Micrococcus luteus -- survival in amber

Exploration of ureolytic airborne bacteria for biocementation applications from different climate zones in Japan

The present study investigated the ureolytic airborne bacteria for microbial induced carbonate precipitation (MICP) applications, seeking resilient strains in order to address the problems of bacterial survivability and adaptability in biocementation treatment and to contribute a robust approach that can effectively stabilize diverse soils. Since the airborne bacteria tend to survive in dynamic environments, they are believed to possess remarkable adaptability in harsh conditions, thus holding great potential for engineering applications. Samplings across diverse climatic zones revealed that approximately 10-20% of the isolates were ureolytic bacteria in each sampling site. A series of characterization tests were conducted on selected strains to study the temperature dependency of urease activity. The results revealed that many of these isolates are unique in many aspects. For instance, some trains of Glutamicibacter sp. were found to precipitate extra-large calcium carbonate crystals that could be beneficial in the cementation of coarse soils. This study stands out from previous research on standard ureolytic bacteria by focusing on the exploration of airborne bacteria. The findings demonstrate that a significant number of ureolytic airborne bacteria have great potential, suggesting that the air can serve as a bacterial isolation source for MICP applications.

Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station

Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.

Micrococcus spp. as a promising source for drug discovery: A review

Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.

The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans

The present research investigated whether accidental contact through stinging with honeybees, wasps, and hornets could represent a microbial hazard for humans. It has been previously suggested that such contact may transmit pathogens causing infections that could even be fatal for some susceptible individuals. Stinging simulation experiments were performed in the lab with live insects collected from the environment in Lemnos Island (north-eastern Greece), while different selective agar media targeting some clinically important bacteria (i.e., Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis/faecium, and Pseudomonas aeruginosa) were used as substrates for microbial recovery and identification. Results revealed none of the target pathogenic bacterial species in the honeybee samples, with bacilli, staphylococci, and micrococci dominating their surveyed microbiota. However, most of the suspect colonies isolated from wasps and hornets belonged to important hygienic indicators (i.e., enterococci, Proteus mirabilis, and coliforms), implying possible contact of these insects with fecal origin materials. To sum up, the microbiota that may be transmitted to humans through stinging appears to differ between honeybees and wasps/hornets, while the isolation from the latter samples of some other important opportunistic pathogens, such as Enterobacter spp. and Klebsiella spp., also known for multidrug resistance, could be an additional reason of concern.

MicroRNAs reshape the immunity of insects in response to bacterial infection

The interaction between bacteria and insects can significantly impact a wide range of different areas because bacteria and insects are widely distributed around the globe. The bacterial-insect interactions have the potential to directly affect human health since insects are vectors for disease transmission, and their interactions can also have economic consequences. In addition, they have been linked to high mortality rates in economically important insects, resulting in substantial economic losses. MicroRNAs (miRNAs) are types of non-coding RNAs involved in regulating gene expression post-transcriptionally. The length of miRNAs ranges from 19 to 22 nucleotides. MiRNAs, in addition to their ability to exhibit dynamic expression patterns, have a diverse range of targets. This enables them to govern various physiological activities in insects, like innate immune responses. Increasing evidence suggests that miRNAs have a crucial biological role in bacterial infection by influencing immune responses and other mechanisms for resistance. This review focuses on some of the most recent and exciting discoveries made in recent years, including the correlation between the dysregulation of miRNA expression in the context of bacterial infection and the progression of the infection. Furthermore, it describes how they profoundly impact the immune responses of the host by targeting the Toll, IMD, and JNK signaling pathways. It also emphasizes the biological function of miRNAs in regulating immune responses in insects. Finally, it also discusses current knowledge gaps about the function of miRNAs in insect immunity, in addition to areas that require more research in the future.

Bacterial Communities in Effluents Rich in Phenol and Their Potential in Bioremediation: Kinetic Modeling

Phenol is used in the manufacturing process of phenolic resins from which residues remain that must be sent for confinement. For that reason, in this study, the wastewater of a resin factory was analyzed to isolate the bacteria present, identify them by molecular methods and finally evaluate their impact on bioremediation treatment. A total of 15 bacteria were isolated, of these, eight belong to the genus Bacillus spp. All bacteria were individually multiplied and inoculated in clusters in 15 L reactors which were carefully monitored for pH, electrical conductivity, chemical oxygen demand and temperature. The acquired data were analyzed using ANOVA with repeated measurements. The first test revealed that native bacterial communities reduce the phenol content by up to 20% and COD by 49%, which is significant with respect to the reactor not being inoculated with bacteria. Furthermore, when a mathematical model was applied to the reactors, it was shown that the bacteria require an adaptation time of approximately 100 h. A second test where the inoculation was interspersed with the addition of lime as a flocculant showed that, even though the reduction in phenol and COD was lower than in the previous test, the difference between treatments and control is statistically significant (α ≤ 0.05).

Comparative Insights into the Antimicrobial, Antioxidant, and Nutritional Potential of the Solanum nigrum Complex

Solanum nigrum is a traditional medicinal plant renowned as a cure for many diseases due to the presence of bioactive compounds. The Solanum nigrum complex refers to a group of more than 30 closely related but morphologically distinct taxa. Five indigenous taxa of this complex were investigated for their medicinal potential by using methanolic extracts. The efficacy of each plant was different for each of the seven bacteria studied. On comparing the MIC values, S. americanum was found to be most potent against Bacillus licheniformis (34 µg/mL), S. chenopodioides against Escherichia coli (78 µg/mL), S. nigrum against Bacillus licheniformis (49 µg/mL) and Escherichia coli (49 µg/mL), S. retroflexum against Escherichia coli (30 µg/mL), and S. villosum against Proteus mirabilis (45 µg/mL). The extracts were also subjected to six antioxidant assays. Moderate scavenging activity was observed by all plants in the DPPH free radical assay, but S. chenopodioides was the most effective. The total phenolic contents of the five plants were comparable, but the gallic acid equivalents of S. americanum and S. nigrum were the highest (26.58 mg/100 g GAE). The highest Trolox equivalent antioxidant capacity was observed for S. retroflexum, with the ABTS assay giving a TEAC value of 33.88 mM/100 g of dry weight. Metal-chelating activity against Fe2+ was observed to be highest for S. chenopodioides (70.37%). The FRAP value of S. nigrum was the highest (8.5 mM FeSO4·7H2O) among all taxa. The lipid peroxidation trend was very similar for all five samples. The results suggest the specified medicinal use of different members of the Solanum nigrum complex, which will also have significant nutritional value.

A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732

Mutants of M. luteus strain ATCC49732 lacking the yellow pigment sarcinaxanthin were observed at an unexpectedly high frequency and the molecular basis was investigated. PCR probing revealed complete deletion of the crt biosynthetic operon in 11/14 mutants. Inverse PCR was used to identify a common breakpoint 35 kb downstream from crt precisely at the end of the right inverted repeat (IRR) of a partial ISMlu8 element that lies between two inversely oriented full-length ISMlu2. Three different breakpoints 5′ to crt were found with the sequence CTAG one bp 5′ to each novel junction. Analysis of 35 genomic sites with single ISMlu8 insertions showed that ISMlu8 transposase has high specificity for CTAG, implicating its key role in formation of the Δcrt deletions. No downstream deletion endpoints were observed at an immediately adjacent ISMlu8 with a nearly identical IRR in the same orientation and slightly closer to the crt operon, indicating that access of ISMlu8 transposase to the ISMlu2-flanked ISMlu8 IRR is greatly enhanced by the surrounding inverted repeat arrangement. The association of high frequency genomic rearrangement with this distinctive natural configuration of ISs from two different IS families offers a new insight into IS element evolutionary potential.

Microbiological Survey of 47 Permanent Makeup Inks Available in the United States

In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on permanent makeup (PMU) inks. We conducted a survey of 47 unopened PMU inks from nine manufacturers and a comparative species-centric co-occurrence network (SCN) analysis using the survey results. Aerobic plate count and enrichment culture methods using the FDA's Bacteriological Analytical Manual (BAM) Chapter 23 revealed that 9 (19%) inks out of 47, from five manufacturers, were contaminated with microorganisms. The level of microbial contamination was less than 250 CFU/g in eight inks and 980 CFU/g in one ink. We identified 26 bacteria that belong to nine genera and 21 species, including some clinically relevant species, such as Alloiococcus otitis, Dermacoccus nishinomiyaensis, Kocuria rosea, and Pasteurella canis. Among the identified microorganisms, the SCN analysis revealed dominance and a strong co-occurrence relation of spore-forming extreme environment survivors, Bacillus spp., with close phylogenetic/phenotypic relationships. These results provide practical insights into the possible microbial contamination factors and positive selection pressure of PMU inks.

Bacterial age distribution in soil - Generational gaps in adjacent hot and cold spots

Resource patchiness and aqueous phase fragmentation in soil may induce large differences local growth conditions at submillimeter scales. These are translated to vast differences in bacterial age from cells dividing every thirty minutes in close proximity to plant roots to very old cells experiencing negligible growth in adjacent nutrient poor patches. In this study, we link bacterial population demographics with localized soil and hydration conditions to predict emerging generation time distributions and estimate mean bacterial cell ages using mechanistic and heuristic models of bacterial life in soil. Results show heavy-tailed distributions of generation times that resemble a power law for certain conditions, suggesting that we may find bacterial cells of vastly different ages living side by side within small soil volumes. Our results imply that individual bacteria may exist concurrently with all of their ancestors, resulting in an archive of bacterial cells with traits that have been gained (and lost) throughout time-a feature unique to microbial life. This reservoir of bacterial strains and the potential for the reemergence of rare strains with specific functions may be critical for ecosystem stability and function.

Propionic acid bacteria in the food industry: An update on essential traits and detection methods

Propionic acid bacteria (PAB) is an umbrella term for a group of bacteria with the ability to produce propionic acid. In the past, due to this common feature and other phenotypic similarities, genetically heterogeneous bacteria were considered as a single genus, Propionibacterium. Members of this genus ranged from "dairy propionibacteria," which are widely known for their role in eye and flavor formation in cheese production, to "cutaneous propionibacteria," which are primarily associated with human skin. In 2016, the introduction of two new genera based on genotypic data facilitated a clear separation of cutaneous (Cutibacterium spp.) from dairy PAB (Propionibacterium spp., Acidipropionibacterium spp.). In light of these taxonomic changes, but with particular emphasis on dairy PAB, this review describes the current state of knowledge about metabolic pathways and other characteristics such as antibiotic resistance and virulence factors. In addition, the relevance of dairy PAB for the food industry and cheese production in particular is highlighted. Furthermore, methods for cultivation, detection, and enumeration are reviewed, incorporating the current taxonomy as well as the potential for routine applications.

Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station

Whole-genome sequences were generated from 96 bacterial strains of 14 species that were isolated from International Space Station surfaces during the Microbial Tracking 2 study. Continued characterization of this closed habitat's microbiome enables tracking of the spread and evolution of secondary pathogens, which is vital for astronaut health.

Whole-genome sequences were generated from 96 bacterial strains of 14 species that were isolated from International Space Station surfaces during the Microbial Tracking 2 study. Continued characterization of this closed habitat's microbiome enables tracking of the spread and evolution of secondary pathogens, which is vital for astronaut health.

Three-electrode galvanic microcells as a new antimicrobial tool

This study presents the first research related to fungal and bacterial growth within electromagnetic fields generated by three-electrode galvanic cells, with PDA growth medium as an electrolyte. We used galvanic microcells constructed with copper, bismuth and zinc metal bars. The configuration of these electrodes was a fundamental agent in the creation of a maximum inhibition zone and in bismuth ion movement. Fungal strains, such as Aspergillus tubingensis and Rhodotorula mucilaginosa, and the bacterium Micrococcus luteus were used as model organisms.

Proteomes of the past: the pursuit of proteins in paleontology

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.

Complete Genome Sequence of Micrococcus luteus Strain SGAir0127, Isolated from Indoor Air Samples from Singapore

Micrococcus luteus strain SGAir0127 was isolated from indoor air samples collected in Singapore. The assembly, based on single-molecule real-time sequencing reads, resulted in two contigs, one chromosomal contig with a length of 2.57 Mbp and one nonchromosomal contig of 8.68 kbp. The genome has a total of 2,564 genes.

Micrococcus luteus strain SGAir0127 was isolated from indoor air samples collected in Singapore. The assembly, based on single-molecule real-time sequencing reads, resulted in two contigs, one chromosomal contig with a length of 2.57 Mbp and one nonchromosomal contig of 8.68 kbp. The genome has a total of 2,564 genes.

Microbial ageing and longevity

Longevity reflects the ability to maintain homeostatic conditions necessary for life as an organism ages. A long-lived organism must contend not only with environmental hazards but also with internal entropy and macromolecular damage that result in the loss of fitness during ageing, a phenomenon known as senescence. Although central to many of the core concepts in biology, ageing and longevity have primarily been investigated in sexually reproducing, multicellular organisms. However, growing evidence suggests that microorganisms undergo senescence, and can also exhibit extreme longevity. In this Review, we integrate theoretical and empirical insights to establish a unified perspective on senescence and longevity. We discuss the evolutionary origins, genetic mechanisms and functional consequences of microbial ageing. In addition to having biomedical implications, insights into microbial ageing shed light on the role of ageing in the origin of life and the upper limits to longevity.

Extracellular DNA Provides Structural Integrity to a Micrococcus luteus Biofilm

Force spectroscopy was used to show that extracellular DNA (eDNA) has a pre-eminent structural role in a biofilm. The adhesive behavior of extracellular polymeric substances to poly(ethylene terephthalate), a model hydrophobic surface, was measured in response to their degradation by hydrolytic enzymes known for their biofilm dispersion potential: DNaseI, protease, cellulase, and mannanase. Only treatment with DNaseI significantly decreased the adhesive force of the model bacterium Micrococcus luteus with the surface, and furthermore this treatment almost completely eliminated any components of the biofilm maintaining the adhesion, establishing a key structural role for eDNA.

Application of next generation sequencing technology on contamination monitoring in microbiology laboratory

The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.

Evolution with a seed bank: The population genetic consequences of microbial dormancy

Dormancy is a bet‐hedging strategy that allows organisms to persist through conditions that are suboptimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long‐term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence the evolutionary dynamics of microorganisms as well as other taxa.

Comparative analysis of airborne bacteria and fungi in two salt mines in Poland

The aim of this work was to determine the genera or species composition and the number of colony forming units of airborne bacteria and fungi, respectively, in two salt mines in Poland "Wieliczka" (Lesser Poland) and "Polkowice-Sieroszowice" (Lower Silesia). Both of them are working environments characterized by extreme conditions, and additionally "Wieliczka," officially placed on the UNESCO World Heritage Sites' list, plays a role of tourist attraction. There are also some curative chambers located in this mine. Air samples were taken once in December 2015, between 6:00 a.m. and 9:00 a.m. There were nine measurement points located about 200 m underground in "Wieliczka" and six measurement points located in the working shafts about 400 m underground in "Polkowice-Sieroszowice." The total volume of each air sample was 150 L. Air samples, collected in individual measurement points of both salt mines, were inoculated on two microbiological media: potato dextrose agar and tryptic soy agar using the impact method. We identified 10 and 3 fungal genera in the "Wieliczka" Salt Mine and in "Polkowice-Sieroszowice," respectively. The most common were fungi of the Penicillium genus. In both mines, the Gram-positive bacteria of genus Micrococcus were detected most frequently. Among identified microorganisms, there were neither pathogenic fungi nor bacteria. The most prevalent microorganisms detected in indoor air were Gram-positive cocci, which constituted up to 80% of airborne microflora. Our results showed that microorganisms recorded in the air samples are not a threat to workers, tourists or patients. Neither pathogens nor potentially pathogenic microorganisms, listed as BSL-2, BSL-3 or BSL-4, were detected. The microbes identified during our analysis commonly occur in such environments as the soil, water and air. Some of the detected bacteria are component of natural microflora of human skin and mucous membranes, and they can cause only opportunistic infections in individuals depending on their health condition.

A Proteomic Signature of Dormancy in the Actinobacterium Micrococcus luteus

Dormancy is a protective state in which diverse bacteria, including Mycobacterium tuberculosis, Staphylococcus aureus, Treponema pallidum (syphilis), and Borrelia burgdorferi (Lyme disease), curtail metabolic activity to survive external stresses, including antibiotics. Evidence suggests dormancy consists of a continuum of interrelated states, including viable but nonculturable (VBNC) and persistence states. VBNC and persistence contribute to antibiotic tolerance, reemergence from latent infections, and even quorum sensing and biofilm formation. Previous studies indicate that the protein mechanisms regulating persistence and VBNC states are not well understood. We have queried the VBNC state of Micrococcus luteus NCTC 2665 (MI-2665) by quantitative proteomics combining gel electrophoresis, high-performance liquid chromatography, and tandem mass spectrometry to elucidate some of these mechanisms. MI-2665 is a nonpathogenic actinobacterium containing a small (2.5-Mb), high-GC-content genome which exhibits a well-defined VBNC state induced by nutrient deprivation. The MI-2665 VBNC state demonstrated a loss of protein diversity accompanied by increased levels of 18 proteins that are conserved across actinobacteria, 14 of which have not been previously identified in VNBC. These proteins implicate an anaplerotic strategy in the transition to VBNC, including changes in the glyoxylate shunt, redox and amino acid metabolism, and ribosomal regulatory processes. Our data suggest that MI-2665 is a viable model for dissecting the protein mechanisms underlying the VBNC stress response and provide the first protein-level signature of this state. We expect that this protein signature will enable future studies deciphering the protein mechanisms of dormancy and identify novel therapeutic strategies effective against antibiotic-tolerant bacterial infections.IMPORTANCE Dormancy is a protective state enabling bacteria to survive antibiotics, starvation, and the immune system. Dormancy is comprised of different states, including persistent and viable but nonculturable (VBNC) states that contribute to the spread of bacterial infections. Therefore, it is imperative to identify how bacteria utilize these different dormancy states to survive antibiotic treatment. The objective of our research is to eliminate dormancy as a route to antibiotic tolerance by understanding the proteins that control dormancy in Micrococcus luteus NCTC 2665. This bacterium has unique advantages for studying dormancy, including a small genome and a well-defined and reproducible VBNC state. Our experiments implicate four previously identified and 14 novel proteins upregulated in VBNC that may regulate this critical survival mechanism.

Effect of different salinity adaptation on the performance and microbial community in a sequencing batch reactor

The performance and microbial community profiles in a sequencing batch reactor (SBR) treating saline wastewater were studied over 300days from 0wt% to 3.0wt% salinity. The experimental results indicated that the activated sludge had high sensitivity to salinity variations in terms of pollutants removal and sedimentation. At 2.0wt% salinity, the system retained a good performance, and 95% removal rate of chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4(+)-N and total phosphorus (TP) could be achieved. Operation before addition salinity revealed the optimal performance and the most microbial diversity indicated by 16S rRNA gene clone library. Sequence analyses illustrated that Candidate_division_TM7 (TM7) was predominant at 2.0 wt% salinity; however, Actinobacteria was more abundant at 3.0wt% salinity.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy

The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11^th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.

Antimicrobial Air Filters Using Natural Euscaphis japonica Nanoparticles

Controlling bioaerosols has become more important with increasing participation in indoor activities. Treatments using natural-product nanomaterials are a promising technique because of their relatively low toxicity compared to inorganic nanomaterials such as silver nanoparticles or carbon nanotubes. In this study, antimicrobial filters were fabricated from natural Euscaphis japonica nanoparticles, which were produced by nebulizing E. japonica extract. The coated filters were assessed in terms of pressure drop, antimicrobial activity, filtration efficiency, major chemical components, and cytotoxicity. Pressure drop and antimicrobial activity increased as a function of nanoparticle deposition time (590, 855, and 1150 µg/cm2(filter) at 3-, 6-, and 9-min depositions, respectively). In filter tests, the antimicrobial efficacy was greater against Staphylococcus epidermidis than Micrococcus luteus; ~61, ~73, and ~82% of M. luteus cells were inactivated on filters that had been coated for 3, 6, and 9 min, respectively, while the corresponding values were ~78, ~88, and ~94% with S. epidermidis. Although statistically significant differences in filtration performance were not observed between samples as a function of deposition time, the average filtration efficacy was slightly higher for S. epidermidis aerosols (~97%) than for M. luteus aerosols (~95%). High-performance liquid chromatography (HPLC) and electrospray ionization-tandem mass spectrometry (ESI/MS) analyses confirmed that the major chemical compounds in the E. japonica extract were 1(ß)-O-galloyl pedunculagin, quercetin-3-O-glucuronide, and kaempferol-3-O-glucoside. In vitro cytotoxicity and disk diffusion tests showed that E. japonica nanoparticles were less toxic and exhibited stronger antimicrobial activity toward some bacterial strains than a reference soluble nickel compound, which is classified as a human carcinogen. This study provides valuable information for the development of a bioaerosol control system that is environmental friendly and suitable for use in indoor environments.

Nonphotosynthetic pigments as potential biosignatures

Previous work on possible surface reflectance biosignatures for Earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on Earth, such as the vegetation red edge. Although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. We present an interdisciplinary study of the diversity and detectability of nonphotosynthetic pigments as biosignatures, which includes a description of environments that host nonphotosynthetic biologically pigmented surfaces, and a lab-based experimental analysis of the spectral and broadband color diversity of pigmented organisms on Earth. We test the utility of broadband color to distinguish between Earth-like planets with significant coverage of nonphotosynthetic pigments and those with photosynthetic or nonbiological surfaces, using both 1-D and 3-D spectral models. We demonstrate that, given sufficient surface coverage, nonphotosynthetic pigments could significantly impact the disk-averaged spectrum of a planet. However, we find that due to the possible diversity of organisms and environments, and the confounding effects of the atmosphere and clouds, determination of substantial coverage by biologically produced pigments would be difficult with broadband colors alone and would likely require spectrally resolved data.

Spectroscopic and biological approach of Ni(II), Cu(II) and Co(II) complexes of 4-methoxy/ethoxybenzaldehyde thiosemicarbazone glyoxime

Two novel vicinal dioxime ligands containing (4-methoxybenzaldehyde thiosemicarbazone glyoxime (L(1)H2) or 4-ethoxybenzaldehyde thiosemicarbazone glyoxime (L(2)H2)) thiosemicarbazone units were synthesized and characterized using (1)H NMR, (13)C NMR, HMQC, MS, infrared and, UV-VIS. spectroscopy, elemental analysis, and magnetic susceptibility measurements. Mononuclear nickel(II), copper(II) and cobalt(II) complexes with a metal:ligand ratio of 1:2 for L(1)H2 and L(2)H2 were also synthesized. The effect of pH and solvent on the absorption spectra of both ligands and complexes was determined. IR spectra show that the ligands act in a bidentate manner and coordinates N4 donor groups of the ligands to Ni(II), Cu(II) and Co(II) ions. The detection of H-bonding (O-H⋯O) in the [M(LH)2] metal complexes by IR spectra supported the square-planar MN4 coordination of mononuclear complexes. The antimicrobial activities of compounds L(1)H2, L(2)H2, and their Ni(II), Cu(II) and Co(II) complexes were evaluated using the disc diffusion method against 12 bacteria and 4 yeasts. The minimal inhibitory concentrations (MICs) against 7 bacteria and 3 yeasts were also determined. Among the test compounds attempted, L(1)H2, [Ni(L1H)2], [Cu(L1H)2], L2H2, [Ni(L2H)2] and [Cu(L2H)2] showed some activities against certain Gram-positive bacteria and some of the yeasts tested.

luxS in bacteria isolated from 25- to 40-million-year-old amber

Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., amber isolates exhibited unique 16S rRNA gene phylogenies. This suggests that luxS may have been acquired by horizontal transfer millions of years ago. Molecular clocks of luxS suggest slow evolutionary rates, similar to those of the 16S rRNA gene and consistent with a conserved gene. Dendograms of the 16S rRNA gene and luxS show two separate clusters for the extant and ancient bacteria, confirming the uniqueness of the latter group.

Whole-Genome Sequencing of Micrococcus luteus Strain Modasa, of Indian Origin

The hydrocarbon-degrading bacterium Micrococcus luteus strain Modasa was isolated from contaminated soil from Modasa, North Gujarat, India. Whole-genome sequencing and analysis provide an insight into the potentially important genes responsible for bioremediation.

Extrachromosomal genetic elements in Micrococcus

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

Photocatalytic elimination of indoor air biological and chemical pollution in realistic conditions

The photocatalytic elimination of microorganisms from indoor air in realistic conditions and the feasibility of simultaneous elimination of chemical contaminants have been studied at laboratory scale. Transparent polymeric monoliths have been coated with sol-gel TiO(2) films and used as photocatalyst to treat real indoor air in a laboratory-scale single-step annular photocatalytic reactor. The analytical techniques used to characterize the air quality and analyze the results of the photocatalytic tests were: colony counting, microscopy and PCR with subsequent sequencing for microbial quantification and identification; automated thermal desorption coupled to gas chromatography with mass spectrometry detection for chemical analysis. The first experiments performed proved that photocatalysis based on UVA-irradiated TiO(2) for the reduction of the concentration of bacteria in the air could compete with the conventional photolytic treatment with UVC radiation, more expensive and hazardous. Simultaneously to the disinfection, the concentration of volatile organic compounds was greatly reduced, which adds value to this technology for real applications. The fungal colony number was not apparently modified.

A bacterial enrichment study and overview of the extractable lipids from paleosols in the Dry Valleys, Antarctica: implications for future Mars reconnaissance

The Dry Valleys of Antarctica are one of the coldest and driest environments on Earth with paleosols in selected areas that date to the emplacement of tills by warm-based ice during the Early Miocene. Cited as an analogue to the martian surface, the ability of the Antarctic environment to support microbial life-forms is a matter of special interest, particularly with the upcoming NASA/ESA 2018 ExoMars mission. Lipid biomarkers were extracted and analyzed by gas chromatography--mass spectrometry to assess sources of organic carbon and evaluate the contribution of microbial species to the organic matter of the paleosols. Paleosol samples from the ice-free Dry Valleys were also subsampled and cultivated in a growth medium from which DNA was extracted with the explicit purpose of the positive identification of bacteria. Several species of bacteria were grown in solution and the genus identified. A similar match of the data to sequenced DNA showed that Alphaproteobacteria, Gammaproteobacteria, Bacteriodetes, and Actinobacteridae species were cultivated. The results confirm the presence of bacteria within some paleosols, but no assumptions have been made with regard to in situ activity at present. These results underscore the need not only to further investigate Dry Valley cryosols but also to develop reconnaissance strategies to determine whether such likely Earth-like environments on the Red Planet also contain life.

Microbial contamination of orthodontic buccal tubes from manufacturers

This study aimed to test the sterility of new unused orthodontic buccal tubes received from manufacturers. Four different types of buccal tubes were used straight from the manufactures package without any additional sterilizing step. Of these buccal tubes tested, three genera of bacteria, implicated as opportunistic pathogens, namely Micrococcus luteus, Staphylococcus haemolyticus and Acinetobacter calcoaceticus were recovered from these buccal tubes. Our data showing microbial contamination on buccal tubes highlights the need of sterilization before clinical use. We also suggest that manufacturers should list the sterility state of orthodontic buccal tubes on their packaging or instructions stating the need for sterilization.

Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy

Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep-sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north-eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910-5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo-reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.