Postdiagenetic Changes in Kerogen Properties and Type by Bacterial Oxidation and Dehydrogenation

A significant part of organic carbon found on the earth is deposited as fossil organic matter in the lithosphere. The most important reservoir of carbon is shale rocks enriched with organic matter in the form of kerogen created during diagenesis. The purpose of this study was to analyze whether the bacterial communities currently inhabiting the shale rocks have had any impact on the properties and type of kerogen. We used the shale rock located on the Fore-Sudetic Monocline, which is characterized by oil-prone kerogen type II. We were able to show that shale rock inhabited by bacterial communities are characterized by oxidized and dehydrated kerogen type III (gas-prone) and type IV (nonproductive, residual, and hydrogen-free). Bacterial communities inhabiting shale rock were dominated by heterotrophs of the Proteobacteria, Firmicutes, and Actinobacteria phyla. Additionally, we detected a number of protein sequences in the metaproteomes of bacterial communities matched with enzymes involved in the oxidative metabolism of aliphatic and aromatic hydrocarbons, which may potentially contribute to the postdiagenetic oxidation and dehydrogenation of kerogen. The kerogen transformation contributes to the mobilization of fossil carbon in the form of extractable bitumen dominated by oxidized organic compounds.     

Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism

Recent developments in whole-cell spectroscopic methods allow rapid characterization of microorganisms of interest to human health, but have yet to be widely applied to marine microbiological studies. In this study of bacteria associated with the kelp Laminaria digitata, we have isolated 18 epiphytic bacterial strains from several thalli, sequenced their 16S rDNA, built corresponding phylogenetic trees, and characterized them using spectroscopic methods. Molecular taxonomy revealed Gram⁺Actinobacteria and Gram⁻Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. Twelve marine reference strains (Gram⁺Firmicutes, and Gram⁻Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes) were treated accordingly. Whole-cell MALDI-TOF MS spectral profiles of 29 of the 30 strains were built into a database against which 16 replicate spectra of each strain were compared and categorized into groups. The proton HR-MAS NMR stack plots allowed visual delineation into taxonomic groups according to their most common peaks, in agreement with identifiable compounds from corresponding D₂O solution spectra. With both methods, these groups corresponded to taxa identified by 16S rDNA sequences, MALDI-TOF MS being more discriminative than HR-MAS NMR. Culture age did not influence the spectral signatures in both approaches. Most cells grown under minimal conditions (VNSS medium) afforded HR-MAS NMR profiles markedly different to those grown in enriched conditions (ZoBell medium), indicating different adaptive metabolic responses between the two media. Spectral signatures obtained under strictly controlled conditions can be used as rapid and reliable tools for taxonomic purposes and as markers of physiological status.     

Distribution and types of bacteria isolated from an inland saltern

The physico-chemical characteristics and bacterial populations of an inland saltern were studied. The well water leading into the ponds of the saltern differed from sea water in its total salinity (18 % (w/v)) and had lower Mg²⁺ and SO₄²⁻ contents and much higher contents of Cl⁻, Ca²⁺ and K⁺A high proportion of halotolerant microorganisms were isolated, although marine bacteria were not found. Most of the halophilic strains isolated appeared to be typical moderate halophiles, and included six groups: Vibrio (39 %), Deleya-Pseudomonas (28 %), Acinetobacter (6.5 %), Flavobacterium (6.5 %), Paracoccus (1.5 %), Planococcus (1.5 %) and non-classified (17 %). All extreme halophiles could be assigned to Hallobacterium (31 %) and Halococcus (68 %).     

Comparison of thrombus,gut, and oral microbiomes in Korean patients with ST-elevation myocardial infarction: a case–control study

ST-segment elevation myocardial infarction (STEMI) is characterized by thrombotic coronary artery occlusions caused by atherosclerotic plaque rupture. The gut microbiome potentially contributes to the pathogenesis of coronary artery diseases. This study investigated the microbial diversity and composition of coronary thrombi in STEMI patients and the composition of the thrombus microbiome relative to that of the oral and gut microbiomes. A case–control study was performed with 22 STEMI patients and 20 age- and sex-matched healthy controls. Coronary thrombi were acquired from STEMI patients via manual thrombus aspiration during primary coronary intervention. Oral swab and stool samples were collected from both groups, and 16S rRNA sequencing and metagenomic microbiome analyses were performed. Microbial DNA was detected in 4 of 22 coronary thrombi. Proteobacteria (p) and Bacteroidetes (p) were the most abundant phyla. The oral and gut microbiomes significantly differed between patients and healthy controls. The patient group presented microbial dysbiosis, as follows: a higher relative abundance of Proteobacteria (p) and Enterobacteriaceae (f) in the gut microbiome and a lower abundance of Firmicutes (p) and Haemophilus (g) in the oral microbiome. Furthermore, 4 significantly abundant genera were observed in the coronary thrombus in the patients: Escherichia, 1.25%; Parabacteroides, 0.25%; Christensenella, 0.0%; and Bacteroides, 7.48%. The present results indicate that the relative abundance of the gut and oral microbiomes was correlated with that of the thrombus microbiome.Subject terms: Genetics research, Myocardial infarction     

Effects of Tebuconazole Application on Soil Microbiota and Enzymes

Identification of pesticide impact on the soil microbiome is of the utmost significance today. Diagnosing the response of bacteria to tebuconazole, used for plant protection, may help isolate the most active bacteria applicable in the bioaugmentation of soils contaminated with this preparation. Bearing in mind the above, a study was undertaken to test the effect of tebuconazole on the diversity of bacteria at all taxonomic levels and on the activity of soil enzymes. It was conducted by means of standard and metagenomic methods. Its results showed that tebuconazole applied in doses falling within the ranges of good agricultural practice did not significantly disturb the biological homeostasis of soil and did not diminish its fertility. Tebuconazole was found to stimulate the proliferation of organotrophic bacteria and fungi, and also the activities of soil enzymes responsible for phosphorus, sulfur, and carbon metabolism. It did not impair the activity of urease responsible for urea hydrolysis, or cause any significant changes in the structure of bacterial communities. All analyzed soil samples were mainly populated by bacteria from the phylum Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, Planctomycetes, and Chloroflexi. Bacteria from the genera Kaistobacter, Arthrobacter, and Streptomyces predominated in the soils contaminated with tebuconazole, whereas these from the Gemmata genus were inactivated by this preparation.     

Polyextremophilic Chitinolytic Activity by a Marine Strain (IG119) of Clonostachys rosea

The investigation for novel unique extremozymes is a valuable business for which the marine environment has been overlooked. The marine fungus Clonostachys rosea IG119 was tested for growth and chitinolytic enzyme production at different combinations of salinity and pH using response surface methodology. RSM modelling predicted best growth in-between pH 3.0 and 9.0 and at salinity of 0–40‰, and maximum enzyme activity (411.137 IU/L) at pH 6.4 and salinity 0‰; however, quite high production (>390 IU/L) was still predicted at pH 4.5–8.5. The highest growth and activity were obtained, respectively, at pH 4.0 and 8.0, in absence of salt. The crude enzyme was tested at different salinities (0–120‰) and pHs (2.0–13.0). The best activity was achieved at pH 4.0, but it was still high (in-between 3.0 and 12.0) at pH 2.0 and 13.0. Salinity did not affect the activity in all tested conditions. Overall, C. rosea IG119 was able to grow and produce chitinolytic enzymes under polyextremophilic conditions, and its crude enzyme solution showed more evident polyextremophilic features. The promising chitinolytic activity of IG119 and the peculiar characteristics of its chitinolytic enzymes could be suitable for several biotechnological applications (i.e., degradation of salty chitin-rich materials and biocontrol of spoiling organisms, possibly solving some relevant environmental issues).     

Comparative Study of Volatile Compounds and Expression of Related Genes in Fruit from Two Apple Cultivars during Different Developmental Stages

Aromatic volatile compounds are important contributors to fruit quality that vary among different cultivars. Herein, headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry was used to determine changes in volatile compounds and related gene expression patterns in “Ruixue” and “Fuji” apples (Malus domestica Borkh.) during fruit development and maturation. Volatile compounds detected in the fruit of both cultivars exhibited similar trends across different developmental stages. In the early stages of “Ruixue” fruit development (60 days after full bloom), there were fewer volatile compounds, mainly aldehydes (87.0%). During fruit maturation (180 days after full bloom), the types and amounts of volatile compounds increased, mainly including esters (37.6%), and alkenes (23.2%). The total volatile concentration, the types of major volatile compounds, and their relative content in both cultivars varied across different stages. Gene expression analysis indicated that the upregulation of MdLOX, MdAAT2, and MdADH3 was associated with increased aroma compound content, especially esters, during fruit development in both cultivars. Changes in the expression of MdArAT, MdACPD, MdADH3, MdAAT2, and MdLOX may lead to differences in volatile compounds between apple cultivars.     

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IF_G); index of petrol effect on soil microorganisms and enzymes (IF_P); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (ID_H). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.     

Chlovalicin B,a Chlorinated Sesquiterpene Isolated from the Marine Mushroom Digitatispora marina

As part of our search for bioactive metabolites from understudied marine microorganisms, the new chlorinated metabolite chlovalicin B (1) was isolated from liquid cultures of the marine basidiomycete Digitatispora marina, which was collected and isolated from driftwood found at Vannøya, Norway. The structure of the novel compound was elucidated by spectroscopic methods including 1D and 2D NMR and analysis of HRMS data, revealing that 1 shares its molecular scaffold with a previously isolated compound, chlovalicin. This represents the first compound isolated from the Digitatispora genus, and the first reported fumagillin/ovalicin-like compound isolated from Basidiomycota. Compound 1 was evaluated for antibacterial activities against a panel of five bacteria, its ability to inhibit bacterial biofilm formation, for antifungal activity against Candida albicans, and for cytotoxic activities against malignant and non-malignant human cell lines. Compound 1 displayed weak cytotoxic activity against the human melanoma cell line A2058 (~50% survival at 50 µM). No activity was detected against biofilm formation or C. albicans at 50 µM, or against bacterial growth at 100 µM nor against the production of cytokines by the human acute monocytic leukemia cell line THP-1 at 50 µM.     

Aronia melanocarpa (Michx.) Elliot,Chaenomeles superba Lindl. and Cornus mas L. Leaf Extracts as Natural Preservatives for Pork Meat Products

The aim of this study was to investigate the possibility of using Aronia melanocarpa, Chaenomeles superba, and Cornus mas leaf extracts as natural preservatives for pork meat products. Pork sausages were stored in modified atmosphere packaging (MAP) (80% N₂ and 20% CO₂) at 4 °C for 29 days. The total psychrotrophic counts (TPC) were determined during the storage period, along with the numbers of Enterobacteriaceae and lactic acid bacteria (LAB). The extracts improved the microbial quality of the meat products but to a lesser extent than sodium nitrate (III). They reduced the amounts of Enterobacteriaceae and LAB. The A. melanocarpa leaf extract showed the strongest preservative effect. The bacterial biodiversity of the meat products was investigated based on high-throughput sequencing of the 16S rRNA gene. Two predominant bacteria phyla were identified, Proteobacteria and Firmucutes, mostly consisting of genera Photobacterium, Brochothrix, and Carnobacterium. The extracts also influenced microbial community in sausages decreasing or increasing bacterial relative abundance. The extracts significantly inhibited lipid oxidation and improved the water-holding capacity of the meat, with C. superba extract showing the strongest influence. In addition, A. melanocarpa and C. superba improved the redness (a*) of the sausages. The results of this study show that A. melanocarpa, C. superba, and C. mas leaf extracts can extend the shelf life of meat products stored in MAP at 4 °C.     

Synthesis of Isothiocyanates Using DMT/NMM/TsO− as a New Desulfurization Reagent

Thirty-three alkyl and aryl isothiocyanates, as well as isothiocyanate derivatives from esters of coded amino acids and from esters of unnatural amino acids (6-aminocaproic, 4-(aminomethyl)benzoic, and tranexamic acids), were synthesized with satisfactory or very good yields (25–97%). Synthesis was performed in a “one-pot”, two-step procedure, in the presence of organic base (Et₃N, DBU or NMM), and carbon disulfide via dithiocarbamates, with 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium toluene-4-sulfonate (DMT/NMM/TsO⁻) as a desulfurization reagent. For the synthesis of aliphatic and aromatic isothiocyanates, reactions were carried out in a microwave reactor, and selected alkyl isothiocyanates were also synthesized in aqueous medium with high yields (72–96%). Isothiocyanate derivatives of L- and D-amino acid methyl esters were synthesized, under conditions without microwave radiation assistance, with low racemization (er 99 > 1), and their absolute configuration was confirmed by circular dichroism. Isothiocyanate derivatives of natural and unnatural amino acids were evaluated for antibacterial activity on E. coli and S. aureus bacterial strains, where the most active was ITC 9e.     

Miniaturized Salinity Gradient Energy Harvesting Devices

Harvesting salinity gradient energy, also known as “osmotic energy” or “blue energy”, generated from the free energy mixing of seawater and fresh river water provides a renewable and sustainable alternative for circumventing the recent upsurge in global energy consumption. The osmotic pressure resulting from mixing water streams with different salinities can be converted into electrical energy driven by a potential difference or ionic gradients. Reversed-electrodialysis (RED) has become more prominent among the conventional membrane-based separation methodologies due to its higher energy efficiency and lesser susceptibility to membrane fouling than pressure-retarded osmosis (PRO). However, the ion-exchange membranes used for RED systems often encounter limitations while adapting to a real-world system due to their limited pore sizes and internal resistance. The worldwide demand for clean energy production has reinvigorated the interest in salinity gradient energy conversion. In addition to the large energy conversion devices, the miniaturized devices used for powering a portable or wearable micro-device have attracted much attention. This review provides insights into developing miniaturized salinity gradient energy harvesting devices and recent advances in the membranes designed for optimized osmotic power extraction. Furthermore, we present various applications utilizing the salinity gradient energy conversion.     

Biological Properties of Latex,Aqueous Extracts and Bee Products of Euphorbia officinarum L.: A Short Review

Euphorbia officinarum L. is a Moroccan endemic plant known as “Tikiout” and “Daghmus” that can also be found in Mauritania, Western Sahara, and Algeria. In the present review, “Euphorbia officinarum”, “metabolites” “hemisynthesis” were the keywords used for the research in the Web search engine Google Scholar and in the database Web of Science. Triterpenes, phytosterols and ingol diterpenes were isolated and identified in the latex of Moroccan E. officinarum. More than sixty triterpenes were obtained by hemisynthesis from natural triterpenes. Some of these derivatives had insecticidal and antimicrobial activity (phytopathogenic bacteria). The total phenol content and the antioxidant and anti-α-glucosidase activities were dependent on the time and temperature of extractions and also on the plant solvent ratio. The antioxidant activity of monofloral honey of E. officinarum origin was attributed to the phenol fraction (this fraction, previously isolated from honey samples, had better activity than the entire honey).     

Short-chain reactive probes as tools to unravel the Pseudomonas aeruginosa quorum sensing regulon

In recent years, the world has seen a troubling increase in antibiotic resistance among bacterial pathogens. In order to provide alternative strategies to combat bacterial infections, it is crucial deepen our understanding into the mechanisms that pathogens use to thrive in complex environments. Most bacteria use sophisticated chemical communication systems to sense their population density and coordinate gene expression in a collective manner, a process that is termed “quorum sensing” (QS). The human pathogen Pseudomonas aeruginosa uses several small molecules to regulate QS, and one of them is N-butyryl-l-homoserine lactone (C₄-HSL). Using an activity-based protein profiling (ABPP) strategy, we designed biomimetic probes with a photoreactive group and a ‘click’ tag as an analytical handle. Using these probes, we have identified previously uncharacterized proteins that are part of the P. aeruginosa QS network, and we uncovered an additional role for this natural autoinducer in the virulence regulon of P. aeruginosa, through its interaction with PhzB1/2 that results in inhibition of pyocyanin production.

Short-chain reactive probes can be used as tools to shed new light on virulence mechanisms in bacterial pathogens.     

Natural Products Produced in Culture by Biosynthetically Talented Salinispora arenicola Strains Isolated from Northeastern and South Pacific Marine Sediments

Laboratory cultures of two ‘biosynthetically talented’ bacterial strains harvested from tropical and temperate Pacific Ocean sediment habitats were examined for the production of new natural products. Cultures of the tropical Salinispora arenicola strain RJA3005, harvested from a PNG marine sediment, produced salinorcinol (3) and salinacetamide (4), which had previously been reported as products of engineered and mutated strains of Amycolatopsis mediterranei, but had not been found before as natural products. An S. arenicola strain RJA4486, harvested from marine sediment collected in the temperate ocean waters off British Columbia, produced the new aminoquinone polyketide salinisporamine (5). Natural products 3, 4, and 5 are putative shunt products of the widely distributed rifamycin biosynthetic pathway.     

Secondary Metabolites of the Genus Amycolatopsis: Structures,Bioactivities and Biosynthesis

Actinomycetes are regarded as important sources for the generation of various bioactive secondary metabolites with rich chemical and bioactive diversities. Amycolatopsis falls under the rare actinomycete genus with the potential to produce antibiotics. In this review, all literatures were searched in the Web of Science, Google Scholar and PubMed up to March 2021. The keywords used in the search strategy were “Amycolatopsis”, “secondary metabolite”, “new or novel compound”, “bioactivity”, “biosynthetic pathway” and “derivatives”. The objective in this review is to summarize the chemical structures and biological activities of secondary metabolites from the genus Amycolatopsis. A total of 159 compounds derived from 8 known and 18 unidentified species are summarized in this paper. These secondary metabolites are mainly categorized into polyphenols, linear polyketides, macrolides, macrolactams, thiazolyl peptides, cyclic peptides, glycopeptides, amide and amino derivatives, glycoside derivatives, enediyne derivatives and sesquiterpenes. Meanwhile, they mainly showed unique antimicrobial, anti-cancer, antioxidant, anti-hyperglycemic, and enzyme inhibition activities. In addition, the biosynthetic pathways of several potent bioactive compounds and derivatives are included and the prospect of the chemical substances obtained from Amycolatopsis is also discussed to provide ideas for their implementation in the field of therapeutics and drug discovery.     

Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles

The aim was to assess plant driven changes in the activity and diversity of microorganisms in the top layer of the zinc and lead smelter waste piles. The study sites comprised two types (flotation waste—FW and slag waste—SW) of smelter waste deposits in Piekary Slaskie, Poland. Cadmium, zinc, lead, and arsenic contents in these technosols were extremely high. The root zone of 8 spontaneous plant species (FW—Thymus serpyllum, Silene vulgaris, Solidago virgaurea, Echium vulgare, and Rumex acetosa; and SW—Verbascum thapsus; Solidago gigantea, Eupatorium cannabinum) and barren areas of each waste deposit were sampled. We observed a significant difference in microbial characteristics attributed to different plant species. The enzymatic activity was mostly driven by plant-microbial interactions and it was significantly greater in soil affected by plants than in bulk soil. Furthermore, as it was revealed by BIOLOG Ecoplate analysis, microorganisms inhabiting barren areas of the waste piles rely on significantly different sources of carbon than those found in the zone affected by spontaneous plants. Among phyla, Actinobacteriota were the most abundant, contributing to at least 25% of the total abundance. Bacteria belonging to Blastococcus genera were the most abundant with the substantial contribution of Nocardioides and Pseudonocardia, especially in the root zone. The contribution of unclassified bacteria was high—up to 38% of the total abundance. This demonstrates the unique character of bacterial communities in the smelter waste.     

Effects of sludge retention time on membrane fouling and microbial community structure in a membrane bioreactor

In this study, the effect of sludge retention time (SRT) on membrane bio-fouling was investigated in a membrane bioreactor (MBR) equipped with a sequential anoxic/anaerobic reactor. Specific cake resistance (α), trans-membrane pressure (TMP), mixed liquor suspended solids (MLSS), particle sizes, extracellular polymer substances bound in sludge (bound-EPS) and their correlations with membrane bio-fouling were studied at different SRTs. As SRT decreased to 20 days, the bound-EPS per unit of biomass increased, and consequently, the value of α increased, which resulted in the rise of TMP. However, the reduction of the bound-EPS content was relatively small as compared to a significant decrease in the value of α at longer SRTs (above 60 days). These observations suggest that colloidal particles significantly contribute to membrane bio-fouling. In addition, the diversity of the microbial community structure of activated sludge in the MBRs was observed using the respiratory quinone profile. The ubiquinone species containing UQ-8, belonging to the class β-Proteobacteria type were the major constituents of the microbial community structure. The mole fraction of menaquinone MK-6, -7 and -8(H2) increased as SRT increased. Thus, the results of this study indicate that growth of microorganisms belonging to the δ- and ?-subclass of Proteobacteria as well as the members of the Cytophaga–Flavobacterium cluster increased at longer SRTs.