Domain Bacteria Research Articles

Precision Design of Antimicrobial Surfaces.

The overall expectation from an antimicrobial surface has been high considering the need for efficiency in preventing the attachment and growth of pathogenic microbes, durability, safety to both humans and environment as well as cost-effectiveness. To date, antimicrobial surface design has been mostly conducted liberally, without rigorous consideration of establishing robust structure-activity relationships for each design strategy or of the use intended for a specific antimicrobial material. However, the variability among the domain bacteria, which is the most diverse of all, alongside the highly dynamic nature of the bacteria-surface interface have taught us that the likelihood of finding universal antimicrobial surfaces is low. In this perspective we discuss some of the current hurdles faced by research in this promising field, emphasizing the relevance and complexity of probing the bacteria-surface interface, and explain why we feel it would greatly benefit from a more streamlined ad-hoc approach.

NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin.

Iron is an important micronutrient that is required by bacteria to proliferate and to cause disease. Many bacterial pathogens forage iron from human hemoglobin (Hb) during infections, which contains this metal within heme (iron–protoporphyrin IX). Several clinically important pathogenic species within the Firmicutes phylum scavenge heme using surface-displayed or secreted NEAr Transporter (NEAT) domains. In this review, we discuss how these versatile proteins function in the Staphylococcus aureus Iron-regulated surface determinant system that scavenges heme-iron from Hb. S. aureus NEAT domains function as either Hb receptors or as heme-binding chaperones. In vitro studies have shown that heme-binding NEAT domains can rapidly exchange heme amongst one another via transiently forming transfer complexes, leading to the interesting hypothesis that they may form a protein-wire within the peptidoglycan layer through which heme flows from the microbial surface to the membrane. In Hb receptors, recent studies have revealed how dedicated heme- and Hb-binding NEAT domains function synergistically to extract Hb’s heme molecules, and how receptor binding to the Hb-haptoglobin complex may block its clearance by macrophages, prolonging microbial access to Hb’s iron. The functions of NEAT domains in other Gram-positive bacteria are also reviewed.

Functional and Mechanistic Characterization of Heterochromatin-like Domains in Bacteria

Functional and Mechanistic Characterization of Heterochromatin-like Domains in Bacteria

Carotenoid Biosynthesis in the Phylum Actinobacteria.

Actinobacteria is the phylum that has the biggest genome in the Bacteria domain and includes many colored species. Their pigment analysis revealed that structurally diverse carotenoids are responsible for their pigmentation. This chapter reviews the biosynthesis of the diverse carotenoids of Actinobacteria. Its carotenoids belong to three different types: 1) carotenoid of C50 chain length, 2) carotenoids with aromatic end groups, and 3) keto carotenoid like canthaxanthin (β,β-carotene-4,4'-dione) or monocyclic keto-γ-carotene derivatives. Species from the genus Rhodococcus are the only known Actinobacteria with a simultaneous pathway to aromatic and to keto carotenoids.

Архейные сообщества мерзлых четвертичных пород морского генезиса на побережье о. Западный Шпицберген

The archaeal composition of permafrost samples taken during drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Gronfjord Bay of Western Spitsbergen has been studied. The study was based on the analysis of the V4 region of the 16S rRNA gene, carried out using next generation sequencing. This is the second part of the work dedicated to the prokaryotic composition of the Western Spitsbergen, the fi rst part was devoted to the domain of Bacteria. The general phyla of the the Archaea domain were Euryarchaeota, Bathyarchaeota, Thaumarchaeota and Asgardarchaeota. As a result of phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea were found. Methanobacteria class of methanogenic archaea was found in the controversial genesis, while methane-oxidizing archaea of the Methanomicrobia class of Methanosarcinales order were found in the marine permafrost of Cape Finneset: ANME-2a, -2b group was found in layers 8.6 and 11.7 m, and a group ANME-2d (Candidatus Methanoperedens) – in a layer of 6.5 m. Ammonium-oxidizing archaea of the phylum Thaumarchaeota was present in all types of permafrost, while Nitrososphaerales was detected in controversial genesis permafrost, and the order-Nitrosopumilales in the marine permafrost or controversial genesis ones. Representatives of phylum Bathyarchaeota were found in the stratigraphicly most ancient samples under this study. Superphylum Asgardarchaeota was met exclusively in the layers of permafrost with marine genesis and was represented by phyla Lokiarchaeota, Thorarchaeota and another group belonging to this superphylum that was not identified by us. The presence in the marine permafrost terrace of Cape Finneset at 11.7 m depth of methane, ethylene and ethane, as well as the composition of the archaeal community gives this layer to assume in it the presence of microbiological processes of the anaerobic oxidation of methane, probably received from Tertiary deposits before freezing. The results obtained are represented the permafrost of Spitsbergen as a rich archive of genetic information of little studied prokaryotic groups.

The evolution of the concept of the intestinal microbial-tissue complex

The human gastrointestinal tract is one of the largest in area — points of contact between the internal environment of the host and environmental factors.The most important functional element of this interaction is the microbial — tissue complex of the gastrointestinal tract, and its permeability is defined as a key option in the implementation of the mechanisms of adaptation and homeostasis.The microbiota is represented in various interpretations by the main four domains (archaea, bacteria or eubacteria, eukaryotes and viruses). The combination of these domains into the Biota taxon suggests the need to use the term biota-tissue complex, which more fully reflects the sophisticated interactions of all microbial-tissue complexes of the body.

Expanding magnetic organelle biogenesis in the domain Bacteria

BackgroundThe discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis.ResultsHere, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria.ConclusionsThese findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.AvdtuUL8bNKQaZ224H3AxpVideo

THERMOPHILIC PROKARYOTIC DIVERSITY OF EYNAL GEOTHERMAL SPRING AND PROTEASE PRODUCTION POTENTIALS OF ISOLATES

Thermophilic microorganisms are quite attractive for the study of biodiversity and evolutionary process as well as biotechnological applications. These organisms provide significant advantages for industrial and biotechnological processes occurring fast and efficiently at high temperatures. Possible potential also is getting increase thanks to isolation of new strains, determination of new metabolites and their pathway. Within the scope of this study, thermophilic bacterial community was investigated with a combination of classical microbiology and molecular biology approaches including fluorescent in situ hybridization, amplified ribosomal DNA restriction analysis, and polymerase chain reaction of 16S rRNA gene. Archaea and Bacteria domain were screened by Fluorescence in situ Hybridization technique. At the end of culture-dependent methodology, Paenibacillus lactis E3.1 (MK573857), Brevibacillus borstelensis E3.2 (MK573871), Paenibacillus naphthalenovorans E2.2 (MK573627), Paenibacillus sp. E3.5 (MK573870) were obtained. Furthermore, these isolates were screened with regards to protease production capabilities. At the end of screening studies, the highest protease activity (300 U/mg) was observed for Paenibacillus lactis E3.1.

Microbial Diversity and Community Structure in Alpine Stream Soil

Investigations of microbial communities over arsenic-polluted soils in an alpine stream are vital to collect pieces of evidence for their in situ-mediated bioremediation. It is the first time that microbial community activities are described in arsenic-polluted soils due to natural and anthropogenic sources along the alpine stream. Greater than 40 phyla from domain bacteria the 16S rRNA Illumina sequencing amplicons are exposed. In overall samples, Unweighted Pair Group Method with Arithmetic Mean (UPGMA) states that the most dominant phyla were Proteobacteria, Cyanobacteria, and Actinobacteria. Our result described that canonical correspondence analysis was used to elaborate more geochemical factors including arsenic, sulfate, total organic carbon, redox potential, and pH influence on the distribution of microbial groups in studies soil samples. Furthermore, Spearman’s rank correlation demonstrates a positive correlation between several specific taxonomic groups, refers to the phylotypes’ possible role in arsenic biogeochemical cycling. The present research could link the knowledge gap and facilitate our understanding for the bioremediation of arsenic at contaminated sites. Highlights We described the microbial communities in arsenic-contaminated soils. CCA revealed that chemical parameters organized microbial communities. The effects of geochemical conditions on microbial community composition were examined.

Characterization of microbial communities in commercial bee pollen used for mass rearing of Bombus impatiens

Bee pollen is a favorable microhabitat for many microorganisms and its dissemination via commercialization must be of important consideration. Here the data presented describe the characterization of bacteria and fungi community structure in seven commercial bee pollen samples from Europe, Mexico, and Chile, obtained from a commercial supplier, which were determined by amplicon-rRNA and ITS analysis. The results show that within the domain Bacteria, the most abundant phyla in all samples were Proteobacteria (24%–91%) and Firmicute (2%–74%), for fungi taxonomy classification was Ascomycota with a relative abundance of 30%–99%, followed by Basidiomycota with a relative abundance of 1%–39%. These results extend our knowledge of the microbial diversity associated with commercial bee pollen used for mass rearing of Bombus impatiens and may be useful in developing procedures for microbial control during its importation.

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.

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense.

CRISPR-associated Rossmann Fold (CARF) and SMODS-associated and fused to various effector domains (SAVED) are key components of cyclic oligonucleotide-based antiphage signaling systems (CBASS) that sense cyclic oligonucleotides and transmit the signal to an effector inducing cell dormancy or death. Most of the CARFs are components of a CBASS built into type III CRISPR-Cas systems, where the CARF domain binds cyclic oligoA (cOA) synthesized by Cas10 polymerase-cyclase and allosterically activates the effector, typically a promiscuous ribonuclease. Additionally, this signaling pathway includes a ring nuclease, often also a CARF domain (either the sensor itself or a specialized enzyme) that cleaves cOA and mitigates dormancy or death induction. We present a comprehensive census of CARF and SAVED domains in bacteria and archaea, and their sequence- and structure-based classification. There are 10 major families of CARF domains and multiple smaller groups that differ in structural features, association with distinct effectors, and presence or absence of the ring nuclease activity. By comparative genome analysis, we predict specific functions of CARF and SAVED domains and partition the CARF domains into those with both sensor and ring nuclease functions, and sensor-only ones. Several families of ring nucleases functionally associated with sensor-only CARF domains are also predicted.

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.

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.

Gut microbial composition changes in bladder cancer patients: A case-control study in Harbin, China.

This study aimed to explore the changes of gut bacteria in bladder cancer patients. Newly diagnosed bladder cancer patients were recruited. All participants completed a questionnaire about personal behavior and diet. Pyrosequencing of the total genomic DNA extracted from human feces was carried out by Illumina HiSeq 2000. The copy number of target DNA for bacteria was determined by real-time quantitative PCR assay. Fecal short chain fatty acids contents were measured by gas chromatography (GC) analysis. The concentrations of lipopolysaccharide and D-lactic acid in serum were determined by enzyme-linked immunosorbent assay kits. Fruit intake was significantly lower than in healthy controls. The numbers of Clostridium cluster XI and Prevotella in bladder cancer patients decreased. The numbers of domain bacteria and Prevotella were significantly and positively associated with fruit intake (r=0.002, p<0.05 for domain bacteria; r=0.004, p<0.05 for Prevotella). The concentration of butyric acid decreased significantly in bladder cancer patients, and the quantities of fecal butyric acid were significantly and positively associated with fruit intake (r=0.610, p<0.01). The concentrations of lipopolysaccharide and D-lactic acid, two sensitive markers of gut permeability, were greater in bladder cancer patients. Dysbiosis of gut microbiota, decreased butyric acid concentrations and impaired intestinal structural integrity were found in bladder cancer patients, which might be associated with inadequate fruit intake.

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.

Origin and Evolution of Polycyclic Triterpene Synthesis.

Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.

CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY

Van Lake, located in Eastern Anatolia Region, is the largest lake in Turkey. This lake features alkaline and saline soda lake. Since there are few studies focused on microbial diversity of alkaline environments, it is very important to reveal the diversity of microorganisms of Van Lake because of the wide range of biotechnological uses of these microorganisms and their ecological roles in lake ecosystem. Next generation sequencing (NGS) allow us to sequence DNA and RNA much more quickly and cheaply than the previously used Sanger sequencing for the rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of Van Lake, by assessing its PCR amplicon of 16S rDNA sequences (V3–V4 regions). The analyses revealed Proteobacteria, Actinobacteria and Verrucomicrobia phyla were most abundant. Archaea members were represented by Euryarchaeota phylum. Results concluded that Bacteria domain were dominant in Van Lake.