Terrestrial Bacteria Research Articles

TESTING OF 24 POTENTIALLY HAZARDOUS WASTES USING 6 ECOTOXICOLOGICAL TESTS

The ecotoxicological characterization of wastes according to the European Waste List (EWL) is part of their assessment as hazardous or non-hazardous. Despite inclusion in national laws no methodological details have been fixed concerning the hazard property HP 14 (“ecotoxic”).This paper intends to discuss the classification of wastes by ecotoxicological testing, using 24 representative samples of solid wastes (identified by their EWL number) with different properties. They were sampled according to standard methods, and, with one exception (galvanic sludge), ecotoxicologically tested. No chemical investigation of the samples was performed but they were characterized according to their properties in the ABANDA data base. Nearly all of these wastes were “mirror entries” in the EWL (i.e., they can be hazardous or not depending on the concentration of hazardous substances). For the ecotoxicological characterization three aquatic tests with eluates (genotoxicity, Algae, Daphnia) as well as three terrestrial tests with solid wastes (bacteria, plants, earthworms) were conducted. All investigations were performed as limit tests with three dilution steps. Algae, plants and terrestrial bacteria were the most sensitive organisms. Since no waste eluate showed any indication of genotoxicity, the genotoxicity test should be replaced by the luminescent bacteria test (ISO 11348-3). Proposals for toxicity criteria as well as hazard classifications were taken from the literature but they were modified according to own experiences. Using these concentration limits for the classification whether these wastes are ecotoxic or not, and using different versions of the hazard classification approach, 15-19 waste samples out of 23 waste samples were classified as ecotoxic (64-83%). It is proposed to perform a plausibility check of the respective HP 14-classification. The procedure used in this contribution (i.e. sampling of the wastes, their ecotoxicological testing as well as their hazard classification) could form the basis of a standardized hazard classification approach as proposed recently in the literature. In summary, this works confirms that ecotoxicological tests are practical and sensitive in order to be used for the ecotoxicological hazard classification of very different wastes.

Mechanisms and Origin of Bacterial Biolumenescence

The origin of bioluminescence in living organisms was first mentioned by Charles Darwin (1859) and remains obscure despite significant success achieved over the past decades. Here we discuss the mechanisms of bacterial bioluminescence. We have the main results from structural and functional analysis of the genes of lux operons, enzymes (luciferase), and mechanisms of bioluminescence in several species of marine bacteria, which belong to three genera, Vibrio, Aliivibrio, and Photobacterium (A. fischeri, V. harveyi, P. leiognathi, and P. phosphoreum), and in terrestrial bacteria of the genus Photorhabdus (Ph. luminescens). The structure and mechanisms for the regulation of the expression of the lux operons are discussed. The fundamental characteristics of luciferase and luciferase-catalyzed reactions (stages of FMNH2 and tetradecanal oxidation, dimensional structure, as well as folding and refolding of the macromolecule) are described. We also discuss the main concepts of the origin of bacterial bioluminescence and its role in the ecology of modern marine fauna, including its involvement in the processes of detoxification of the reactive oxygen species and DNA repair, as well as the bait hypothesis.

Evaluation of meteorites as habitats for terrestrial microorganisms: Results from the Nullarbor Plain, Australia, a Mars analogue site

Unambiguous identification of biosignatures on Mars requires access to well-characterized, long-lasting geochemical standards at the planet’s surface that can be modified by theoretical martian life. Ordinary chondrites, which are ancient meteorites that commonly fall to the surface of Mars and Earth, have well-characterized, narrow ranges in trace element and isotope geochemistry compared to martian rocks. Given that their mineralogy is more attractive to known chemolithotrophic life than the basaltic rocks that dominate the martian surface, exogenic rocks (e.g., chondritic meteorites) may be good places to look for signs of prior life endemic to Mars. In this study, we show that ordinary chondrites, collected from the arid Australian Nullarbor Plain, are commonly colonized and inhabited by terrestrial microorganisms that are endemic to this Mars analogue site. These terrestrial endolithic and chasmolithic microbial contaminants are commonly found in close association with hygroscopic veins of gypsum and Mg-calcite, which have formed within cracks penetrating deep into the meteorites. Terrestrial bacteria are observed within corrosion cavities, where troilite (FeS) oxidation has produced jarosite [KFe3(SO4)2(OH)6]. Where terrestrial microorganisms have colonized primary silicate minerals and secondary calcite, these mineral surfaces are heavily etched. Our results show that inhabitation of meteorites by terrestrial microorganisms in arid environments relies upon humidity and pH regulation by minerals. Furthermore, microbial colonization affects the weathering of meteorites and production of sulfate, carbonate, Fe-oxide and smectite minerals that can preserve chemical and isotopic biosignatures for thousands to millions of years on Earth. Meteorites are thus habitable by terrestrial microorganisms, even under highly desiccating environmental conditions of relevance to Mars. They may therefore be useful as chemical and isotopic “standards” that preserve evidence of life, thereby providing the possibility of universal context for recognition of microbial biosignatures on Earth, Mars and throughout the solar system.

Sponge-Inspired Dibromohemibastadin Prevents and Disrupts Bacterial Biofilms without Toxicity.

Since the banning of several families of compounds in antifouling (AF) coatings, the search for environmentally friendly AF compounds has intensified. Natural sources of AF compounds have been identified in marine organisms and can be used to create analogues in laboratory. In a previous study, we identified that dibromohemibastadin-1 (DBHB) is a promising AF molecule, leading to the inhibition of the activity of phenoloxidase, an enzyme involved in the attachment of mussels to surfaces. This paper describes the activity of the DBHB on biofilm formation and its detachment and on bacterial adhesion and communication: quorum sensing. DBHB has an anti-biofilm activity without affecting adhesion of marine and terrestrial bacteria at a dose of 10 µM. Moreover, DBHB activity on quorum sensing (QS) is demonstrated at doses of 8 and 16 µM. The activity of DBHB on QS is compared to kojic acid, a quorum sensing inhibitor already described. This compound is a promising environmentally friendly molecule potentially useful for the inhibition of microfouling.

Assessment of Aliphatic Hydrocarbons in Sediments of Shatt Al-Arab River, Southern Iraq, North East Arabian Gulf

Shatt Al-Arab River is one of the important rivers for water supply, industry and irrigation in Basrah City, south of Iraq. It's also supply drinking water to users in the region. Despite the significance of this river, there is a lack of previous studies dealing with petroleum pollution especially for geochemical studies of organic matter in the river sediments using molecular tracer methods. Therefore, the identification and quantification of petroleum hydrocarbons in this river at the elemental and molecular levels will be of the utmost interest. Sediments were analyzed in nine Shatt Al-Arab River stations. Texture was silty clay or silty sand. TOC and TN ranged from 0.39-0.90 and 0.02-0.16%. OM varied from 17.43-34.36 µg g-1 dw, representing 0.27-0.87% of TOC. AHs ranged from 3.19-10.27 µg g-1 dw and constituted 16.07-29.88% of OM. Total n-alkanes concentrations ranged from 0.08-42.58 µg g-1 dw with carbon numbers from C11-C34 were identified. N-alkanes content was relatively moderate compared to sites contaminated with oil worldwide. Dominance of even carbon number n-alkanes (C11-C20) with CPI and LMW/HMW values close to unity, indicated to oil-related n-alkanes. This was verified by the values of U/R (1.27-2.45), pri/phy (0.82-1.00), C17/pri (0.70-1.94) and C18/phy (0.95-1.56) ratios and the presence of UCM. Biogenic contributions were detected within the n-alkanes distribution of C17-C31 and CPI and LMW/HMW values of <1 that mainly related to terrestrial plants, phytoplankton, algae and bacteria sources, confirmed by TAR (0.79-2.15) and C31/C19 ratio (0.28-1.62) values. However, the contribution from biogenic hydrocarbons is overshadowed by petroleum origin n-alkanes. This was obvious by the presence of UCM. PCA showed concordant results with n-alkanes ratios indicating mixed n-alkanes sources in sediments. Hopanes and steranes in sediments displayed similar signatures that were characteristic of mature organic matter contribution from oil contaminations.

A new isoflavone from the roots of Ficus auriculata

A new isoflavone, 5,7,4′-trihydroxy-3′-hydroxymethylisoflavone (1), together with three known isoflavones, 3′-formyl-5,4′-dihydroxy-7-methoxyisoflavone (2), ficuisoflavone (3) and alpinumisoflavone (4), were isolated from the roots of Ficus auriculata. Among them, 1 is a rare isoflavone containing 16 carbon atoms on the carbon skeleton. The structure of 1 was elucidated by extensive spectroscopic methods and the known compounds were identified by comparisons with data reported in the literature. All compounds were evaluated for their antibacterial activities against five terrestrial pathogenic bacteria in vitro. Compounds 1–4 showed significant antibacterial activities against various terrestrial pathogenic bacteria with MIC values ranging from 1.30 to 39.93 μM.

Chemical Structure of the Lipid A component of Pseudomonas sp. strain PAMC 28618 from Thawing Permafrost in Relation to Pathogenicity

Climate change causes permafrost thawing, and we are confronted with the unpredictable risk of newly discovered permafrost microbes that have disease-causing capabilities. Here, we first characterized the detailed chemical structure of the lipid A moiety from a Pseudomonas species that was isolated from thawing arctic permafrost using MALDI-based mass spectrometric approaches (i.e., MALDI-TOF MS and MALDI-QIT-TOF MSn). The MALDI multi-stage mass spectrometry (MS) analysis of lipid A extracted from the Pseudomonas sp. strain PAMC 28618 demonstrated that the hexaacyl lipid A ([M−H]− at m/z 1616.5) contains a glucosamine (GlcN) disaccharide backbone, two phosphates, four main acyl chains and two branched acyl chains. Moreover, the lipid A molecule–based structural activity relationship with other terrestrial Gram-negative bacteria indicated that strain PAMC 28618 has an identical lipid A structure with the mesophilic Pseudomonas cichorii which can cause rot disease in endive (Cichorium endivia) and that their bacterial toxicities were equivalent. Therefore, the overall lipid A validation process provides a general strategy for characterizing bacteria that have been isolated from arctic permafrost and analyzing their respective pathogenicities.

Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility.

Every spacecraft sent to Mars is allowed to land viable microbial bioburden, including hardy endospore-forming bacteria resistant to environmental extremes. Earth's stratosphere is severely cold, dry, irradiated, and oligotrophic; it can be used as a stand-in location for predicting how stowaway microbes might respond to the martian surface. We launched E-MIST, a high-altitude NASA balloon payload on 10 October 2015 carrying known quantities of viable Bacillus pumilus SAFR-032 (4.07 × 107 spores per sample), a radiation-tolerant strain collected from a spacecraft assembly facility. The payload spent 8 h at ∼31 km above sea level, exposing bacterial spores to the stratosphere. We found that within 120 and 240 min, spore viability was significantly reduced by 2 and 4 orders of magnitude, respectively. By 480 min, <0.001% of spores carried to the stratosphere remained viable. Our balloon flight results predict that most terrestrial bacteria would be inactivated within the first sol on Mars if contaminated spacecraft surfaces receive direct sunlight. Unfortunately, an instrument malfunction prevented the acquisition of UV light measurements during our balloon mission. To make up for the absence of radiometer data, we calculated a stratosphere UV model and conducted ground tests with a 271.1 nm UVC light source (0.5 W/m2), observing a similarly rapid inactivation rate when using a lower number of contaminants (640 spores per sample). The starting concentration of spores and microconfiguration on hardware surfaces appeared to influence survivability outcomes in both experiments. With the relatively few spores that survived the stratosphere, we performed a resequencing analysis and identified three single nucleotide polymorphisms compared to unexposed controls. It is therefore plausible that bacteria enduring radiation-rich environments (e.g., Earth's upper atmosphere, interplanetary space, or the surface of Mars) may be pushed in evolutionarily consequential directions. Key Words: Planetary protection—Stratosphere—Balloon—Mars analog environment—E-MIST payload—Bacillus pumilus SAFR-032. Astrobiology 17, 337–350.

Preparation of Antioxidant Peptides from Salmon Byproducts with Bacterial Extracellular Proteases.

Bacterial extracellular proteases from six strains of marine bacteria and seven strains of terrestrial bacteria were prepared through fermentation. Proteases were analyzed through substrate immersing zymography and used to hydrolyze the collagen and muscle proteins from a salmon skin byproduct, respectively. Collagen could be degraded much more easily than muscle protein, but it commonly showed weaker antioxidant capability. The hydrolysate of muscle proteins was prepared with crude enzymes from Pseudoalteromonas sp. SQN1 displayed the strongest activity of antioxidant in DPPH and hydroxyl radical scavenging assays (74.06% ± 1.14% and 69.71% ± 1.97%), but did not perform well in Fe2+ chelating assay. The antioxidant fractions were purified through ultrafiltration, cation exchange chromatography, and size exclusion chromatography gradually, and the final purified fraction U2-S2-I displayed strong activity of antioxidant in DPPH, hydroxyl radical scavenging assays (IC50 = 0.263 ± 0.018 mg/mL and 0.512 ± 0.055 mg/mL), and oxygen radical absorption capability assay (1.960 ± 0.381 mmol·TE/g). The final purified fraction U2-S2-I possessed the capability to protect plasmid DNA against the damage of hydroxyl radical and its effect was similar to that of the original hydrolysis product. It indicated that U2-S2-I might be the major active fraction of the hydrolysate. This study proved that bacterial extracellular proteases could be utilized in hydrolysis of a salmon byproduct. Compared with collagen, muscle proteins was an ideal material used as an enzymatic substrate to prepare antioxidant peptides.

Coupled Biosynthesis of Volatiles and Salinosporamide A in Salinispora tropica.

Terrestrial bacteria, especially actinomycetes, are known to be prolific producers of volatile compounds. We show here that bacteria from ocean sediments can also release complex bouquets of volatiles. The actinomycete Salinispora tropica produces cyclohexenyl compounds not previously known in nature, such as methyl cyclohex-2-ene-1-carboxylate (9), methyl 2-(cyclohex-2-en-1-yl)acetate (10), methyl (E/Z)-2-(cyclohex-2-en-1-ylidene)acetate (11/12), and related alcohols 8 and 13. These compounds were identified by GC/MS and confirmed by synthesis. In addition, rare spiroacetals, aromatic compounds, short-chain acids and esters, alcohols, and various cyclic compounds were produced by the bacteria. The biosynthesis of the cyclohexenyl compounds is closely coupled to that of cyclohexenylalanine (4), a building block of salinosporamide A, a proteasome inhibitor produced by S. tropica. Analysis of S. tropica strains that harbor knockouts of the salinosporamide biosynthetic genes salX and salD, coupled with feeding experiments, revealed that 3-(cyclohex-2-en-1-yl)-2-oxopropanoic acid (60) and 3-(cyclohex-2-en-1-ylidene)-2-oxopropanoic acid (isomers 61 and 62) are important intermediates in the biosynthesis of salinosporamide A, 4, and 8-13.

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces.

ABSTRACTWe show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.

Variochelins, Lipopeptide Siderophores from Variovorax boronicumulans Discovered by Genome Mining.

Photoreactive siderophores have a major impact on the growth of planktonic organisms. To date, these molecules have mainly been reported from marine bacteria, although evidence is now accumulating that some terrestrial bacteria also harbor the biosynthetic potential for their production. In this paper, we describe the genomics-driven discovery and characterization of variochelins, lipopeptide siderophores from the bacterium Variovorax boronicumulans, which thrives in soil and freshwater habitats. Variochelins are different from most other lipopeptide siderophores in that their biosynthesis involves a polyketide synthase. We demonstrate that the ferric iron complex of variochelin A possesses photoreactive properties and present the MS-derived structures of two degradation products that emerge upon light exposure.

Characterization of a New M13 Metallopeptidase from Deep-Sea Shewanella sp. E525-6 and Mechanistic Insight into Its Catalysis.

Bacterial extracellular peptidases are important for bacterial nutrition and organic nitrogen degradation in the ocean. While many peptidases of the M13 family from terrestrial animals and bacteria are studied, there has been no report on M13 peptidases from marine bacteria. Here, we characterized an M13 peptidase, PepS, from the deep-sea sedimentary strain Shewanella sp. E525-6, and investigated its substrate specificity and catalytic mechanism. The gene pepS cloned from strain E525-6 contains 2085 bp and encodes an M13 metallopeptidase. PepS was expressed in Escherichia coli and purified. Among the characterized M13 peptidases, PepS shares the highest sequence identity (47%) with Zmp1 from Mycobacterium tuberculosis, indicating that PepS is a new member of the M13 family. PepS had the highest activity at 30°C and pH 8.0. It retained 15% activity at 0°C. Its half life at 40°C was only 4 min. These properties indicate that PepS is a cold-adapted enzyme. The smallest substrate for PepS is pentapeptide, and it is probably unable to cleave peptides of more than 30 residues. PepS prefers to hydrolyze peptide bonds with P1′ hydrophobic residues. Structural and mutational analyses suggested that His531, His535 and Glu592 coordinate the catalytic zinc ion in PepS, Glu532 acts as a nucleophile, and His654 is probably involved in the transition state stabilization. Asp538 and Asp596 can stablize the orientations of His531 and His535, and Arg660 can stablize the orientation of Asp596. These results help in understanding marine bacterial peptidases and organic nitrogen degradation.

Biogenic and Anthropogenic Lipid Markers in Sediments from a Marsh Habitat Associated with the LCP Chemicals Superfund Site in Brunswick, Georgia, USA

Sediment samples from a salt marsh habitat in the vicinity of Linden Chemical Plant (LCP) Superfund site in Brunswick Georgia, USA, were analyzed for the composition of total solvent extracts and sources of lipid compounds. Stable isotope analysis of carbon and nitrogen and gas chromatography-mass spectrometry analysis infer past multiple sources of organic matter (OM) from aquatic and terrestrial origin, e.g., phytoplankton, bacteria, and land plants, as well as anthropogenic contamination. The n-alkane and n-alkanol distributions in the sediment samples were dominated by long-chain homologues maximizing at C25–C27 for alkanes (carbon preference index (CPI) ∼1) and C32 for n-alkanols indicating inputs from higher plants, but also microbial and petroleum-related sources. Fatty acid distribution was characterized by short-chain (< C18) and branched homologues indicative of bacterial origin. The high abundance of dehydroabietic acid and anthropogenic contaminants, including alkylphenols, are indicative of the effects of past industrial activities in the LCP marsh area in Brunswick, Georgia.

Protein composition of the cell envelope of the bacterium Shewanella frigidimarina Pi 2-35 (Gammaproteobacteria: Shewanellaceae)

The protein composition of the outer (OM) and cytoplasmic (CM) membranes of the cell envelope of the psychrotolerant marine bacterium Shewanella frigidimarina Pi 2-35, which was isolated from a sample of sea ice from the Amur Bay (Sea of Japan), was analyzed using SDS-PAGE. The cell envelope of this microorganism has been found to contain high molecular weight proteins, cytochromes, which were extracted with detergents of different types. It is shown that the composition of the CM of S. frigidimarina Pi 2-35 does not depend on the cultivation temperature. Proteins with a molecular weight (MW) within the range of 30–50 kDa, which is characteristic for nonspecific porins of terrestrial Gram-negative bacteria, were detected only in the OM of bacteria that were cultivated at a low temperature (6–8°C). Two porin-like proteins, PZW (MW 40 kDa) and PLYS (MW 34.5 kDa), were isolated from the OM by extraction with the 0.5% non-ionic detergent Zwittergent 3-14 and by digestion of the peptidoglycan layer of the cell envelope with lysozyme, respectively. The use of the bilayer lipid membrane (BLM) technique showed that both proteins exhibit a pore-forming activity. The efficiency of channel formation and the pattern of fluctuations of current in the BLM indicate that the isolated porins are not identical in their functional properties.

IN-VITRO ANTI-INFLAMMATORY ACTIVITIES OF EXTRACTS FROM BACTERIA ASSOCIATED WITH MARINE SPONGES: THEONELLA SP.

In recent years, high numbers of research focusing on secondary metabolites produced by terrestrial bacteria towards anti-inflammatory properties but, minority of them used bacteria associated to marine organism. In this study, 25 bacteria colonies were isolated from sponge Theonella sp. which was collected from Bidong Island, Terengganu. Cytotoxicity and anti-inflammatory activity of secondary metabolites produced by these bacteria were studied using macrophage cell lines: RAW 264.7 .Macrophage plays a role in mammalian immune system by providing defense against a foreign harmful substance for example Lipopolysaccharides (LPS) which induces production of pro-inflammatory mediators such as nitric oxide (NO). Inhibition of NO production in LPS stimulated RAW 264.7 cells is highly established assay to screen for anti-inflammatory activity. All isolates were cultured and supernatants were collected for the extraction of secondary metabolites using diaion HP-20 to obtain crude extracts. Evaluations of the cytotoxicity effect of the extracts on RAW 264.7 were done using MTT assay. The highest concentration sample producing lowest toxicity effect was used for anti-inflammatory assay. Macrophages were induced with LPS before treated with different concentrations of crude metabolites in anti-inflammatory assay. The effects of crude secondary metabolites extracted to the induced macrophage were monitored by observing the inhibition level of Nitric Oxide (NO) released by RAW 264.7 into supernatant and estimated from nitrate standard curve. A preliminary assay revealed that isolate label with TM1.8 and TM 1.9 possesses anti-inflammatory activities of 112.06% and 109.7% respectively for every 1ug/L sample. The result suggested that these two crude extracts were more effective in inhibiting NO production compared to positive control N-Monomethyl-L-arginine Monoacetate (L-NMMA) which showed an inhibitory activity at 87.41% for every 1ug/L sample.

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments.

One-carbon compounds such as methanol, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are significant intermediates in biogeochemical cycles. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds; therefore, we analyzed the diversity of terrestrial bacteria that utilize methanol, DMS and DMSO as carbon and energy source using culture-dependent and culture-independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera Hyphomicrobium, Methylobacterium, Pseudomonas, Hydrogenophaga, Rhodococcus, Flavobacterium and Variovorax were isolated, denaturing gradient gel electrophoresis revealed the dominance of Thiobacillus, Rhodococcus, Flavobacterium and Bacteroidetes species. Furthermore, methylotrophic communities that degrade methanol or DMS are not shaped by terrestrial habitat type. Rhizosphere and soil samples showed dominance of Methylophilus spp. and Methylovorus spp. for methanol enrichments; Cytophaga spp., Pseudomonas tremae and Thiobacillus thioparus for DMS enrichments.

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula

Bacterial populations transported from ground environments to the atmosphere get dispersed throughout downwind areas and can influence ecosystem dynamics, human health, and climate change. However, the vertical bacterial distribution in the free troposphere was rarely investigated in detail. We collected aerosols at altitudes of 3000 m, 1000 m, and 10 m over the Noto Peninsula, Japan, where the westerly winds carry aerosols from continental and marine areas. During the sampling period on March 10, 2012, the air mass at 3000 m was transported from the Chinese desert region by the westerly winds, and a boundary layer was formed below 2000 m. Pyrosequencing targeting 16S rRNA genes (16S rDNA) revealed that the bacterial community at 3000 m was predominantly composed of terrestrial bacteria, such as Bacillus and Actinobacterium species. In contrast, those at 1000 m and 10 m included marine bacteria belonging to the classes Cyanobacteria and Alphaproteobacteria. The entire 16S rDNA sequences in the clone libraries were identical to those of the terrestrial and marine bacterial species, which originated from the Chinese desert region and the Sea of Japan, respectively. The origins of air masses and meteorological conditions contribute to vertical variations in the bacterial communities in downwind atmosphere.

Structure and Effects of Cyanobacterial Lipopolysaccharides.

Lipopolysaccharide (LPS) is a component of the outer membrane of mainly Gram-negative bacteria and cyanobacteria. The LPS molecules from marine and terrestrial bacteria show structural variations, even among strains within the same species living in the same environment. Cyanobacterial LPS has a unique structure, since it lacks heptose and 3-deoxy-d-manno-octulosonic acid (also known as keto-deoxyoctulosonate (KDO)), which are present in the core region of common Gram-negative LPS. In addition, the cyanobacterial lipid A region lacks phosphates and contains odd-chain hydroxylated fatty acids. While the role of Gram-negative lipid A in the regulation of the innate immune response through Toll-like Receptor (TLR) 4 signaling is well characterized, the role of the structurally different cyanobacterial lipid A in TLR4 signaling is not well understood. The uncontrolled inflammatory response of TLR4 leads to autoimmune diseases such as sepsis, and thus the less virulent marine cyanobacterial LPS molecules can be effective to inhibit TLR4 signaling. This review highlights the structural comparison of LPS molecules from marine cyanobacteria and Gram-negative bacteria. We discuss the potential use of marine cyanobacterial LPS as a TLR4 antagonist, and the effects of cyanobacterial LPS on humans and marine organisms.

Biosynthesis and ecological functions of diketopiperazine natural products from marine actinomycetes

Molecules featuring 2,5-diketopiperazine (DKP) scaffolds are common in Nature and have been isolated from a variety of fungi and bacteria. These cyclodipeptides offer a range of medicinal activities, including antimicrobial, anticancer, and immunosuppressant effects. Cyclodipeptide synthases (CDPSs) were recently revealed as a novel family of small (˜30 kDa) enzymes that assemble DKPs from aminoacyl-tRNA substrates diverted from primary metabolic pathways. Although bioinformatics analyses of microbial genomes suggest that CDPSs are widespread amongst terrestrial and marine bacteria, fewer than a dozen CDPSs have been biochemically characterized. Here, we present the biochemical characterization of two CDPSs from a marine-derived Nocardiopsis sp. actinomycete. Our data reveal that both of these phylogenetically distinct CDPSs are highly selective for tryptophan-charged tRNA substrates to yield exclusively cyclo(L-Trp-L-Trp). We also present results from field and laboratory experiments probing cyclo(L-Trp-L-Trp) and other microbial DKPs as mediators of interactions between marine microorganisms. Together, our data provide insights into the prevalent, yet understudied CDPS enzyme family and suggest important adaptive functions of corresponding DKP metabolites.