene, and neo-α-carotene. However, there is still controversy about the nature of the pathways for carotenogenesis in haloarchaea. During the last decade, the number of haloarchaeal genomes fully sequenced and assembled has increased significantly. Although some of these genomes are not fully annotated, and many others are drafts, this information provides a new approach to exploring the capability of haloarchaea to produce carotenoids. This work conducts a deeply bioinformatic analysis to establish a hypothetical metabolic map connecting all the potential pathways involved in carotenogenesis in haloarchaea. Special interest has been focused on the synthesis of bacterioruberin in members of the Haloferax genus. The main finding is that in almost all the genus analyzed, a functioning alternative mevalonic acid (MVA) pathway provides isopentenyl pyrophosphate (IPP) in haloarchaea. Then, the main branch to synthesized carotenoids proceeds up to lycopene from which β-carotene or bacterioruberin (and its precursors: monoanhydrobacterioriberin, bisanhydrobacterioruberin, dihydrobisanhydrobacteriuberin, isopentenyldehydrorhodopsin, and dihydroisopenthenyldehydrorhodopsin) can be made.

Changes in the Phylogenetic Structure of the Metabolically Active Prokaryotic Soil Complex Induced by Oil Pollution

Molecular genetic techniques (FISH and metabarcoding) were used to investigate comparative biodiversity in the prokaryotic complex of soil microcosms of gray forest, chestnut, and chernozem soils before and after oil pollution. At the level of high-rank taxonomic units, the structure of prokaryotic communities from different soil types was similar. In oil-polluted microcosms microbial diversity decreased, and the metbolically active dominants of the Bacteria and Archaea domains changed compared to the control samples. A specific bacterial complex was found to emerge in experimental samples of all soil types, with predominance of the Gammaproteobacteria and Actinobacteria, as well as of archaea, among which Thaumarchaeota and Crenarchaeota prevailed. Members of the soil prokaryotic complex active and inactive in respect to oil pollution were determined. Our results indicate similar succession responses of microbial communities from different soil type to oil pollution.