Marine Samples Research Articles

Determination of Bisphenol A (BPA) in the Port of Gdynia Waters Using Gas Chromatography Coupled with Mass Spectrometry (GC-MS)

This paper presents a procedure for the determination of bisphenol A (BPA) in seawater. Gas chromatography coupled with mass spectrometry (GC-MS) was used as the analytical method, preceded by analyte isolation via solid-phase extraction (SPE). Initially, the best conditions for extraction, derivatization, and GC-MS analysis were established. The need for derivatization in the determination of BPA was investigated, and for this reason, two methods of sample preparation were compared: with and without the derivatization step. The parameters of the two methods of sample preparation were compared with each other, and a more efficient method was chosen for the analysis of marine water samples. Afterwards, the validation process was carried out and the following parameters were determined: limit of detection (LOD), limit of quantification (LOQ), linearity, precision, reproducibility, and repeatability. Finally, the results of the determination of bisphenol A in water samples collected from five harbor basins of the Port of Gdynia using an unmanned mobile research unit, HydroDron-1, were presented. The identified concentrations ranged from 0.01 µg/L to 0.03 µg/L, depending on the investigated area.

A study to determine effect of metal ions for optimization of L-Asparaginase producers for bioprocessing

The present study encompasses isolation of marine bacteria from marine soil samples collected from Chirala, Coastal area of Andhra Pradesh. Work includes isolation, screening, morphological and molecular characterization of selected L- Asparaginase producers. Purified enzyme was used for enzyme kinetic studies. Marine soil sample was collected in sterile bottle and brought to the lab bench and a total of 12 morphologically distinct bacterial colonies were isolated from collected marine soil samples and coded as Chirala Marine Bacteria. All 12 Chirala Marine Bacteria isolates were qualitatively screened for L-Asparaginase production. Out of 12 Chirala marine bacteria isolates, 9 isolates show positive response to L-Asparaginase activity. Effect of inducers i.e. carbon, nitrogen, aminoacids, phosphates and metal ions was studied.

Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding

Fungi in the phylum Cryptomycota have been recovered in numerous environmental DNA (eDNA) surveys but are only known from five described genera of intracellular parasites. These fungi are common in aquatic and soil habitats, but little is known about their relative diversity and specificity among particular habitats. We surveyed Cryptomycota from 80 eDNA samples including freshwater, soil, and marine habitats using Cryptomycota-preferential primers coupled with long-amplicon PacBio sequencing (1.2 kb of the 18S rRNA gene region). We found that freshwater samples were the most diverse, comprising 175 operational taxonomic units (OTUs) of Cryptomycota and also showed a high abundance of the related algae-parasitic group Aphelidiomycota, while marine samples were the least diverse with 25 OTUs. The composition of Cryptomycota communities was influenced by habitat, with freshwater and soil showing statistically distinct communities. Phylogenetic analyses showed that the present survey recovered most previously sampled major clades of Cryptomycota, but most (61%) OTUs were novel to this study, indicative of an extensive diversity of the group that remains largely uncharacterized.

MARINE RADIOCARBON CALIBRATION IN POLAR REGIONS: A SIMPLE APPROXIMATE APPROACH USING MARINE20

ABSTRACTThe Marine20 radiocarbon (14C) age calibration curve, and all earlier marine 14C calibration curves from the IntCal group, must be used extremely cautiously for the calibration of marine 14C samples from polar regions (outside ∼ 40ºS–40ºN) during glacial periods. Calibrating polar 14C marine samples from glacial periods against any Marine calibration curve (Marine20 or any earlier product) using an estimate of ${\rm{\Delta R}}$, the regional 14C depletion adjustment, that has been obtained from samples in the recent (non-glacial) past is likely to lead to bias and overconfidence in the calibrated age. We propose an approach to calibration that aims to address this by accounting for the possibility of additional, localized, glacial 14C depletion in polar oceans. We suggest, for a specific polar location, bounds on the value of ${\rm{\Delta }}{{\rm{R}}_{20}}\left( {\rm{\theta }} \right)$ during a glacial period. The lower bound ${\rm{\Delta R}}_{20}^{{\rm{Hol}}}$ may be based on 14C samples from the recent non-glacial (Holocene) past and corresponds to a low-depletion glacial scenario. The upper bound, ${\rm{\Delta R}}_{20}^{{\rm{GS}}}$, representing a high-depletion scenario is found by increasing ${\rm{\Delta R}}_{20}^{{\rm{Hol}}}$ according to the latitude of the 14C sample to be calibrated. The suggested increases to obtain ${\rm{\Delta R}}_{20}^{{\rm{GS}}}$ are based upon simulations of the Hamburg Large Scale Geostrophic Ocean General Circulation Model (LSG OGCM). Calibrating against the Marine20 curve using the upper and lower ${\rm{\Delta }}{{\rm{R}}_{20}}$ bounds provide estimates of calibrated ages for glacial 14C samples in high- and low-depletion scenarios which should bracket the true calendar age of the sample. In some circumstances, users may be able to determine which depletion scenario is more appropriate using independent paleoclimatic or proxy evidence.

A dietary perspective of cat-human interactions in two medieval harbors in Iran and Oman revealed through stable isotope analysis

Cats are hypercarnivorous, opportunistic animals that have adjusted to anthropogenic environments since the Neolithic period. Through humans, either by direct feeding and/or scavenging on food scraps, the diet of cats has been enriched with animals that they cannot kill themselves (e.g., large mammals, fish). Here, we conducted carbon and nitrogen stable isotope ratio analysis to reconstruct the diet of medieval cats and investigate cat-human interactions in two medieval harbor sites (Qalhât, Oman and Siraf, Iran). The analysis included 28 cat individuals and 100 associated marine and terrestrial faunal samples pertaining to > 30 taxa. The isotopic results indicate a high marine protein-based diet for the cats from Qalhât and a mixed marine-terrestrial (C4) diet for the cats from Siraf. Cats at these sites most likely scavenged on both human food scraps and refuse related to fishing activities, with differences in the two sites most likely associated with the availability of marine resources and/or the living conditions of the cats. By shedding light on the dietary habits of cats from two medieval harbors in the Arabian Gulf and Gulf of Oman, this study illustrates the potential of stable isotope analysis in reconstructing human-cat interactions in the past.

A Review of Marine In Situ Sensors and Biosensors

The exploration of the ocean is essential for the exploitation of marine resources and the sustainable development of human society. In order to assess both the health and the resources of the marine environment, a variety of chemical and biological sampling is needed. Traditionally, marine samples are collected on site and transported to a laboratory for analysis. Analytical methods are often tedious, and it is difficult to know the in situ real-time status. This review provides a comprehensive summary of the development of in situ chemical and biological sensors for the typical compounds in the ocean, including methane, radon, ferrous ion, carbon dioxide, microorganisms, pollutants, nutrients and seafood. Different types of sensors for each compound are highlighted, such as novel electrochemical and optical sensors. Commercial status of different sensors is introduced, and performance of representative sensors is compared and discussed deeply. The advantages and disadvantages of each sensing technique are analyzed and evaluated in detail. Finally, future prospects and work directions are presented, such as the deployment of these in situ sensors on fixed and/or moving platforms, development of microfluidic sensors and exploration of new antifouling materials and methods. This paper could serve as a resource for developing more advanced in situ chemical sensors and biosensors for marine scientific research, as well as related practical applications for monitoring marine resource exploration and exploitation and for environmental protection.

First Report of Caligus minimus Otto, 1821 (Copepoda: Siphonostomatoida: Caligidae) from Plankton Samples Collected from Türkiye

During a plankton sampling conducted off the northeastern Mediterranean coast of Türkiye, a single female copepod, Caligus minimus Otto, 1821 was collected from a marine plankton sample. C. minimus is a well-known species of the genus Caligus O.F. Müller, 1785 which has been previously reported as a parasite from nine marine fish species belonging to eight different families. To date, however, C. minimus has never been reported from plankton samples. In this study, the general morphology based on the key diagnostic characters of the planktonic C. minimus is presented using confocal laser scanning microscope (CLSM) images. This is the first report of C. minimus from plankton samples off Turkish waters and global marine environments.

Leisingera thetidis sp. nov., isolated from coastal water.

A Gram-strain-negative, strictly aerobic, rod-shaped, catalase-positive, oxidase-positive and pinkish beige colony-forming bacterial strain designated as BMJM1T was isolated from a marine sample collected from coastal water near Tongyeong, Republic of Korea. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that BMJM1T represents a member of the genus Leisingera as it is closely related to Leisingera daeponensis KCTC 12794T (98.27%), Leisingera caerulea DSM 24564T (97.98%), Leisingera aquaemixtae KCTC 32538T (97.91%), Leisingera methylohalidivorans DSM 14336T (97.26%) and Leisingera aquimarina DSM 24565T (97.25%). Optimal growth occurred at 25-30°C, pH 7.0 and with 2% NaCl. Digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values between strain BMJM1T and the closely related species of the genus Leisingera were below 40 and 90%, respectively, which are far below the thresholds to delineate a novel species. The predominant fatty acids (>10%) are summed feature 8 (C18:1ω7c and/or C18:1ω6c) (68.4%) and C14:1iso E (11.6%). The major polar lipids were phosphatidylethanolamine and phospholipid. The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 64.0%. On the basis of the results of the polyphasic taxonomic characterisation, BMJM1T represents a novel species of the genus Leisingera, for which the name is Leisingera thetidis sp. nov. is proposed, with that type strain BMJM1T (= KCTC 92110T = GDMCC 1.2992T).

Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.

The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.

Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters.

The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.

Compound-Specific 1D 1H NMR Pulse Sequence Selection for Metabolomics Analyses.

NMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) 1H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T2 filter to suppress macromolecule signals and reduce the humped curve in the spectrum. 1D nuclear Overhauser enhancement spectroscopy (NOESY) is another method for water suppression that is used routinely in plant samples with fewer macromolecules than in biofluid samples. Other common 1D 1H NMR methods such as 1D 1H presat and 1D 1H ES have simple pulse sequences; their acquisition parameters can be set easily. The proton with presat has just one pulse and the presat block causes water suppression, while other 1D 1H NMR methods including those mentioned above have more pulses. However, it is not well known in metabolomics studies because it is used only occasionally and in a few types of samples by metabolomics experts. Another effective method is excitation sculpting to suppress water. Herein, we evaluate the effect of method selection on signal intensities of commonly detected metabolites. Different classes of samples including biofluid, plant, and marine samples were investigated, and recommendations on the advantages and limitations of each method are presented.

Use of yellow mombin (Spondias mombin L.) in marination: Effect on quality properties of Boston butt pork during refrigerated storage

This research aimed to evaluate the effect of yellow mombin (Spondias mombin L.) juice as a marinade liquid on the quality properties of Boston butt pork during refrigerated storage. Yellow mombin juice was used as a marinade liquid at different concentrations: 0% (C0), 50% (C50), 75% (C75), and 100% (C100) in Boston butt pork samples which were analyzed for technological properties, proximate composition, and sensory characteristics on day 0 of storage. In addition, the pH, lipid oxidation, textural, and microbiological analyzes were carried out during refrigerated storage for 21 days. The results showed that the pH of the marinated samples was affected by yellow mombin juice (P < 0.05), with final values of 4.65 (C50), 4.56 (C75), and 4.39 (C100). Regarding the texture properties, C75 and C100 had the lowest values for hardness during storage. In addition, C100 had the lowest total aerobic mesophilic (5.69 log CFU g−1), total aerobic psychrophilic (7.10 log CFU g−1), and Enterobacteriaceae (5.30 log CFU g−1) counts at the end of storage. Regarding sensory properties, samples C50 and C75 were the best-rated marinated samples regarding overall acceptability and purchase intention. Therefore, the use of 75% yellow mombin juice (C75) as a marinade liquid could be a viable alternative for marinating Boston butt pork.

A targeted liquid cultivation method for previously uncultured non-colony forming microbes

A large number of microbes are not able to form colonies using agar-plating methods, which is one of the reasons that cultivation based on solid media leaves the majority of microbial diversity in the environment inaccessible. We developed a new Non-Colony-Forming Liquid Cultivation method (NCFLC) that can selectively isolate non-colony-forming microbes that exclusively grow in liquid culture. The NCFLC method involves physically separating cells using dilution-to-extinction (DTE) cultivation and then selecting those that could not grow on a solid medium. The NCFLC was applied to marine samples from a coastal intertidal zone and soil samples from a forest area, and the results were compared with those from the standard direct plating method (SDP). The NCFLC yielded fastidious bacteria from marine samples such as Acidobacteriota, Epsilonproteobacteria, Oligoflexia , and Verrucomicrobiota . Furthermore, 62% of the isolated strains were potential new species, whereas only 10% were novel species from SDP. From soil samples, isolates belonging to Acidobacteriota and Armatimonadota (which are known as rare species among identified isolates) were exclusively isolated by NCFLC. Colony formation capabilities of isolates cultivated by NCFLC were tested using solid agar plates, among which approximately one-third of the isolates were non-colony-forming, approximately half-formed micro-colonies, and only a minority could form ordinary size colonies. This indicates that the majority of the strains cultivated by NCFLC were previously uncultured microbial species unavailable using the SDP method. The NCFCL method described here can serve as a new approach to accessing the hidden microbial dark matter.

Unravelling the complex sub-ice geology of the Wilkes Subglacial Basin region of East Antarctica from marine sediment provenance analyses

AbstractDeciphering the sub-ice geology in the Wilkes Subglacial Basin region is important for understanding solid earth-ice sheet evolution and for assessing geological ties between East Antarctica and formerly contiguous Australia. We analyse marine sediment samples derived from drill site U1359 of Integrated Oceanic Drilling Program Expedition 318. Our study reports for the first time that the inland sediment source area comprises a complex mafic igneous terrain and a metamorphosed Precambrian subglacial basement. Pyroxene geochemical analyses confirm the presence of tholeiitic to calc-alkaline basalts. The high-grade part of the subglacial terrain contains upper amphibolite to granulite facies rocks that are comparable to Archaean to Palaeoproterozoic rocks exposed in the Terre Adélie Craton and the formerly adjacent Gawler Craton in Australia. Chemical Th-U-total Pb isochron method (CHIME) ages extracted from a subhedral monazite grain associated with the low-grade biotite-muscovite schist rock fragment provide a unimodal age of 799 ± 13 Ma. Rare occurrences of 800 Ma age in the Terre Adélie Craton and/or George V Coast provide evidence for the presence of at least one late Neoproterozoic magmato-metamorphic event in the interior of Wilkes Land. The affinity of the unexposed geological domains of Wilkes Land, East Antarctica, with their Australian counterparts is discussed in the context of the Rodinia supercontinent.

Genesis and interaction of magmas at Nishinoshima volcano in the Ogasawara arc, western Pacific: new insights from submarine deposits of the 2020 explosive eruptions

Sudden changes of eruption styles and magma compositions at arc volcanoes are enigmatic processes. Nishinoshima volcano, western Pacific, has had historical eruptions in 1973–1974 and from 2013 on and off to the present day. These eruptions were characterized by effusive Strombolian eruptions of andesite magmas until mid-June 2020, when they suddenly transitioned to violent explosive Strombolian eruptions that produced tephra fallout over a wide area. To understand this transition, we conducted marine surveys and sampling of the extensive submarine deposits of the tephra fallout. Our new data demonstrate that the full compositional range of the 2020 eruptions spans from basalt to dacite. We present evidence for magma mixing of newly injected basalt with andesite magmas. Nishinoshima consists of an andesitic main edifice surrounded by basaltic knolls: previous studies have shown that Nishinoshima andesite compositions can be generated by olivine fractionation of primary andesitic magmas that result from partial melting of hydrous mantle at relatively low pressures under the thin crust of the Ogasawara arc; knoll basalt compositions can be generated by partial melting of mantle at greater depths and were interpreted as older events of the volcano. We show that basalt magmas could have been generated throughout the entire history of Nishinoshima. In addition, we show that andesites from Nishinoshima and nearby Nishinoshima-Minami Knoll, which are only ∼8 km apart, have distinct subduction components. Together, these data improve our understanding of the diverse primary magmas responsible for the construction and continuing eruptive activity of an active island arc volcano.

Effect of antibiotics, antibiotic-resistant bacteria, and extracellular antibiotic resistance genes on the fate of ARGs in marine sediments

Surface runoff is a prevalent source via which emerging pollutants (i.e., antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs)) enter marine sediments. However, few studies have investigated the effect of emerging pollutants on the fate of ARGs in marine sediments. Therefore, three systems were established to measure the relative abundances of four common ARGs (i.e., blaTEM, tetA, tetC, and aphA) and the integron-integrase gene (intI1) after exposure to emerging pollutants in marine sediments from the Bohai Sea, the Yellow Sea, the East China Sea, and the South China Sea in China. The results revealed that antibiotic exposure could decrease the relative abundance of most ARGs (including blaTEM, tetA, and tetC) in these marine sediment samples. The exceptions were the relative abundance of blaTEM in the Bohai Sea marine sediments under ampicillin exposure and tetC in the Yellow Sea marine sediments under tetracycline exposure, which increased significantly. Among marine sediments challenged with ARB, the relative abundance of aphA in all four marine sediments displayed a decreasing trend, whereas the abundances of blaTEM and tetA in the marine sediments from the Bohai Sea and the South China Sea showed an increasing trend. The relative abundance of tetA in the marine sediments from the Yellow Sea and the East China Sea dropped markedly when exposed to extracellular ARG (eARG). Significant changes in blaTEM abundance were observed in the four marine sediments under eARG exposure. Gene aphA abundance showed the same trend as the intI1 abundance. IntI1 showed a decreasing trend under the exposure of antibiotic, ARB, or eARG, apart from the East and the South China Sea marine sediments under ampicillin conditions and the South China Sea marine sediments under RP4 plasmid condition. These findings suggest that dosing with emerging pollutants does not increase ARG abundance in marine sediments.

Examining the performance of three ballast water compliance monitoring devices for quantifying live organisms in both regulated size classes (≥50μm and ≥10-

A number of ballast water compliance monitoring devices (CMDs) have been made commercially available to verify the efficacy of ballast water management systems by quantifying the living organisms for both plankton size classes (≥50μm and ≥10-<50μm). This study aimed to examine whether new CMDs can provide a reliable indication of compliance regarding Regulation D-2 and to evaluate their performance for indicative analysis of organisms by assessing their accuracy (comparison to microscopy) and precision (comparison within measurement). Challenge fresh water samples were collected in four locations of Lake Ontario, Canada, whereas marine challenge water samples were collected around the Bay of Fundy, New Brunswick, Canada. Ballast water samples were collected from ships visiting several ports across Canada. Overall, accuracy was higher (>80%) in estimating organisms from prepared-challenge water (Ballast Eye and BallastWISE) than from ballast water samples (>70%) (B-QUA only). The sensitivity ranged from 50 to 100% for the ≥50μm organism size class, whereas for the ≥10-<50μm organism size class, it was higher for freshwater samples (>75%) than for marine samples (>50%). The performance of CMDs should be assessed under real-world conditions for a better understanding and to improve their use.

Experimental and molecular investigation of water adsorption controls in marine and lacustrine shale reservoirs

The restriction of hydrocarbon migration within shale reservoirs by pre-adsorbed water necessitates an investigation into water adsorption control mechanisms within shales. In this study, water vapor adsorption isotherms obtained from marine and lacustrine shale samples along with isotherms from their organic matter and experimentally verified kerogen molecular models were used to evaluate water adsorption mechanisms, with simulated wet kerogen-quartz nanocomposites. Furthermore, these were also used to investigate organic matter-inorganic interaction controls on water adsorption. Pore size distribution (PSD) controls on water distribution in organic matter were obtained via water vapor adsorption and low-pressure nitrogen adsorption analysis, along with small angle neutron scattering (SANS) analysis. The results reveal water adsorption is linked to changes in mesopore volume within organic matter and porosity in kerogen models. PSD obtained from the shales only reveal mesopore controls at high RH, with water adsorption mainly controlled by oxygen functional groups in organic matter pores and swelling clays. Inorganic controls on water adsorption are also observed in adsorbed water not tightly bound to the shale surface due to a high montmorillonite content in clay interlayers, and organic matter interaction with quartz with a negative relationship between the adsorbed water and the quartz content. Collectively, these findings indicate that CO2 migration in shale reservoirs could be inhibited by water that is distributed in potential CO2 adsorption sites within organic matter pores and montmorillonite.

Comparative Study on the Primary Control Factors of Nanopores in Transitional and Deep Marine Shale in the Southeastern Sichuan Basin, China

The deep marine shale from the Silurian Longmaxi Formation and transitional shale from the Permian Longtan Formation in the Sichuan Basin are two promising targets for shale gas exploration in China. In this study, nanopore characteristics for deep marine and transitional shale samples collected from the same well in the southeastern Sichuan Basin are investigated and compared via field emission scanning electron microscopy imaging, low-pressure gas adsorption, total organic carbon measurement, and X-ray diffraction. Results show that clay-related pores are well developed, pores within organic matter (OM) are rare, and shrinkage cracks along the OM-edge are widely prevalent in transitional shales. The deep marine shale is rich in bubble-like OM pores. The transitional shale has a larger pore volume but a lower specific surface area compared to the deep marine shale. The nanoporosity of the transitional shales is primarily controlled by clay and OM content. In deep marine shale, OM is the primary contributor to nanoporosity. Higher nanoporosity in the deep marine shales than in the middle-shallow ones was observed in this study. This occurrence is attributed to the high fluid pressure and the resulting superior preservation conditions for nanopores in deep marine shale formations.

Evaluation of DNA extraction methods and direct PCR in metabarcoding of mock and marine bacterial communities.

Recent advances in new molecular biology methods and next-generation sequencing (NGS) technologies have revolutionized metabarcoding studies investigating complex microbial communities from various environments. The inevitable first step in sample preparation is DNA extraction which introduces its own set of biases and considerations. In this study, we assessed the influence of five DNA extraction methods [B1: phenol/chloroform/isoamyl extraction, B2 and B3: isopropanol and ethanol precipitations, respectively-both modifications of B1, K1: DNeasy PowerWater Kit (QIAGEN), K2: modified DNeasy PowerWater Kit (QIAGEN) and direct PCR approach (P) that completely circumvents this step on community composition and DNA yield of mock and marine sample communities from the Adriatic Sea]. B1-B3 methods generally produced higher DNA yields and more similar microbial communities, but with higher interindividual variability. Each method demonstrated significant differences in a specific community structure, where rare taxa seem to play a crucial role. There was not one superior method closest to the theoretically expected mock community composition, they all demonstrated skewed ratios, but in a similar way which might be attributed to other factors, such as primer bias or 16S rRNA gene count for specific taxa. Direct PCR represents an interesting approach when high throughput in sample processing is required. We emphasize the importance of making a cautious decision about the choice of the extraction method or direct PCR approach, but even more importantly its consistent application throughout the study.