METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data.

BACKGROUND: With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing. RESULTS: We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results. CONCLUSION: Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.

Estimating internal phosphorus loading for a water quality model using chemical characterisation of sediment phosphorus and contrasting oxygen conditions.

The Finnish Archipelago Sea (AS) has long been subject to intensive anthropogenic phosphorus (P) loading. The area suffers from seasonal hypoxia and cyanobacterial blooms despite reductions in nutrient discharge from the catchment and point sources. Internal loading may even dominate the P budget. Previous estimates of internal P loading have limitations (e.g., in spatial coverage and infrequent measurements). We present the first area-wide estimates of the magnitude of internal P loading based on the long-term release of P stored in the sediments. Modelling the internal P loading in the AS is challenging due to the complexity of biogeochemical processes in the sediment-water interface, as well as the heterogenic topography of the seafloor. Instead, we calculated estimates of internal P loading based on data from previous studies on sequential chemical extraction of sediment P, sediment physical characteristics (e.g., organic content, location of muddy seabed substrates), and near-bottom oxygen (O2) conditions. The estimates in three scenarios of contrasting O2 conditions were based on potentially mobile P pools in the sediments, recycled from sediment to water (i.e., loosely-bound or exchangeable P, P bound to reducible iron oxy(hydr)oxides, and labile organic P). The potentially mobile P pools were determined by chemical extraction methods (modified from Psenner et al., 1984 and Ruttenberg, 1992). The internal P loading under presumable O2 conditions was estimated to be fivefold that of waterborne P input to the AS; comparable to previous estimates for hypoxic areas in the Baltic Sea. Our estimates revealed wide spatial variability in the internal P loading, depending on O2 conditions and seabed sediment substrate. The site-specific P release estimates are included in a water quality model used by regional authorities, which increases the model's reliability for estimating the impact of human activities on the water quality across the AS.

Natural peloids originating from subsea depths of 200 m in the hupo basin, South Korea: physicochemical properties for potential pelotherapy applications.

The present study firstly reports surface sediment from the subsea depth of 200 m as a potential natural peloid. The fine-silt sediment exhibited a consistent clay mineral composition dominated by illite, chlorite, kaolinite, and diatomite. The most abundant clay mineral was illite/mica, with other minerals loosely packed in a face-to-face orientation. The thermal conductivity, specific heat capacity, and cation-exchange capacity of the sediment were in the range 0.855-0.885 W/m K, 2.718-2.821 J/g °C, and 23.06-32.96 cmol/kg, respectively. The concentrations of most toxic elements in the sediment were considerably lower than the limits set by domestic cosmetic regulations and other international standards. The analyzed samples exhibited similar properties to those of previously reported peloids, thus making them suitable for use in the field of pelotherapy; furthermore, the consistency in data across a wide peloid-distribution area is expected to enable economically viable mining. Future investigations should aim to to evaluate the long-term effects on the skin, the bioavailability of potentially hazardous substances, and the therapeutic efficacy for various skin conditions.

Microplastic ingestion and its effects οn sea urchin Paracentrotus lividus: A field study in a coastal East Mediterranean environment.

Microplastics (MPs) are recognized as an increasing threat to the marine environment, but little is known about their effects on benthic organisms, including sea urchins, when ingested. For this purpose, wild sea urchins (P. lividus) and seafloor sediment samples were investigated across three coastal areas of Zakynthos Island (Ionian Sea), each exposed to different anthropogenic pressures, revealing a consistent pattern in MP abundance, shape, and color. Biomarkers related to oxidative stress, neurotoxicity, and genotoxicity showed no significant effects of MP ingestion in the sea urchins, except for a positive correlation between GST activity and ingested MPs, suggesting a possible activation of their detoxification system in response to MP ingestion. While MP concentrations in sea urchins and sediments were within the low range reported in the global literature, it remains crucial to conduct further investigations in areas with MP pollution approaching predicted levels to fully comprehend the potential effects of MP pollution on marine organisms.

Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment.

Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.

Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.

Transuranic nuclides Pu, Am and Cm isotopes, and 90Sr in seafloor sediments off the Fukushima Daiichi Nuclear Power Plant during the period from 2012 to 2019.

The 238Pu, 239+240Pu, 241Am, 242Cm, 243+244Cm and 90Sr concentrations in seafloor surface sediments collected at three sampling stations off the Fukushima Daiichi Nuclear Power Plant (FDNPP) site during the period from 2012 to 2019 were determined to elucidate the impacts of the FDNPP accident onto their concentrations in coastal sediments and to discuss the sources of the measured radionuclides. The 239+240Pu, 241Pu and 241Am concentrations and 240Pu/239Pu atom ratios in a sediment core were also determined to allow comparison of their inventories between this study and previously reported values and to identify the Pu sources. The 238Pu, 239+240Pu, 241Am and 90Sr concentrations showed no remarkable temporal variations; no significant increases in concentrations after the FDNPP accident were observed; these concentrations were comfortably within the previously reported concentration range; and no detectable 242Cm and 243+244Cm amounts were observed in surface sediments. The observed 238Pu/239+240Pu activity ratios were approximately two orders of magnitudes lower than those for the damaged FDNPP reactor core inventories and the observed values in terrestrial samples after the accident. The 239+240Pu, 241Pu and 241Am inventories in the sediment core were 389 ± 5, 503 ± 33 and 214 ± 3 Bq m-2, respectively. The 239+240Pu inventory was about an order of magnitude greater than the expected cumulative deposition density of global fallout from atmospheric nuclear weapons testing due to an enhanced scavenging effect. The 240Pu/239Pu atom ratios in the sediment core ranged from 0.239 to 0.246 with a mean value of 0.242 ± 0.002; these ratios were clearly greater than the mean global fallout ratio of 0.18. The results for 238Pu/239+240Pu activity ratios and 240Pu/239Pu atom ratios reflected a mixture of global fallout and Pacific Proving Grounds (PPG) close-in fallout Pu rather than Fukushima accident-derived Pu. The sediment column inventory for 239+240Pu originating from the PPG close-in fallout was calculated as 166 Bq m-2, which corresponded to 43% of the total inventory. A significant amount of the PPG-derived Pu has been transported by ocean currents and then preferentially scavenged in the coastal waters of Japan.

Distribution of heavy metals in seafloor sediments on the East China Sea inner shelf: Seasonal variations and typhoon impact.

Based on concentrations and distributions of heavy metals, grain size and loss on ignition (LOI) in the seafloor sediments acquired during three surveys in winter and in summer (before and after typhoon Morakot) in the mud deposition center off the Fujian-Zhejiang coast, East China Sea, the seasonal and typhoon-induced variations of heavy metals in seafloor sediments are discussed. It is found that different concentrations of heavy metals occurred in seafloor sediments, but their distribution patterns were similar, gradually decreasing from near-shore to offshore. The distribution of heavy metals was correlated with grain size and LOI in seafloor sediments, which showed significant seasonal variations and typhoon's impact. Based on these results, a conceptual evolution model was built about the seasonal and typhoon's impact on the deposition environment of heavy metals, which has implications for understanding the migration, settling, and burial processes of heavy metals in the sea.