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1
Cottrell, Matthew T., Jessica A. Moore, and David L. Kirchman. "Chitinases from Uncultured Marine Microorganisms." Applied and Environmental Microbiology 65, no. 6 (June 1, 1999): 2553–57. http://dx.doi.org/10.1128/aem.65.6.2553-2557.1999.
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ABSTRACT Our understanding of the degradation of organic matter will benefit from a greater appreciation for the genes encoding enzymes involved in the hydrolysis of biopolymers such as chitin, one of the most abundant polymers in nature. To isolate representative and abundant chitinase genes from uncultivated marine bacteria, we constructed libraries of genomic DNA isolated from coastal and estuarine waters. The libraries were screened for genes encoding proteins that hydrolyze a fluorogenic analogue of chitin, 4-methylumbelliferyl β-d-N,N′-diacetylchitobioside (MUF-diNAG). The abundance of clones capable of MUF-diNAG hydrolysis was higher in the library constructed with DNA from the estuary than in that constructed with DNA from coastal waters, although the abundance of positive clones was also dependent on the method used to screen the library. Plaque assays revealed nine MUF-diNAG-positive clones of 75,000 screened for the estuarine sample and two clones of 750,000 for the coastal sample. A microtiter plate assay revealed approximately 1 positive clone for every 500 clones screened in the coastal library. The number of clones detected with the plaque assay was consistent with estimates of the portion of culturable bacteria that degrade chitin. Our results suggest that culture-dependent methods do not greatly underestimate the portion of marine bacterial communities capable of chitin degradation.
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Tassara, Eleonora, Caterina Oliveri, Luigi Vezzulli, Carlo Cerrano, Lian Xiao, Marco Giovine, and Marina Pozzolini. "2D Collagen Membranes from Marine Demosponge Chondrosia reniformis (Nardo, 1847) for Skin-Regenerative Medicine Applications: An In Vitro Evaluation." Marine Drugs 21, no. 8 (July 28, 2023): 428. http://dx.doi.org/10.3390/md21080428.
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Research in tissue engineering and regenerative medicine has an ever-increasing need for innovative biomaterials suitable for the production of wound-dressing devices and artificial skin-like substitutes. Marine collagen is one of the most promising biomaterials for the production of such devices. In this study, for the first time, 2D collagen membranes (2D-CMs) created from the extracellular matrix extract of the marine demosponge Chondrosia reniformis have been evaluated in vitro as possible tools for wound healing. Fibrillar collagen was extracted from a pool of fresh animals and used for the creation of 2D-CMs, in which permeability to water, proteins, and bacteria, and cellular response in the L929 fibroblast cell line were evaluated. The biodegradability of the 2D-CMs was also assessed by following their degradation in PBS and collagenase solutions for up to 21 days. Results showed that C. reniformis-derived membranes avoided liquid and protein loss in the regeneration region and also functioned as a strong barrier against bacteria infiltration into a wound. Gene expression analyses on fibroblasts stated that their interaction with 2D-CMs is able to improve fibronectin production without interfering with the regular extracellular matrix remodeling processes. These findings, combined with the high extraction yield of fibrillar collagen obtained from C. reniformis with a solvent-free approach, underline how important further studies on the aquaculture of this sponge could be for the sustainable production and biotechnological exploitation of this potentially promising and peculiar biopolymer of marine origin.
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Sobecky, Patricia A., Tracy J. Mincer, Michelle C. Chang, Aresa Toukdarian, and Donald R. Helinski. "Isolation of Broad-Host-Range Replicons from Marine Sediment Bacteria." Applied and Environmental Microbiology 64, no. 8 (August 1, 1998): 2822–30. http://dx.doi.org/10.1128/aem.64.8.2822-2830.1998.
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ABSTRACT Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888–895, 1997). In the present study we isolated 1.8- to 2.3-kb fragments that contain functional replication origins from one relatively large (30-kb) and three small (<10-kb) naturally occurring plasmids present in different marine isolates. 16S rRNA sequence analyses indicated that the four plasmid-bearing marine isolates belonged to the α and γ subclasses of the classProteobacteria. Three of the marine sediment isolates are related to the γ-3 subclass organisms Vibrio splendidusand Vibrio fischeri, while the fourth isolate may be related to Roseobacter litoralis. Sequence analysis of the plasmid replication regions revealed the presence of features common to replication origins of well-characterized plasmids from clinical bacterial isolates, suggesting that there may be similar mechanisms for plasmid replication initiation in the indigenous plasmids of gram-negative marine sediment bacteria. In addition to replication inEscherichia coli DH5α and C2110, the host ranges of the plasmid replicons, designated repSD41, repSD121, repSD164, and repSD172, extended to marine species belonging to the generaAchromobacter, Pseudomonas,Serratia, and Vibrio. While sequence analysis of repSD41 and repSD121 revealed considerable stretches of homology between the two fragments, these regions do not display incompatibility properties against each other. The replication origin repSD41 was detected in 5% of the culturable plasmid-bearing marine sediment bacterial isolates, whereas the replication origins repSD164 and repSD172 were not detected in any plasmid-bearing bacteria other than the parental isolates. Microbial community DNA extracted from samples collected in November 1995 and June 1997 and amplified by PCR yielded positive signals when they were hybridized with probes specific for repSD41 and repSD172 replication sequences. In contrast, replication sequences specific for repSD164 were not detected in the DNA extracted from marine sediment microbial communities.
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Valdés-Castro, Valentina, Humberto E. González, Ricardo Giesecke, Camila Fernández, and Verónica Molina. "Assessment of Microbial Community Composition Changes in the Presence of Phytoplankton-Derived Exudates in Two Contrasting Areas from Chilean Patagonia." Diversity 14, no. 3 (March 7, 2022): 195. http://dx.doi.org/10.3390/d14030195.
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Patagonian fjords and channels in southern Chile are heterogeneous ecosystems characterized by the interaction of estuarine and marine waters influencing physical-chemical conditions and biological assemblages. Besides salinity, microbial communities from estuarine and marine origin are naturally subjected to changing organic matter quality and variable nutrient concentrations. In this study, we tackle the response of the bacterial community from estuarine and marine origins associated with two size classes (<0.7 µm and <1.6 µm) to the addition of sterile phytoplankton-derived exudates (PDE) compared to control conditions (no addition). Picoplanktonic cell abundance, active bacterial composition analyzed through 16S rRNA sequencing, changes in dissolved organic carbon (DOC) and δ13C were determined over 5 and 15 days after PDE addition. Our results showed that the active marine bacteria were richer and more diverse than their estuarine counterparts, and were dominated by Alphaproteobacteria and Gammaproteobacteria, respectively. PDE addition in both the fractions and the sample origin resulted in an enrichment throughout the incubation of Rhodobacteracea and Cryimorphaceae families, whereas Epsilonproteobacteria (Arcobacteraceae) were mainly favored in the estuarine experiments. Picoplankton abundance increased with time, but higher cell numbers were found in PDE treatments in both size classes (>2 × 105 cell mL−1). In all the experiments, DOC concentration decreased after eight days of incubation, but shifts in δ13C organic matter composition were greater in the estuarine experiments. Overall, our results indicate that despite their different origins (estuarine versus marine), microbial communities inhabiting the fjord responded to PDE with a faster effect on marine active bacteria.
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Mostafa, Yasser S., Sulaiman A. Alrumman, Kholod A. Otaif, Saad A. Alamri, Mohamed S. Mostafa, and Taher Sahlabji. "Production and Characterization of Bioplastic by Polyhydroxybutyrate Accumulating Erythrobacter aquimaris Isolated from Mangrove Rhizosphere." Molecules 25, no. 1 (January 1, 2020): 179. http://dx.doi.org/10.3390/molecules25010179.
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The synthesis of bioplastic from marine microbes has a great attendance in the realm of biotechnological applications for sustainable eco-management. This study aims to isolate novel strains of poly-β-hydroxybutyrate (PHB)-producing bacteria from the mangrove rhizosphere, Red Sea, Saudi Arabia, and to characterize the extracted polymer. The efficient marine bacterial isolates were identified by the phylogenetic analysis of the 16S rRNA genes as Tamlana crocina, Bacillus aquimaris, Erythrobacter aquimaris, and Halomonas halophila. The optimization of PHB accumulation by E. aquimaris was achieved at 120 h, pH 8.0, 35 °C, and 2% NaCl, using glucose and peptone as the best carbon and nitrogen sources at a C:N ratio of 9.2:1. The characterization of the extracted biopolymer by Fourier-transform infrared spectroscopy (FTIR), Nuclear magnetic resonance (NMR), and Gas chromatography-mass spectrometry (GC-MS) proves the presence of hydroxyl, methyl, methylene, methine, and ester carbonyl groups, as well as derivative products of butanoic acid, that confirmed the structure of the polymer as PHB. This is the first report on E. aquimaris as a PHB producer, which promoted the hypothesis that marine rhizospheric bacteria were a new area of research for the production of biopolymers of commercial value.
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Ramesh, Chatragadda, Bhushan Rao Tulasi, Mohanraju Raju, Narsinh Thakur, and Laurent Dufossé. "Marine Natural Products from Tunicates and Their Associated Microbes." Marine Drugs 19, no. 6 (May 26, 2021): 308. http://dx.doi.org/10.3390/md19060308.
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Marine tunicates are identified as a potential source of marine natural products (MNPs), demonstrating a wide range of biological properties, like antimicrobial and anticancer activities. The symbiotic relationship between tunicates and specific microbial groups has revealed the acquisition of microbial compounds by tunicates for defensive purpose. For instance, yellow pigmented compounds, “tambjamines”, produced by the tunicate, Sigillina signifera (Sluiter, 1909), primarily originated from their bacterial symbionts, which are involved in their chemical defense function, indicating the ecological role of symbiotic microbial association with tunicates. This review has garnered comprehensive literature on MNPs produced by tunicates and their symbiotic microbionts. Various sections covered in this review include tunicates’ ecological functions, biological activities, such as antimicrobial, antitumor, and anticancer activities, metabolic origins, utilization of invasive tunicates, and research gaps. Apart from the literature content, 20 different chemical databases were explored to identify tunicates-derived MNPs. In addition, the management and exploitation of tunicate resources in the global oceans are detailed for their ecological and biotechnological implications.
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Zhang, Hongcai, Zekai Wang, Xi Yu, Junwei Cao, Tianqiang Bao, Jie Liu, Chengwen Sun, Jiahua Wang, and Jiasong Fang. "The Phylogeny and Metabolic Potentials of a Lignocellulosic Material-Degrading Aliiglaciecola Bacterium Isolated from Intertidal Seawater in East China Sea." Microorganisms 12, no. 1 (January 11, 2024): 144. http://dx.doi.org/10.3390/microorganisms12010144.
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Lignocellulosic materials are composed of cellulose, hemicellulose and lignin and are one of the most abundant biopolymers in marine environments. The extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, a novel lignin-degrading bacterial strain, LCG003, was isolated from intertidal seawater in Lu Chao Harbor, East China Sea. Phylogenetically, strain LCG003 was affiliated with the genus Aliiglaciecola within the family Alteromonadaceae. Metabolically, strain LCG003 contains various extracellular (signal-fused) glycoside hydrolase genes and carbohydrate transporter genes and can grow with various carbohydrates as the sole carbon source, including glucose, fructose, sucrose, rhamnose, maltose, stachyose and cellulose. Moreover, strain LCG003 contains many genes of amino acid and oligopeptide transporters and extracellular peptidases and can grow with peptone as the sole carbon and nitrogen source, indicating a proteolytic lifestyle. Notably, strain LCG003 contains a gene of dyp-type peroxidase and strain-specific genes involved in the degradation of 4-hydroxy-benzoate and vanillate. We further confirmed that it can decolorize aniline blue and grow with lignin as the sole carbon source. Our results indicate that the Aliiglaciecola species can depolymerize and mineralize lignocellulosic materials and potentially play an important role in the marine carbon cycle.
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Champion, Marie, Emilie Portier, Karine Vallée-Réhel, Isabelle Linossier, Eric Balnois, Guillaume Vignaud, Xavier Moppert, Claire Hellio, and Fabienne Faÿ. "Anti-Biofilm Activity of a Hyaluronan-like Exopolysaccharide from the Marine Vibrio MO245 against Pathogenic Bacteria." Marine Drugs 20, no. 11 (November 21, 2022): 728. http://dx.doi.org/10.3390/md20110728.
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Biofilms, responsible for many serious drawbacks in the medical and marine environment, can grow on abiotic and biotic surfaces. Commercial anti-biofilm solutions, based on the use of biocides, are available but their use increases the risk of antibiotic resistance and environmental pollution in marine industries. There is an urgent need to work on the development of ecofriendly solutions, formulated without biocidal agents, that rely on the anti-adhesive physico-chemical properties of their materials. In this context, exopolysaccharides (EPSs) are natural biopolymers with complex properties than may be used as anti-adhesive agents. This study is focused on the effect of the EPS MO245, a hyaluronic acid-like polysaccharide, on the growth, adhesion, biofilm maturation, and dispersion of two pathogenic model strains, Pseudomonas aeruginosa sp. PaO1 and Vibrio harveyi DSM19623. Our results demonstrated that MO245 may limit biofilm formation, with a biofilm inhibition between 20 and 50%, without any biocidal activity. Since EPSs have no significant impact on the bacterial motility and quorum sensing factors, our results indicate that physico-chemical interactions between the bacteria and the surfaces are modified due to the presence of an adsorbed EPS layer acting as a non-adsorbing layer.
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Guerra, LV, F. Savergnini, FS Silva, MC Bernardes, and MAC Crapez. "Biochemical and microbiological tools for the evaluation of environmental quality of a coastal lagoon system in Southern Brazil." Brazilian Journal of Biology 71, no. 2 (May 2011): 461–68. http://dx.doi.org/10.1590/s1519-69842011000300016.
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This study aimed to evaluate the environmental quality of surface water of the Maricá Lagoon System through physicochemical, biochemical and microbiological parameters, in order to assess its environmental quality. Marine influence over the system was evidenced by the salinity and temperature gradients, where the most distant point, in Maricá Lagoon, presented the largest protein, lipid and biopolymeric carbon concentrations. Biopolymers, with predominance of lipids, presented a pattern that differs from the literature for coastal sediments. The concentration of thermotolerant coliforms characterised Maricá Lagoon and Boqueirão Channel as unfit for bathing (60.0 and 66.3 cells.mL-1, respectively). The bacterioplankton in the system proved to be predominantly heterotrophic, a consumer of organic matter, with fermentative, denitrifying and sulfate-reducing metabolism. No esterase enzyme activity was detected, despite the presence of active metabolism, measured by the electron transport system (average of 0.025 µgO2.h-1.mL-1). The bacterial biomass (autotrophic, heterotrophic and coliforms), bacterial respiratory activity and biopolymer parameters evinced a spatial degradation pattern in the Maricá Lagoon System, where the points with less water renewal are the most impacted.
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Wibowo, Joko Tri, Asep Bayu, Widya Dwi Aryati, Carla Fernandes, Arry Yanuar, Anake Kijjoa, and Masteria Yunovilsa Putra. "Secondary Metabolites from Marine-Derived Bacteria with Antibiotic and Antibiofilm Activities against Drug-Resistant Pathogens." Marine Drugs 21, no. 1 (January 12, 2023): 50. http://dx.doi.org/10.3390/md21010050.
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The search for new antibiotics against drug-resistant microbes has been expanded to marine bacteria. Marine bacteria have been proven to be a prolific source of a myriad of novel compounds with potential biological activities. Therefore, this review highlights novel and bioactive compounds from marine bacteria reported during the period of January 2016 to December 2021. Published articles containing novel marine bacterial secondary metabolites that are active against drug-resistant pathogens were collected. Previously described compounds (prior to January 2016) are not included in this review. Unreported compounds during this period that exhibited activity against pathogenic microbes were discussed and compared in order to find the cue of the structure–bioactivity relationship. The results showed that Streptomyces are the most studied bacteria with undescribed bioactive compounds, followed by other genera in the Actinobacteria. We have categorized the structures of the compounds in the present review into four groups, based on their biosynthetic origins, as polyketide derivatives, amino acid derivatives, terpenoids, as well as compounds with mixed origin. These compounds were active against one or more drug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), vancomycin-resistant Enterococci (VRE), multidrug-resistant Mycobacterium tuberculosis (MDR-TB), and amphotericin B-resistant Candida albicans. In addition, some of the compounds also showed activity against biofilm formation of the test bacteria. Some previously undescribed compounds, isolated from marine-derived bacteria during this period, could have a good potential as lead compounds for the development of drug candidates to overcome multidrug-resistant pathogens.
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Wörmer, Lars, Tatsuhiko Hoshino, Marshall W. Bowles, Bernhard Viehweger, Rishi R. Adhikari, Nan Xiao, Go-ichiro Uramoto, et al. "Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial." Science Advances 5, no. 2 (February 2019): eaav1024. http://dx.doi.org/10.1126/sciadv.aav1024.
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Marine sediments host an unexpectedly large microbial biosphere, suggesting unique microbial mechanisms for surviving burial and slow metabolic turnover. Although dormancy is generally considered an important survival strategy, its specific role in subsurface sediments remains unclear. We quantified dormant bacterial endospores in 331 marine sediment samples from diverse depositional types and geographical origins. The abundance of endospores relative to vegetative cells increased with burial depth and endospores became dominant below 25 m, with an estimated population of 2.5 × 1028to 1.9 × 1029endospores in the uppermost kilometer of sediment and a corresponding biomass carbon of 4.6 to 35 Pg surpassing that of vegetative cells. Our data further identify distinct endospore subgroups with divergent resistance to burial and aging. Endospores may shape the deep biosphere by providing a core population for colonization of new habitats and/or through low-frequency germination to sustain slow growth in this environment.
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Burroughs, A. Max, and L. Aravind. "Innate immunity and bacterial conflict: the deep origins of cGAS-STING signaling and discovery of uncharacterized animal immunity pathways." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 68.25. http://dx.doi.org/10.4049/jimmunol.204.supp.68.25.
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Abstract Just as animal innate immunity pits endogenous response pathways against invading extragenic threats, microbiomes are governed by myriad pathways mediating inter-genomic resource procurement, collectively known as ‘conflict systems.’ Leveraging the continually-increasing amount of genome data, we have probed such systems and in the process uncovered the evolutionary origins of core components of animal immunity. This includes the discovery that cyclic-nucleotide synthesizing enzymes like human cGAS and OAS1 and their receptors like STING were acquired from comparable conflict-triggered nucleotide signaling systems in bacteria. While our analyses point to previously-unknown diversity animal innate immunity, particularly in marine invertebrates, this diversity pales in contrast to bacterial pathways which contain a wealth of completely uncharacterized nucleotide synthetase enzymes, nucleotide receptors, and response effector domains. Further, studies from our group point to entirely-uncharacterized components of the animal innate immunity response that have also been acquired from bacterial conflict systems. These include the viral RNA-acting human Leng9 phosphoesterase and the human N4BP2L1 nucleotide kinase. These studies also uncover a connection between immunity-driven second messenger nucleotide generation and a previously-unrecognized receptor domain in the human apoptotic factor MAP3K5.
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Gu, Ailiang, and Christopher John Eastoe. "The Origins of Sulfate in Cenozoic Non-Marine Evaporites in the Basin and-Range Province, Southwestern North America." Geosciences 11, no. 11 (November 3, 2021): 455. http://dx.doi.org/10.3390/geosciences11110455.
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Cenozoic evaporites (gypsum and anhydrite) in southwestern North America have wide ranges of δ34S (−30 to +22‰; most +4 to +10‰) and δ18OSO4 (+3 to +19‰). New data are presented for five basins in southern Arizona. The evaporites were deposited in playas or perennial saline lakes in closed basins of Oligocene or younger age. Very large accumulations in Picacho, Safford and Tucson Basins have isotope compositions plotting close to a linear δ34S-δ18OSO4 relationship corresponding to mixing of two sources of sulfur: (1) sulfate recycled from Permian marine gypsum and (2) sulfate from weathering of Laramide-age igneous rocks that include porphyry copper deposits. In the large evaporites, sulfate with δ34S > +10‰ is dominantly of Permian or Early Cretaceous marine origin, but has locally evolved to higher values as a result of bacterial sulfate reduction (BSR). Sulfate with δ34S < −10‰ formed following exposure of sulfides, possibly formed during supergene enrichment of a porphyry copper deposit by BSR, and have values of δ18OSO4 higher than those of local acid rock drainage because of participation of evaporated water in BSR. Accumulations of 30 to 100 km3 of gypsum in Picacho and Safford Basins are too large to explain as products of contemporaneous erosion of Permian and Laramide source materials, but may represent recycling of Late Cretaceous to Miocene lacustrine sulfate.
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Han, Heejun, Jeomshik Hwang, and Guebuem Kim. "Characterizing the origins of dissolved organic carbon in coastal seawater using stable carbon isotope and light absorption characteristics." Biogeosciences 18, no. 5 (March 16, 2021): 1793–801. http://dx.doi.org/10.5194/bg-18-1793-2021.
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Abstract. In order to determine the origins of dissolved organic matter (DOM) occurring in the seawater of Sihwa Lake, we measured the stable carbon isotope ratios of dissolved organic carbon (DOC-δ13C) and the optical properties (absorbance and fluorescence) of DOM in two different seasons (March 2017 and September 2018). Sihwa Lake is enclosed by a dike along the western coast of South Korea, and the water is exchanged with the Yellow Sea twice a day through the sluice gates. The DOC concentrations were generally higher in lower-salinity waters in both periods, and excess of DOC was also observed in 2017 in high-salinity waters. Here, the excess DOC represents any DOC concentrations higher than those in the incoming open-ocean seawater. The excess DOC occurring in the lower-salinity waters originated mainly from marine sediments of tidal flats, based on the DOC-δ13C values (-20.7±1.2 ‰) and good correlations among the DOC, humic-like fluorescent DOM (FDOMH), and NH4+ concentrations. However, the origins of the excess DOC observed in 2017 appear to be from two different sources: one mainly from marine sources such as biological production based on the DOC-δ13C values (−19.1 ‰ to −20.5 ‰) and the other mainly from terrestrial sources by land–seawater interactions based on its depleted DOC-δ13C values (−21.5 ‰ to −27.8 ‰). This terrestrial DOM source observed in 2017 was likely associated with DOM on the reclaimed land, which experienced extended exposure to light and bacterial degradation as indicated by the higher spectral slope ratio (SR) of light absorbance and no concurrent increases in the FDOMH and NH4+ concentrations. Our study demonstrates that the combination of these biogeochemical tools can be a powerful tracer of DOM sources and characteristics in coastal environments.
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Do, Thanh Ngoc, and Luan Thi Bui. "Correlations between geochemical characteristics of source rocks and chemical compositions of crude oils from LD field, block 15-1/05, Cuu Long basin." Science and Technology Development Journal - Natural Sciences 1, T3 (September 30, 2017): 109–20. http://dx.doi.org/10.32508/stdjns.v1it3.457.
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LD field is the second oil discovery on offshore Block 15-1/05, which is located 15 kilometres East-North East of the first discovery (LDN field). The major aim of this study is to evaluate correlations between accumulated hydrocarbons and source rocks of LD structure, in order to verify their potential for generating oil and gas. Therefore, the authors have synthesized and analyzed geochemical and biomarker characteristics, structures, and chemical compositions of crude oils and source rock extracts by gas chromatography–mass spectrometry analysis to interpret hydrocarbon origins of the LD field. Oil samples and source rock hydrocarbon extracts were from LD-1X/LD-1Xst and LD-3X/LD-3Xbis well of the LD field. Based on biomarker distributions, five oil samples as well as nineteen studied extracts from source rocks indicated predominant non-marine algal organic substances as well as contributions of bacterial and higher plant input. Such samples are characterized by the presence of oleananes, high concentration of C27 steranes compared to C29 and C28 steranes, and the presence of 4-methyl C30-steranes low to moderate concentration. Those evidences show that the oil samples are derived from a single source unit.
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Beckett, Stephen J., and Hywel T. P. Williams. "Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks." Interface Focus 3, no. 6 (December 6, 2013): 20130033. http://dx.doi.org/10.1098/rsfs.2013.0033.
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Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins.
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De la Iglesia, Rodrigo, Isidora Echenique-Subiabre, Susana Rodríguez-Marconi, Juan Pablo Espinoza, Peter von Dassow, Osvaldo Ulloa, and Nicole Trefault. "Distinct oxygen environments shape picoeukaryote assemblages thriving oxygen minimum zone waters off central Chile." Journal of Plankton Research 42, no. 5 (August 17, 2020): 514–29. http://dx.doi.org/10.1093/plankt/fbaa036.
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Abstract Oxygen minimum zones (OMZs) support ocean biogeochemical cycles of global importance. The OMZ off central Chile is characterized by seasonally variable oxygen concentrations due to upwelling events. Bacterial and archaeal communities from this area have been previously described; however, picoeukaryote communities remain largely unexplored. In order to improve our knowledge on picoeukaryote ecology and the effect of controlling factors on its community structure, environmental parameters and 18S rRNA metabarcoding analyses were performed in water samples collected at several depths at a time series station on the continental shelf in March, May and August. Our results showed that oxygen, nitrate, silicate and temperature are relevant factors shaping the picoeukaryote community structure. Overall, according to our sequence dataset, the OMZ was dominated by Dinophyceae members including marine parasitic dinoflagellates. Moreover, dysoxic and suboxic conditions were enriched by fungi and phagotrophic protists from Ustilaginomycetes, Bicoecea and Choanoflagellatea. The latter is particularly relevant in the understanding of metazoan evolution and the origins of multicellularity in low-oxygen environments. Picoeukaryote communities changed significantly over the 3 months sampled with variations in water column stratification, including the occurrence of a winter bloom of Mamiellales. Altogether, this study reveals a great diversity and dynamics of picoeukaryotes inhabiting a coastal OMZ.
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Maki, Teruya, Kazutaka Hara, Ayumu Iwata, Kevin C. Lee, Kei Kawai, Kenji Kai, Fumihisa Kobayashi, et al. "Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events." Atmospheric Chemistry and Physics 17, no. 19 (October 9, 2017): 11877–97. http://dx.doi.org/10.5194/acp-17-11877-2017.
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Abstract. Aerosol particles, including airborne microorganisms, are transported through the free troposphere from the Asian continental area to the downwind area in East Asia and can influence climate changes, ecosystem dynamics, and human health. However, the variations present in airborne bacterial communities in the free troposphere over downwind areas are poorly understood, and there are few studies that provide an in-depth examination of the effects of long-range transport of aerosols (natural and anthropogenic particles) on bacterial variations. In this study, the vertical distributions of airborne bacterial communities at high altitudes were investigated and the bacterial variations were compared between dust events and non-dust events.Aerosols were collected at three altitudes from ground level to the free troposphere (upper level: 3000 or 2500 m; middle level: 1200 or 500 m; and low level: 10 m) during Asian dust events and non-dust events over the Noto Peninsula, Japan, where westerly winds carry aerosols from the Asian continental areas. During Asian dust events, air masses at high altitudes were transported from the Asian continental area by westerly winds, and laser imaging detection and ranging (lidar) data indicated high concentrations of non-spherical particles, suggesting that dust-sand particles were transported from the central desert regions of Asia. The air samples collected during the dust events contained 10–100 times higher concentrations of microscopic fluorescent particles and optical particle counter (OPC) measured particles than in non-dust events. The air masses of non-dust events contained lower amounts of dust-sand particles. Additionally, some air samples showed relatively high levels of black carbon, which were likely transported from the Asian continental coasts. Moreover, during the dust events, microbial particles at altitudes of > 1200 m increased to the concentrations ranging from 1. 2 × 106 to 6. 6 × 106 particles m−3. In contrast, when dust events disappeared, the microbial particles at > 1200 m decreased slightly to microbial-particle concentrations ranging from 6. 4 × 104 to 8. 9 × 105 particles m−3.High-throughput sequencing technology targeting 16S rRNA genes (16S rDNA) revealed that the bacterial communities collected at high altitudes (from 500 to 3000 m) during dust events exhibited higher diversities and were predominantly composed of natural-sand/terrestrial bacteria, such as Bacillus members. During non-dust periods, airborne bacteria at high altitudes were mainly composed of anthropogenic/terrestrial bacteria (Actinobacteria), marine bacteria (Cyanobacteria and Alphaproteobacteria), and plant-associated bacteria (Gammaproteobacteria), which shifted in composition in correspondence with the origins of the air masses and the meteorological conditions. The airborne bacterial structures at high altitudes suggested remarkable changes in response to air mass sources, which contributed to the increases in community richness and to the domination of a few bacterial taxa.
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Lacroix, Gilles L., and Derek Knox. "Distribution of Atlantic salmon (Salmo salar) postsmolts of different origins in the Bay of Fundy and Gulf of Maine and evaluation of factors affecting migration, growth, and survival." Canadian Journal of Fisheries and Aquatic Sciences 62, no. 6 (June 1, 2005): 1363–76. http://dx.doi.org/10.1139/f05-055.
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Atlantic salmon (Salmo salar) postsmolts surveyed by surface trawling in the Bay of Fundy and Gulf of Maine during 20012003 were aggregated in several areas in the Bay of Fundy and dispersed over a broader area in the Gulf of Maine. Postsmolt distribution reflected the major surface-current vectors and was independent of origin (wild vs. hatchery, inner vs. outer Bay of Fundy). Migration proceeded without disruption, and marked wild postsmolts from both the inner and outer Bay of Fundy were recaptured in the outer Bay of Fundy and the Gulf of Maine, where their distribution overlapped the commercial fishery for Atlantic herring (Clupea harengus). Marked postsmolts of wild origin were recaptured more frequently than those of hatchery origin but the overall density was low, and no schools of postsmolts were encountered that could offer protection from predators. Temperature and salinity in postsmolt habitat were favourable for growth and survival. Postsmolts were in excellent condition and had no bacterial or viral pathogens or salmon lice (Lepeophtheirus salmonis). They were feeding on pelagic prey (amphipods, euphausiids, and fish larvae) and the period of accelerated marine growth had started, indicating that environmental conditions and food supply were not limiting growth and survival.
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Del Cortona, Andrea, Christopher J. Jackson, François Bucchini, Michiel Van Bel, Sofie D’hondt, Pavel Škaloud, Charles F. Delwiche, et al. "Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds." Proceedings of the National Academy of Sciences 117, no. 5 (January 7, 2020): 2551–59. http://dx.doi.org/10.1073/pnas.1910060117.
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The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Sageman, Bradley B., and Erle G. Kauffman. "Benthic community analysis and the prediction of organic carbon content in Mesozoic black shale facies." Paleontological Society Special Publications 6 (1992): 258. http://dx.doi.org/10.1017/s2475262200008182.
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The burial and preservation of significant quantities of marine organic matter in epicontinental basins results from low bottom water oxygen levels, and moderate to low sedimentation rates of fine-grained siliciclastic sediment under at least moderately productive waters. Because benthic biotas are extremely sensitive to such factors as bottom water oxygen, grain size, substrate consistency and sedimentation rate, there is a potentially predictive relationship between biofacies and Corg potential of marine strata. High-resolution biological, sedimentological and geochemical studies of Mesozoic organic-rich black shale facies, comprising major hydrocarbon source rocks, allow characterization of this relationship: a) A series of recurrent, bivalve-dominated benthic communities are defined based on trends in diversity, abundance, equitability and trophic specialization. They comprise biofacies which reflect oxygen and substrate gradients in time and space, and thus the Corg preservation potential of marine sediments/strata. The biotas are surprisingly robust in terms of population size and inferred biomass, and demonstrably colonized the benthic zone (as opposed to pseudoplanktic origins). They include both resident communities of taxa specifically adapted to low oxygen (dysoxic) conditions through physiological and anatomical means (e.g., expanded oxygen adsorptive surfaces), or possibly through bacterial chemosymbiosis, and event communities of less tolerant taxa reflecting short-term improvements in benthic conditions; b) many organic-rich sequences contain common event biofacies, indicating a dynamic benthic environment with frequent short-term fluctuations in oxygen and substrate. These are attributable to mixing during large storms, productivity blooms, rapid deposition from mass flows, or reduced sedimentation during condensation/bypass events. However, increasing frequency of events is not necessarily correlated with decrease in Corg levels; c) comparison of trends in the quantity and quality of Corg to biofacies patterns indicate that the most favorable Corg preservation is associated with “benthic boundary biofacies.” These biofacies represent a redox boundary at or near the sediment-water interface and a predominantly dysoxic to episodically oxic water column. The “benthic boundary” may have been associated with the presence of microbial (mainly sulphur bacterial) mats on the substrate surface, which could have regulated its position and contributed to the pool of sedimented Corg; d) mapping of benthic boundary biofacies in time and space within a basin makes possible correlation of Corg preservation potential to paleogeography and sea level history. Although the results of such analyses from the Greenhorn Formation, Western Interior basin, suggest highest Corg burial and preservation in fine-grained shale facies of distal offshore environments during sea level rise, high Corg is not necessarily associated with an anoxic water column. This suggests the need for reappraisal of stagnant basin scenarios for source rock formation. The most important factors in Corg accumulation and preservation may be the development of benthic boundaries and consequent maintenance of anoxia below the sediment-water interface in fine-grained, organic-rich substrates, and the contribution of bacteria to the flux of Corg into the sediment.
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Rodela, T. M., J. S. Ballantyne, and P. A. Wright. "Carrier-mediated urea transport across the mitochondrial membrane of an elasmobranch (Raja erinacea) and a teleost (Oncorhynchus mykiss) fish." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 294, no. 6 (June 2008): R1947—R1957. http://dx.doi.org/10.1152/ajpregu.00251.2007.
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In osmoregulating teleost fish, urea is a minor nitrogen excretory product, whereas in osmoconforming marine elasmobranchs it serves as the major tissue organic solute and is retained at relatively high concentrations (∼400 mmol/l). We tested the hypothesis that urea transport across liver mitochondria is carrier mediated in both teleost and elasmobranch fishes. Intact liver mitochondria in rainbow trout ( Oncorhynchus mykiss) demonstrated two components of urea uptake, a linear component at high concentrations and a phloretin-sensitive saturable component [Michaelis constant ( Km) = 0.58 mmol/l; maximal velocity ( Vmax) = 0.12 μmol·h−1·mg protein−1] at lower urea concentrations (<5 mmol/l). Similarly, analysis of urea uptake in mitochondria from the little skate ( Raja erinacea) revealed a phloretin-sensitive saturable transport ( Km= 0.34 mmol/l; Vmax= 0.054 μmol·h−1·mg protein−1) at low urea concentrations (<5 mmol/l). Surprisingly, urea transport in skate, but not trout, was sensitive to a variety of classic ionophores and respiration inhibitors, suggesting cation sensitivity. Hence, urea transport was measured in the reverse direction using submitochondrial particles in skate. Transport kinetics, inhibitor response, and pH sensitivity were very similar in skate submitochondrial particle submitochondrial particles ( Km= 0.65 mmol/l, Vmax= 0.058 μmol·h−1·mg protein−1) relative to intact mitochondria. We conclude that urea influx and efflux in skate mitochondria is dependent, in part, on a bidirectional proton-sensitive mechanism similar to bacterial urea transporters and reminiscent of their ancestral origins. Rapid equilibration of urea across the mitochondrial membrane may be vital for cell osmoregulation (elasmobranch) or nitrogen waste excretion (teleost).
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Besednova, NN, TS Zaporozhets, TA Kuznetsova, NV Krylova, ID Makarenkova, AK Gazha, TP Smolina, LA Ivanushko, and EV Persiyanova. "Biologically Active Substances from Marine Hydrobionts of the Pacific Ocean as the Basis for Developing New Medicines." ЗДОРОВЬЕ НАСЕЛЕНИЯ И СРЕДА ОБИТАНИЯ - ЗНиСО / PUBLIC HEALTH AND LIFE ENVIRONMENT, May 2021, 78–83. http://dx.doi.org/10.35627/2219-5238/2021-338-5-78-83.
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Introduction: Since 1970s, a school of thought on management of innate and acquired immunity systems using biologically active substances of the Far East marine origin has been developed by the Immunology Laboratory of Somov Research Institute of Epidemiology and Microbiology of the Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor). Biopolymers, which constitute the structural basis of live marine organisms and sustain numerous vital processes, draw special attention as potential candidates for pharmaceutical forms. The objective of our study was to summarize the results of long-term research on biologically active substances (BAS) from marine aquatic organisms (hydrobionts) of the Pacific Ocean as the basis for developing medicinal preparations for infectious disease prevention and treatment and dietary supplements for food and functional food products. Methods: We have selected and analyzed 46 principal published works of the researchers of the Institute found in electronic databases (Web of Science, PubMed, and eLibrary) using appropriate keywords. Results: We established that over 500 substances from various hydrobionts of the Pacific Ocean including invertebrates, fish, algae, marine bacteria (polycationic and polyanionic polysaccharides of brown and red algae), pectins (colloidal carbohydrates of high molecular weight and complex structure), lipopolysaccharides and polysaccharides from marine proteobacteria, glycoproteins, proteoglycans, glycolipids, low-molecular compounds of marine origin (sulfated polyoxysteroids, peptides, beta-glucans, nucleic acids, amino acid complexes, naphthoquinones and spinochromes of sea urchins) had been studied for their biological properties over the past almost half a century. The studies produced abundant new data on immunomodulatory, antibacterial, antiviral, antitumor, anti-adhesive, anti-endotoxic, pro-apoptotic, hepatoprotective, and hypolipidemic properties of biologically active substances, substantiated feasibility of designing innovative BAS-based medicines, and developed environmentally safe functional food products and dietary supplements. Conclusions: Biologically active substances from marine hydrobionts are a promising source for the development of novel domestic pharmaceuticals.
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Li, Minchun, Wei Xie, Chuanlun Zhang, and Kedong Yin. "Linking Bacterial Communities to Optical-Derived Properties of Porewater DOM in Sediments in the Coastal East China Sea." Frontiers in Marine Science 9 (June 21, 2022). http://dx.doi.org/10.3389/fmars.2022.919368.
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Bacterial communities and porewater dissolved organic matter (DOM) pool are intimately interactive in sedimentary environments. Estuarine coastal regions are an interactive area between terrestrial and marine influences in terms of DOM origins and freshness. Yet, we know little about the relationships between the bacterial communities and DOM in those regions. In this study, porewater DOM samples were collected from 42 sites in the coastal East China Sea. The porewater DOM optical properties were determined by fluorescence and absorption spectra, while the corresponding bacterial community compositions of those sediments were examined by 16S rRNA gene high-throughput sequencing. The results showed that bacterial species richness was positively correlated with multiple terrestrial indicators based on the optical properties of DOM, which implied that heterogeneous DOM from terrestrial origins might harbor a wider spectrum of bacterial taxa in marine sediments. The analysis of the co-occurrence network of the bacterial communities showed that the edges and density for samples with low DOM freshness were 3.4 times and 3 times those for the samples with high DOM freshness, respectively. This suggested that the connection among the bacterial taxa under the lower DOM freshness condition were enhanced and that reduced freshness of DOM may encourage more complimentary utilization of resources. The findings provide a new insight into such interactive processes of heterogeneous organic matter utilization meditated by microorganisms in coastal sediments.
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Satari, Leila, Alba Guillén, Adriel Latorre-Pérez, and Manuel Porcar. "Beyond Archaea: The Table Salt Bacteriome." Frontiers in Microbiology 12 (October 29, 2021). http://dx.doi.org/10.3389/fmicb.2021.714110.
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Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.
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Erkorkmaz, Burak Adnan, Daniella Gat, and Yinon Rudich. "Aerial transport of bacteria by dust plumes in the Eastern Mediterranean revealed by complementary rRNA/rRNA-gene sequencing." Communications Earth & Environment 4, no. 1 (February 6, 2023). http://dx.doi.org/10.1038/s43247-023-00679-8.
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AbstractProcesses influencing the transport of airborne bacterial communities in the atmosphere are poorly understood. Here, we report comprehensive and quantitative evidence of the key factors influencing the transport of airborne bacterial communities by dust plumes in the Eastern Mediterranean. We extracted DNA and RNA from size-resolved aerosols sampled from air masses of different origins, followed by qPCR and high-throughput amplicon sequencing of 16 S ribosomal RNA gene and transcripts. We find that airborne bacterial community composition varied with air mass origin and particle size. Bacterial abundance, alpha diversity and species richness were higher in terrestrially influenced air masses than in marine-influenced air masses and higher in the coarse particle fraction (3.0 to 10.0 µm) than in the fine fraction (0.49 to 1.5 µm). This suggests that airborne bacteria mainly were associated with dust particles or transported as cell aggregates. High abundances of rRNA from human, animal and plant pathogen taxa indicate potential ecological impacts of atmospheric bacterial transport.
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Darya, Mehrnoosh, Mehdi Haji Abdolrasouli, Morteza Yousefzadi, Mir Masoud Sajjadi, Iman Sourinejad, and Maaroof Zarei. "Antifouling coating based on biopolymers (PCL/ PLA) and bioactive extract from the sea cucumber Stichopus herrmanni." AMB Express 12, no. 1 (February 27, 2022). http://dx.doi.org/10.1186/s13568-022-01364-3.
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AbstractAn important challenge to decrease the toxic effects of the common biocides in marine environments and to achieve suitable ecofriendly natural antifouling coatings is to find effective natural antifoulants and efficient biodegradable coatings. In this study, antifouling activities of nine bioactive extracts (non-polar to polar) from different organs of the sea cucumber Stichopus herrmanni were tested against five bacterial strains, barnacle and brine shrimp larvae. The ethyl acetate extract of the body wall showed the highest in-vitro antifouling activity including high antibacterial and anti-barnacle activities and low toxicity against the brine shrimp as non-target organism. Based on these results, 10 phr of the ethyl acetate extract from S.herrmanni was added to different coatings consisting of polycaprolactone (PCL)/polylactic acid (PLA) blends containing various compositions of PLA (0, 10, and 20 wt.%). Polyvinyl chloride panels were coated with the prepared antifouling coatings and immersed in seawater for three months. Panel coated with PCL 80% /PLA 20% containing 10 phr of the antifoulant (panel-5), showed the highest resistance against fouling settlement with fouling coverage of 41.66% (P < 0.05). In addition, the lowest fouling weight was measured in panel-5 as well (81.00 ± 9.85 g) (P < 0.05). These findings indicate the antibacterial and antifouling potential of semi-polar bioactive extracts from the S. herrmanni body wall as natural antifoulants, as well as the enhanced antifouling performance of PCL/the natural antifoulant coatings by adding PLA. Graphical Abstract
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Gopal, Judy, Manikandan Muthu, Thirumalai Dhakshanamurthy, Ki Jun Kim, Nazim Hasan, Seong Jung Kwon, and Sechul Chun. "Sustainable ecofriendly phytoextract mediated one pot green recovery of chitosan." Scientific Reports 9, no. 1 (September 25, 2019). http://dx.doi.org/10.1038/s41598-019-50133-z.
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Abstract Chitin and chitosan are biopolymers that have diverse applications in medicine, agriculture, food, cosmetics, pharmaceuticals, wastewater treatment and textiles. With bio-origins, they easily blend with biological systems and show exemplified compatibility which is mandatory when it comes to biomedical research. Chitin and chitosan are ecofriendly, however the processes that are used to recover them aren’t ecofriendly. The focus of this work is to attempt an ecofriendly, sustainable phytomediated one pot recovery of chitosan from commercial chitin and from crab and shrimp shells and squid pen solid wastes. Graviola extracts have been employed, given the fact file that their active ingredients acetogenins actively interact with chitin in insects (resulting in its application as an insecticide). With that as the core idea, the graviola extracts were chosen for orchestrating chitin recovery and a possible chitin to chitosan transformation. The results confirm that graviola extracts did succeed in recovery of chitosan nanofibers from commercial chitin flakes and recovery of chitosan particles directly from solid marine wastes of crab, shrimp and squids. This is a first time report of a phyto-extract mediated novel chitosan synthesis method.
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Gupta, Annika Durve, Shivani Kakkar Khanna, and Pooja Gupta. "Isolation and Characterization of Extracellular Chitinase Produced by Chitinolytic Bacteria Isolated from Soil Samples." Asian Journal of Microbiology and Biotechnology, May 3, 2023, 16–24. http://dx.doi.org/10.56557/ajmab/2023/v8i28225.
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Chitin is one of the most common biopolymers found in both marine and terrestrial habitats. Chitinase enzyme has gained popularity due to its diverse biotechnological applications, particularly in agriculture for the biocontrol of phytopathogenic fungi and harmful insects. In this work bacteria producing chitinase enzyme were isolated from soil and water samples. Three bacterial isolates C2, C3, and C4 were found to be Gram-negative coccobacilli while bacterial isolate C9 was found to be Gram-positive cocci. The optimum pH and temperature for all the isolates were studied. The effect of pH, temperature, substrate variation, and incubation period on enzyme activity was studied. The activity of the chitinase enzyme for all the bacterial isolates increased with an increase in temperature up to 37°C. However, a further rise in reaction temperature caused a loss of chitinase activity. Michaelis-Menten plot and Line weaver Burk plot were constructed to calculate the Km and Vmax values. Partial Purification of the chitinase enzyme was carried out and the enzyme activity, protein content, specific activity, and purification fold were estimated. It was observed that the enzyme activity of the crude sample was less than the fractionated sample. The highest enzyme activity was found to be at a 40% fraction. Of the four isolates, C2 was the best in its enzyme activity. The future prospect is the production of chitinases at an industrial scale for various biotechnological applications. Chitinase-producing isolates have the ability to produce chitinase between temperatures 22ºC and 40ºC which is the field temperature for the cultivation of most the crop, so it may be applicable to field conditions against plant pathogenic fungi which is the major problem for agricultural food production. The management of seafood waste businesses may potentially benefit from the usage of this enzyme.
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Elsayis, Asmaa, Sahar W. M. Hassan, Khaled M. Ghanem, and Heba Khairy. "Suggested Sustainable Medical and Environmental Uses of Melanin Pigment From Halotolerant Black Yeast Hortaea werneckii AS1." Frontiers in Microbiology 13 (April 13, 2022). http://dx.doi.org/10.3389/fmicb.2022.871394.
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The marine ecosystem is a complex niche with unique environmental circumstances. Microbial communities from the sea are one of the main origins of compounds with tremendous capabilities. Marine yeasts have the ability to produce secondary metabolites that are architecturally distinct from those found in terrestrial species. Melanin pigment synthesized by marine halotolerant black yeast Hortaea werneckii AS1 isolated from Mediterranean salt lakes in Alexandria, Egypt was found to exert a radical scavenging effect on 2,2-diphenyl-1-picrylhydrazyl (DPPH) with an IC50 of 61.38 μg/ml. Furthermore, it showed no cytotoxicity toward human skin fibroblast cell line (HSF) with an IC50 value above 0.1 mg/ml. The antimicrobial capability of the pigment was revealed against the tested number of bacterial and fungal strains with the highest inhibition zone of 25 mm against Aeromonas sp. and a growth inhibition percentage up to 63.6% against Aspergillus niger. From an environmental impact point of view, the pigment disclosed a heavy metal removal efficiency of 85.7, 84.8, and 81.5% for Pb2+, Cd2+, and Ni2+, respectively, at 100 mg/L metal concentration. The previously mentioned results suggested melanin from H. werneckii AS1 as a promising biocompatible candidate in various medical, cosmetics, pharmaceutical, and environmental applications.
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Panwar, Pratibha, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, et al. "Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community." Microbiome 8, no. 1 (August 9, 2020). http://dx.doi.org/10.1186/s40168-020-00889-8.
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Abstract Background Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. Results The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Conclusion Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.
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Ghaly, Timothy M., Sasha G. Tetu, and Michael R. Gillings. "Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites." Communications Biology 4, no. 1 (August 9, 2021). http://dx.doi.org/10.1038/s42003-021-02489-0.
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AbstractIntegrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites (attCs) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attCs from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attCs that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attCs cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For example, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons.
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Tarquinio, Flavia, Océane Attlan, Mathew A. Vanderklift, Oliver Berry, and Andrew Bissett. "Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds." Frontiers in Microbiology 12 (September 21, 2021). http://dx.doi.org/10.3389/fmicb.2021.703014.
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Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Killops, S. D., A. N. Bishop, E. W. Tegelaar, K. Urdal, M. R. K. Ghammari, and J. W. H. Weijers. "Sedimentary diterpane origins—inferences from oils of varying source depositional environment and age." Frontiers in Geochemistry 1 (August 31, 2023). http://dx.doi.org/10.3389/fgeoc.2023.1241784.
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The potential of C20 tricyclic and tetracyclic diterpane distributions in oils (and by extension, rock extracts) to aid the interpretation of sources of organic matter and depositional environments—spanning carbonate, marl, freshwater and saline lacustrine, normal marine and transitional—from Neoproterozoic to Neogene, is investigated using GC-MS and GC-MS-MS analysis of a range of oils of known origin. Contributions from gymnosperms are readily distinguished by abundant characteristic tricyclics and/or tetracyclics [e.g., 5β(H)-rimuane, 5β(H)-rosane, isopimarane and phyllocladanes]. Even at low levels, phyllocladane appears a reliable indicator of Carboniferous or younger source. A fairly uniform, limited range of diterpanes at relatively low abundance is observed in oils from other sources, with the 13β(H),14α(H)-cheilanthane often being the most abundant C20 diterpane associated with carbonates and marls. Other tricyclics include the previously proposed 8β-methyl-13α-ethylpodocarpane and a series of unidentified compounds, mostly sharing mass spectra with abundant fragment ions at m/z 123, 163 and 191, together with methyl (m/z 261), but not ethyl, loss from the molecular ion. This limited range of tricyclics suggests a common group of source organisms (probably bacterial) and or diagenetic transformation resulting in a few thermodynamically stable products. It may explain why pimarane is at most a trace component, despite pimaroids being widely occurring natural products. Where gymnosperms have made little contribution, C20 tetracyclic diterpanes are typically sparse and comprise beyerane, atisanes and possibly also 16α(H)-kaurane (which co-elutes with the first of the pair of atisane isomers), with beyerane usually the most abundant in terms of m/z 276→123 response. These compounds are not detected in oils from Neoproterozoic and Cambrian carbonates, but analysis of more samples is required to confirm this trend. Despite some caveats, diterpane distributions can provide useful information related to age and depositional environment as well as providing a tool for oil-oil correlation.
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Möller, Lars, Yevhen Vainshtein, Bettina Meyer, John Neidhardt, A. Murat Eren, Kai Sohn, and Ralf Rabus. "Rich microbial and depolymerising diversity in Antarctic krill gut." Microbiology Spectrum, March 11, 2024. http://dx.doi.org/10.1128/spectrum.04035-23.
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ABSTRACT With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter , also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire. IMPORTANCE The Antarctic krill ( Euphausia superba ) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
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Liu, Siwei, Shan Yu, Xindi Lu, Hailin Yang, Yuanyuan Li, Xuemin Xu, Hailong Lu, and Yunxin Fang. "Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea." Frontiers in Microbiology 13 (October 25, 2022). http://dx.doi.org/10.3389/fmicb.2022.1032851.
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Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.
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Meng, Xiangyu, Fangyi Chen, Ming Xiong, Hua Hao, and Ke-Jian Wang. "A new pathogenic isolate of Kocuria kristinae identified for the first time in the marine fish Larimichthys crocea." Frontiers in Microbiology 14 (April 25, 2023). http://dx.doi.org/10.3389/fmicb.2023.1129568.
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In recent years, new emerging pathogenic microorganisms have frequently appeared in animals, including marine fish, possibly due to climate change, anthropogenic activities, and even cross-species transmission of pathogenic microorganisms among animals or between animals and humans, which poses a serious issue for preventive medicine. In this study, a bacterium was clearly characterized among 64 isolates from the gills of diseased large yellow croaker Larimichthys crocea that were raised in marine aquaculture. This strain was identified as K. kristinae by biochemical tests with a VITEK 2.0 analysis system and 16S rRNA sequencing and named K. kristinae_LC. The potential genes that might encode virulence-factors were widely screened through sequence analysis of the whole genome of K. kristinae_LC. Many genes involved in the two-component system and drug-resistance were also annotated. In addition, 104 unique genes in K. kristinae_LC were identified by pan genome analysis with the genomes of this strain from five different origins (woodpecker, medical resource, environment, and marine sponge reef) and the analysis results demonstrated that their predicted functions might be associated with adaptation to living conditions such as higher salinity, complex marine biomes, and low temperature. A significant difference in genomic organization was found among the K. kristinae strains that might be related to their hosts living in different environments. The animal regression test for this new bacterial isolate was carried out using L. crocea, and the results showed that this bacterium could cause the death of L. crocea and that the fish mortality was dose-dependent within 5 days post infection, indicating the pathogenicity of K. kristinae_LC to marine fish. Since K. kristinae has been reported as a pathogen for humans and bovines, in our study, we revealed a new isolate of K. kristinae_LC from marine fish for the first time, suggesting the potentiality of cross-species transmission among animals or from marine animals to humans, from which we would gain insight to help in future public prevention strategies for new emerging pathogens.
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Worden, Paul J., Daniel R. Bogema, Melinda L. Micallef, Jeffrey Go, Ania T. Deutscher, Maurizio Labbate, Timothy J. Green, et al. "Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak." Microbial Genomics 8, no. 12 (December 7, 2022). http://dx.doi.org/10.1099/mgen.0.000883.
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The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium , Pseudoalteromonas , Shewanella and Vibrio genera, with Vibrio species making up more than two-thirds of all species identified. Construction of a phylogenomic tree, ANI analysis, and pan-genome analysis of the 57 isolates represents the most comprehensive culture-based phylogenomic survey of Vibrios during a PO summer mortality event in Australian waters and revealed large genomic diversity in many of the identified species. Our analysis revealed limited and inconsistent associations between isolate species and their geographical origins, or host health status. Together with ANI and pan-genome results, these inconsistencies suggest that to determine the role that microbes may have in Pacific oyster summer mortality events, isolate identification must be at the taxonomic level of strain. Our WGS data (specifically, the accessory genomes) differentiated bacterial strains, and coupled with associated metadata, highlight the possibility of predicting a strain’s environmental niche and level of pathogenicity.
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Dong, Xiyang, Jayne E. Rattray, D. Calvin Campbell, Jamie Webb, Anirban Chakraborty, Oyeboade Adebayo, Stuart Matthews, et al. "Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep." Nature Communications 11, no. 1 (November 17, 2020). http://dx.doi.org/10.1038/s41467-020-19648-2.
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AbstractAt marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
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Tawfeek, Walaa S., Amina S. Kassab, Lamiaa A. Okasha, Mohamed Abdelsalam, and Ahmed H. Sherif. "The phenotypic and genetic characteristics of Pseudomonas anguilliseptica strains associated with mortalities in farmed sea bream and sea bass." Aquaculture International, December 11, 2023. http://dx.doi.org/10.1007/s10499-023-01360-9.
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AbstractTo investigate the presence of Pseudomonas anguilliseptica, one hundred specimens of sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) were collected alongside water samples during episodes of widespread fish mortality in marine fish farms located in the northern region of Egypt. This study documented the clinical and postmortem manifestations observed in moribund sea bream and sea bass, thus providing evidence for the occurrence of a septicemic-hemorrhagic bacterial disease. Fourteen strains of P. anguilliseptica were isolated and characterized from both sea bream and sea bass specimens. The conventional bacteriology methods were employed to retrieve the causative bacterial agent and subsequently evaluate its phenotypic traits. Moreover, sequencing of the 16 S rRNA was conducted to characterize the identified microorganism. Furthermore, multilocus sequence analysis (MLSA) was employed to confirm the identity of P. anguilliseptica and elucidate the phylogenetic interrelationship among various strains. Regardless of their source or the fish species from which the strains were obtained, these isolates showed a high level of phenotypic homogeneity. MLSA displayed a genetic homogeneity among isolates despite their different geographic origins. Antibiogram revealed the sensitivity of some P. anguilliseptica strains for antibiotics (florfenicol, trimethoprim, sulfamethoxazole, cefotaxime, and ciprofloxacin). Isolated strains were harboring some antibiotic-resistant genes, with the most prevalent being tetA gene, followed by ermB gene. Water physico-chemical parameters (low temperature and salinity fluctuation) were convenient for bacterial growth. In addition, P. anguilliseptica strains could resist several antibiotics and harbored antibiotic-resistant genes, resulting in difficulties in fish treatment.
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Zafeiropoulos, Haris, Laura Gargan, Christina Pavloudi, Evangelos Pafilis, and Jens Carlsson. "Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter!" ARPHA Conference Abstracts 4 (March 4, 2021). http://dx.doi.org/10.3897/aca.4.e64966.
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Environmental DNA (eDNA) metabarcoding has been commonly used in recent years (Jeunen et al. 2019) for the identification of the species composition of environmental samples. By making use of genetic markers anchored in conserved gene regions, universally present acrooss the species of large taxonomy groups, eDNA metabarcoding exploits both extra- and intra-cellular DNA fragments for biodiversity assessment. However, there is not a truly “universal” marker gene that is capable of amplifying all species across different taxa (Kress et al. 2015). The mitochondrial cytochrome C oxidase subunit I gene (COI) has many of the desirable properties of a “universal" marker and has been widely used for assessing species identity in Eukaryotes, especially metazoans (Andjar et al. 2018). However, a great number of COI Operational Taxonomic Units (OTUs) or/and Amplicon Sequence Variants (ASVs) retrieved from such studies do not match reference sequences and are often referred to as “dark matter” (Deagle et al. 2014). The aim of this study was to discover the origins and identities of these COI dark matter sequences. We built a reference phylogenetic tree that included as many COI-sequence-related information across the tree of life as possible. An overview of the steps followed is presented in Fig. 1a. Briefly, the Midori reference 2 database was used to retrieve eukaryotes sequences (183,330 species). In addition, the API of the BOLD database was used as source for the corresponding Bacteria (559 genera) and Archaea (41 genera) sequences. Consensus sequences at the family level were constructed from each of these three initial COI datasets. The COI-oriented reference phylogenetic tree of life was then built by using 1,240 consensus sequences with more than 80% of those coming from eukaryotic taxa. Phylogeny-based taxonomic assignment was then used to place query sequences. The a) total number of sequences, b) sequences assigned to Eukaryotes and c) unassigned subsets of OTUs, from marine and freshwater samples, retrieved during in-house metabarcoding experiments, were placed in the reference tree (Fig. 1b). It is clear that a large proportion of sequences targeting the COI region of Eukaryotes actually represents bacterial branches in the phylogenetic tree (Fig. 1b). We conclude that COI metabarcoding studies targeting Eukaryotes may come with a great bias derived from amplification and sequencing of bacterial taxa, depending on the primer pair used. However, for the time being, publicly available bacterial COI sequences are far too few to represent the bacterial variability; thus, a reliable taxonomic identification of them is not possible. We suggest that bacterial COI sequences should be included in the reference databases used for the taxonomy assignment of OTUs/ASVs in COI-based eukaryote metabarcoding studies to allow for bacterial sequences that were amplified to be excluded enabling researchers to exclude non-target sequences. Further, the approach presented here allows researchers to better understand the unknown unknowns and shed light on the dark matter of their metabarcoding sequence data.
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Mandragutti, Teja, and G. Sudhakar. "Selective isolation and genomic characterization of biopolymer producer—a novel feature of halophile Brachybacterium paraconglomeratum MTCC 13074." Journal of Genetic Engineering and Biotechnology 21, no. 1 (February 28, 2023). http://dx.doi.org/10.1186/s43141-023-00484-y.
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Abstract Background Biopolymers like polyhydroxyalkanoates (PHA) are the best natural macromolecules to use as alternative to the synthetic polymers. Many prokaryotes accumulate PHA as cytoplasmic intracellular granules and their accumulation is triggered by starving conditions. The PHAs are ecofriendly and used to create biodegradable plastics. The microbial synthesized PHA had acquired global importance in industrial and biomedical sectors. Results Ten different bacterial strains were isolated for the screening of PHA producers from the estuarine region of the Bay of Bengal, Suryalanka in Bapatla. A yellowish slimy circular colony known as M4 is actively growing on selective minimal media and was screened for polymeric granules in its cytoplasm using Sudan Black B and confirmed with the fluorescent dye Nile blue A. All of the isolates were biochemically tested and isolate M4 is the most capable of growing at high NaCl concentrations (3.2 percent) and tests positive for catalase, methyl red. The M4 strain revealed clear hydrolysis of gelatin, starch, and casein. The 16S rRNA sequencing revealed that M4 is 99.72% of identity to Brachybacterium paraconglomeratum LMG 19861(T) in BLAST and the obtained strain was assigned with accession no. MTCC 13074 and deposited in NCBI with accession no. MW899045. The chief cellular fatty acids found in M4 were C14:0, C15:0, C16:0, C18:1cis-9, C18:0, iso-C15: 0, iso-C14: 0, anteiso-C17: 0 and C18:1-7. Crotonic acid formation from M4-PHB extract was detected at 235nm in a UV spectrophotometer. Methanolysis was done, and derivatives of polyhydroxybutyric acid (PHB) in the extract were analyzed using GC-MS. Increasing viscosity was seen in the extracts which confirms the presence of polymer in the extracts. Thermogravimetric analysis was studied to determine the thermal profile of the PHB in the extract of M4. Conclusion In the study, the selective screening and extraction of ecofriendly PHB from M4 strain was highlighted. Brachybacterium paraconglomeratum is a novel strain showed its uniqueness by producing few monomeric derivatives of PHB. The strain was reporting for the first time as PHA producer. B. paraconglomeratum has promising characteristics according to its metabolic profile. In addition, this study also helps to understand the diversity of bacteria isolated from marine sources.
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Liu, Yanting, Qiang Zheng, Wenxin Lin, and Nianzhi Jiao. "Characteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to Chromids." mSystems 4, no. 5 (September 10, 2019). http://dx.doi.org/10.1128/msystems.00358-19.
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ABSTRACT Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent a bacteriochlorophyll a-containing functional group. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In this study, 13 Roseobacter clade genomes from seven genera that harbored exPGCs were used to analyze the characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs among PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing puf operons. Furthermore, the two different types of operons were observed within different strains of the same Tateyamaria and Jannaschia genera. The PufC-containing and PufX-containing operons were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of the Jannaschia strains comprised superoperons without evidence of insertion and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Finally, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within the Roseobacter clade. IMPORTANCE The evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of chlorophototrophy in bacteria. This report advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.
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Grote, Jana, J. Cameron Thrash, Megan J. Huggett, Zachary C. Landry, Paul Carini, Stephen J. Giovannoni, and Michael S. Rappé. "Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade." mBio 3, no. 5 (September 18, 2012). http://dx.doi.org/10.1128/mbio.00252-12.
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ABSTRACTSAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world’s oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade’s origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade.IMPORTANCEThe SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.