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Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.

Over half of the organic carbon on Earth’s surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including mercury resistance proteins. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.

Marine sediments may represent a sink of persistent organic pollutants including polychlorinated biphenyls (PCBs), toxic compounds prone to reductive or oxidative biodegradation pathways depending on the degree of chlorination and the positions of the chlorine atoms on the biphenyl rings. Superficial marine sediments can be subjected to episodic sediment resuspension by boat traffic and wind action causing the exposure of the underlying anaerobic layer to oxygen. Under these dynamic conditions, a deeper knowledge of the adaptation capability of the autochthonous microbial communities towards severe changes of the reaction environment is required. Insights into the metabolic potential of sediment community members may contribute greatly to the definition of efficient and reliable in situ bioremediation strategies. In this study, an anaerobic PCB-dechlorinating microbial consortium, developed from the chronically polluted marine sediment of Mar Piccolo (Taranto, Italy), was used to evaluate the response of the sediment microbiome to the imposition of aerobic conditions after prolonged anaerobic incubation. Compared to the anaerobic control, a dramatic change in microbiome composition, with a marked increase of Alphaproteobacteria of up to 39.2 % of total operational taxonomic units (OTUs) was revealed by high-throughput 16S rRNA gene sequencing. Accordingly, a decrement of low chlorinated PCBs (up to 58.3 ± 7.5 % for PCB 18) and the concomitant appearance of genes coding for PCB-degrading biphenyl dioxygenase (bph) were observed at the end of the aerobic incubation, suggesting the occurrence of oxidative PCB biodegradation processes.

A novel actinobacterium producing biosurfactant, designated OTB305T, was isolated from marine sediment sampled at Otsuchi Bay, Iwate Prefecture, Japan and its taxonomic position was examined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences exhibited that strain OTB305T was closely related to Streptomyces bohaiensis JCM 19630T (98.8 %) and Streptomyces lonarensis DSM 42084T (98.8 %). The chemotaxonomic characteristics of strain OTB305T corresponded to those of the genus Streptomyces as follows: the diamino acid of the cell-wall peptidoglycan was ll-diaminopimelic acid; whole-cell hydrolysates contained glucose and lacked characteristic major sugars; the predominant isoprenoid quinones were MK-9(H8) and MK-9(H6); the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unidentified phospholipid; the major cellular fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c; and the genomic DNA G+C content was 72.83 mol%. However, genomic relatedness analysis based on the average nucleotide identity and some phenotypic characteristics revealed that strain OTB305T was distinguished from closely related Streptomyces species. Therefore, strain OTB305T represents a novel species of the genus Streptomyces , for which the name Streptomyces otsuchiensis sp. nov. is proposed. The type strain is OTB305T (=NBRC 113255T=TBRC 9682T).

In this study, marine sediment (MS) was successfully used as a source of methanogenic bacteria for the anaerobic digestion (AD) of chicken manure (CM). Using MS showed high production in liquid and semi-solid conditions. Even in solid conditions, 169.3 mL/g volatile solids of chicken manure (VS-CM) was produced, despite the accumulation of ammonia (4.2 g NH3-N/kg CM). To the best of our knowledge, this is the highest methane production from CM alone, without pretreatment, in solid conditions (20%). Comparing MS to Ozouh sludge (excess activated sewage sludge) (OS), using OS under semi-solid conditions resulted in higher methane production, while using MS resulted in more ammonia tolerance (301 mL/gVS-CM at 8.58 g NH3-N/kg). Production optimization was carried out via a response surface methodology (RDM) model involving four independent variables (inoculum ratio, total solid content, NaCl concentration, and incubation time). Optimized methane production (324.36 mL/gVS-CM) was at a CM:MS ratio of 1:2.5 with no NaCl supplementation, 10% total solid content, and an incubation time of 45 days.

The former manganese ferroalloy plant and the remaining tailings are affecting the quality of the environment in Šibenik Bay, Croatia, even though industrial activities ceased more than 25 years ago. This study has revealed that the main manganese mineral phases present in the recently collected tailings, as well as in the dust collected on the roof of the plant during the production period, are bustamite and Mn-oxides. The same type of Mn mineral phases was also found in recently collected sediments from Šibenik Bay. Detailed chemical and phase analyses (XRD, BCR sequential analysis, aqua regia and lithium borate fusion) of the dust sample revealed high manganese values (24.1%), while granulometric analysis showed that 50% of the particles are smaller than PM2.5. The influence of the tailings is visible in the sediment, but the concentrations of the potentially toxic elements determined by the sequential BCR analysis are within the legal limits. Some higher values (20.3 g/kg Mn, 595 mg/kg Pb and 494 mg/kg Zn) are detected in the tailings, which are still exposed to weathering and as such should be additionally monitored. On the other hand, this material contains a considerable number of elements that could be considered lucrative (∑ REE up to 700 mg/kg, Mn up to 23 g/kg, Fe up to 37 g/kg and Al up to 25 g/kg), opening the possibility of reuse and recovery.

Marine Streptomyces species are underexplored for their pigment molecules and genes. In this study, we report the genome of the undecylprodigiosin biosynthesizing gene cluster carrying Streptomyces sp. strain BSE6.1, displaying antioxidant, antimicrobial, and staining properties. This Gram-positive obligate aerobic bacterium was isolated from the coastal sediment of the Andaman and Nicobar Islands, India. Pink to reddish pigmented colonies with whitish powdery spores on both agar and broth media are the important morphological characteristics of this bacterium. Growth tolerance to NaCl concentrations was 2 to 7%. The assembled genome of Streptomyces sp. BSE6.1 contains one linear chromosome 8.02 Mb in length with 7157 protein-coding genes, 82 tRNAs, 3 rRNAs and at least 11 gene clusters related to the synthesis of various secondary metabolites, including undecylprodigiosin. This strain carries type I, type II, and type III polyketide synthases (PKS) genes. Type I PKS gene cluster is involved in the biosynthesis of red pigment undecylprodigiosin of BSE6.1, similar to the one found in the S. coelicolor A3(2). This red pigment was reported to have various applications in the food and pharmaceutical industries. The genome of Streptomyces sp. BSE6.1 was submitted to NCBI with a BioProject ID of PRJNA514840 (Sequence Read Archive ID: SRR10849367 and Genome accession ID: CP085300).

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

Sediment from a log pond located in south Finland contained 15 000 to 50 000 mg/kg dry weight of C10 -C40 hydrocarbons. It was unclear whether they originated from the hydraulic fluid of the log hoist or the wood extractives. In the present study, methods of effect-directed analysis were used for the identification of toxicants. A combination of fractionation, biotesting, and chemical analyses revealed that the key toxicant of log pond sediment was retene, a dialkyl-substituted phenanthrene derived from wood resin acids. In addition, the most toxic fraction included 3 other wood-originated diterpenic compounds. Typical wood extractives such as sesquiterpenes and odd-carbon number alkanes in the range C21 -C33 were identified in the fraction, which showed minor genotoxic potency. The most polar fraction contained triterpenes and showed estrogenic activity. No evidence for the presence of hydraulic fluid in sediment was found. The study also indicated that in cases where the organic matter content of sediment or soil is high, using the results of standard mineral oil analysis in risk management can lead to incorrect actions because standard methods do not differentiate petroleum hydrocarbons from biogenic hydrocarbons. Environ Toxicol Chem 2019;9999:1-11. © 2019 SETAC.

Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA. Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs. IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.

Microplastics (MPs) quantification in benthic marine sediments is typically performed by time-consuming and moderately accurate mechanical separation and microscopy detection. In this paper, we describe the results of our innovative Polymer Identification and Specific Analysis (PISA) of microplastic total mass, previously tested on either less complex sandy beach sediment or less demanding (because of the high MPs content) wastewater treatment plant sludges, applied to the analysis of benthic sediments from a sublittoral area north-west of Leghorn (Tuscany, Italy). Samples were collected from two shallow sites characterized by coarse debris in a mixed seabed of Posidonia oceanica, and by a very fine silty-organogenic sediment, respectively. After sieving at &lt, 2 mm the sediment was sequentially extracted with selective organic solvents and the two polymer classes polystyrene (PS) and polyolefins (PE and PP) were quantified by pyrolysis-gas chromatography-mass spectrometry (Pyr-GC/MS). A contamination in the 8–65 ppm range by PS could be accurately detected. Acid hydrolysis on the extracted residue to achieve total depolymerization of all natural and synthetic polyamides, tagging of all aminated species in the hydrolysate with a fluorophore, and reversed-phase high performance liquid chromatography (HPLC) (RP-HPLC) analysis, allowed the quantification within the 137–1523 ppm range of the individual mass of contaminating nylon 6 and nylon 6,6, based on the detected amounts of the respective monomeric amines 6-aminohexanoic acid (AHA) and hexamethylenediamine (HMDA). Finally, alkaline hydrolysis of the residue from acid hydrolysis followed by RP-HPLC analysis of the purified hydrolysate showed contamination by polyethylene terephthalate (PET) in the 12.1–2.7 ppm range, based on the content of its comonomer, terephthalic acid.

Microbial cell counting provides essential information for the study of cell abundance profiles and biogeochemical interactions with the surrounding environments. However, it often requires labor-intensive and time-consuming processes, particularly for subseafloor sediment samples, in which non-cell particles are abundant. We developed a rapid and straightforward method for staining microbial intracellular DNA by SYBR Green I (SYBR-I) to enumerate cells by flow cytometry (FCM). We initially examined the efficiency of microbial cell staining at various dye/sediment ratios (volume ratio of SYBR-I/sediment [vSYBR/vSed]). Non-cell particles in sediment strongly and preferentially adsorbed SYBR-I dye, resulting in the unsuccessful staining of microbial cells when an insufficient ratio (106 cells cm–3). Samples with low cell abundance (

Microplastic pollution is increasingly recognized as a prominent threat to marine life. Understanding the role of bioturbators is crucial to determine to what extent marine sediments can act as a microplastic sink. The presence of microplastics has been documented in holothurians, but no study has investigated how the ingestion-egestion process influences their bioavailability. Using the Mediterranean deposit-feeder, Holothuria tubulosa, as a model system, we assessed if, upon ingestion, plastic particles are accumulated in pseudofeces and if the passage through the digestive tract reduces their size. To this end, the number, shape and colour of plastic particles was compared between pseudofeces and surrounding surficial sediments collected along the edges of a seagrass meadow. Pseudofeces were enriched in plastic fragments with respect to surficial sediments, suggesting a selective ingestion of fragments over fibres. By contrast, there was no difference in the size or colour of plastic particles between pseudofeces and sediments. In addition, by means of a laboratory experiment, we evaluated how microplastic resuspension rates from pseudofeces compares with those from surficial sediments. Under standard water movement conditions, the resuspension of labelled microplastics from pseudofeces was much greater than that from sediments (i.e., about 92% and 26% at the end of the experimental trial). Greater relative abundance of fine material (i.e., pelite) in pseudofeces than sediments could explain their physical instability and, hence, their lower microplastic retention. Our results suggest that pseudofeces of H. tubulosa not only represent a hotspot for plastic fragment concentration, but, due to their surficial deposition and rapid dissolution, they could also promote their transfer to the water column. Ingestion and egestion of microplastics by this sea cucumber, although not altering their size, may thus enhance their bioavailability.

Microorganisms and burrowing animals exert a pronounced impact on the cycling of redox sensitive metals in coastal sediments. We hypothesized that the iron biogeochemical cycle and associated sedimentary microbial community will respond to seasonal changes in a bioturbated intertidal mudflat. In this study, we monitored the spatiotemporal dynamics of porewater and highly reactive solid phase iron with the corresponding prokaryotic and eukaryotic sedimentary microbial communities over one annual cycle from November 2015 to November 2016. Continuous and seasonally variable pools of both porewater Fe(II) and highly reactive iron (FeHR) were observed throughout the seasons with significant increases of Fe(II) and FeHR in response to increased sediment temperature in summer months. Maximum concentrations of Fe(II) and FeHR were predominantly confined to the upper 5 cm of sediment throughout the year. Iron-oxidizing and -reducing microorganisms were present and stable temporally, and exhibited a depth-dependent stratification likely due to availability of Fe(II) and FeHR pools, respectively. Zetaproteobacteria, presumptive lithotrophic iron-oxidizing bacteria, were present at abundances around 0.5–1% in the top 5 cm of sediment with decline abundance with depth. As a whole the microbial community was relatively stable across the seasons, and showed strongest separation with depth, probably driven by changes in oxygen availability and organic matter. The Deltaproteobacteria, principally taxa known to be associated with sulfur and iron cycling, were prevalent, especially at >5 cm depth. Gammaproteobacteria and Bacteroidetes were also abundant, with putatively aerobic members especially prevalent in the cm of the sediment. The relative abundance of diatoms, estimated from abundance of 18S rRNA gene counts, showed evidence of a seasonal signal possibly tied to spring and fall blooms. Overall, analysis of phytoplankton found significant abundance at depth, likely due to the feeding and bio-mixing activity of marine worms. Macro-, and meiofauna, consistent with expected taxa, were detected throughout the year via 18S gene counts, and showed some seasonal variations that may influence sedimentary iron transformations by active microbial grazing. In summary, this analysis revealed relatively consistent temporal and spatial trends in iron geochemistry and microbial and macrobial community composition, while also indicating a complex dynamic of microbial and macrobial interactions are responsible for maintaining these processes.

This study is aimed to determine the distribution, diversity and bioprospecting aspects of marine pigmented bacteria (MPB) isolated from pristine Andaman Islands, India. A total of 180 samples including seawater, sediment, marine plants, invertebrates, and vertebrates were collected and investigated for isolating pigmented bacteria. Results revealed that sediment, invertebrates, and seawater samples were colonized with a greater number of pigmented bacteria pertains to 27.9 &times, 103 CFU/mL, 24.1 &times, 103 CFU/mL and 6.7 &times, 103 CFU/mL respectively. Orange (21.6 &times, 103 CFU/mL) and red (8.0 &times, 103 CFU/mL) MPB were predominant than other pigmented bacteria. Fourteen potential MPB were selected based on their intense pigmentation and tested for bioactive nature and food colorant applications. Out of 14, two red pigmented strains BSE6.1 &amp, S2.1 displayed potential multifaceted applications, such as antibacterial, antioxidant, food colorant, and staining properties. Brown pigmented strains CO8 and yellow pigmented strain SQ2.3 have displayed staining properties. Chemical characterization of red pigment using TLC, HP-LC, GC-MS, FT-IR and 1H-NMR analysis revealed prodigiosin as a main chemical constituent. Pure form of prodigiosin compound fractions obtained from both the strains displayed effective antibacterial activity against different human pathogens. MIC and MBC assays revealed that S2.1 requires 300 &micro, g and 150 &micro, g, respectively, and BSE6.1 require 400 &micro, g concentrations of pigment compound for complete inhibition of S. aureus subsp. aureus. On the basis of 16S rRNA sequence analysis, strains S2.1 and BSE6.1 were identified as Zooshikella sp. and Streptomyces sp. and assigned under the GenBank accession numbers: MK680108 and MK951781 respectively.

The relationship between predominant physiological types of prokaryotes in marine sediments and propionate degradation through sulfate reduction, fermentation, and methanogenesis was studied in marine sediments. Propionate conversion was assessed in slurries containing sediment from three different biogeochemical zones of Aarhus Bay, Denmark. Sediment slurries were amended with 0, 3, or 20 mM sulfate and incubated at 25 &deg, C and 10 &deg, C for 514&ndash, 571 days. Methanogenesis in the sulfate zone and sulfate reduction in the methane zone slurries was observed. Both processes occurred simultaneously in enrichments originating from samples along the whole sediment. Bacterial community analysis revealed the dominance of Desulfobacteraceae and Desulfobulbaceae members in sulfate-amended slurries incubated at 25&deg, C and 10&deg, C. Cryptanaerobacter belonging to the Peptococcaceae family dominated sulfate-free methanogenic slurries at 25&deg, C, whereas bacteria related to Desulfobacteraceae were dominant at 10&deg, C. Archaeal community analysis revealed the prevalence of different genera belonging to Methanomicrobiales in slurries incubated at different temperatures and amended with different sulfate concentrations. Methanosarcinaceae were only detected in the absence of sulfate. In summary, Aarhus Bay sediment zones contain sulfate reducers, syntrophs, and methanogens interacting with each other in the conversion of propionate. Our results indicate that in Aarhus Bay sediments, Cryptanaerobacter degraded propionate in syntrophic association with methanogens.

28 páginas, 6 figuras, 1 tabla. -- This is a post-peer-review, pre-copyedit version of an article published in Antonie van Leeuwenhoek. The final authenticated version is available online at: http://dx.doi.org/10.1007/s10482-019-01349-6, A novel actinobacterial strain, designated S2509T, was isolated from marine sediment collected by a dredge at a depth of 45 m along Melet River offshore of the southern Black Sea coast, Ordu, Turkey. The cell wall peptidoglycan of strain was found to contain mesodiaminopimelic acid and 3-OH-diaminopimelic acid. The whole cell sugars detected were arabinose, glucose, rhamnose, ribose and xylose. The diagnostic phospholipids of strain S2509T were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The predominant menaquinones were identified as MK-9(H8), MK-9(H6), MK-10(H8), MK9(H4), MK-10(H4) and MK-10(H6). The major cellular fatty acids were found to be iso-C16:0, iso-C15:0 and 10-methylC17:0. The taxonomic position of the strain was established using a polyphasic approach, showing that S2509T strain belongs to the genus Micromonospora. Phylogenetic analysis based on the 16S rRNA gene sequence of strain S2509T showedthatitis closely related to the type strain of Micromonospora chokoriensis DSM 45160T (99.37% sequence similarity), and phylogenetically clustered with Micromonospora inaquosa LB39T (99.37%), Micromonospora lupini Lupac 14NT (99.16%), Micromonospora violae NEAU-zh8T (99.23%) and Micromonospora taraxaci NEAU-P5T (99.03%). The phylogenetic analysis based on the gyrB gene sequence of strain S2509T confirmed its close relationship with M. chokoriensis JCM 13247T (96.5% sequence similarity). Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the strain S2509T represents a novel species in the genus Micromonospora, for which the name Micromonospora orduensis sp. nov. is proposed. The type strain is S2509T (=DSM 45926T = KCTC 29201T), AV is gratefully acknowledge support from Ondokuz Mayis University (Project No. PYO. FEN. 1901.12.014) and the School of Biology (Newcastle University). LC thanks the University of Salamanca for a postdoctoral fellowship. Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk), which is supported by the BBSRC (Grant Number BB/L024209).

The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples—dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.

The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate&ndash, methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 &deg, C and 25 &deg, C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.

Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfur-oxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O2 cell–1 day–1. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.

Understanding the effects of hydrodynamic forcing on organic matter (OM) composition is important for assessment of organic carbon (OC) burial in marginal seas on regional and global scales. Here we examine the relationships between regional oceanographic conditions (bottom shear stress), and the physical characteristics (mineral surface area and grain size) and geochemical properties (OC content [OC%] and carbon isotope compositions [13C, 14C]) of a large suite of surface sediments from the Chinese marginal seas to assess the influence of hydrodynamic processes on the fate of OM on shallow continental shelves. Our results suggest that 14C content is primarily controlled by organo‐mineral interactions and hydrodynamically driven resuspension processes, highlighted by (i) positive correlations between 14C content and OC% (and surface area) and (ii) negative correlations between 14C content and grain size (and bottom shear stress). Hydrodynamic processes influence 14C content due to both OC aging during lateral transport and accompanying selective degradation of OM associated with sediment (re) mobilization, these effects being superimposed on the original 14C characteristics of carbon source. Our observations support the hypotheses of Blair and Aller (2012, https://doi.org/10.1146/annurev‐marine‐120709‐142717) and Leithold et al. (2016, https://doi.org/10.1016/j.earscirev.2015.10.011) that hydrodynamically driven sediment translocation results in greater OC 14C depletion in broad, shallow marginal seas common to passive margin settings than on active margins. On a global scale, this may influence the extent to which continental margins act as net carbon sources and sinks. Our findings thus suggest that hydrodynamic processes are important in shaping the nature, dynamics, and magnitude of OC export and burial in passive marginal seas.

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization, and will be increasingly important as climate warming causes more rapid glacial melt. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had ‘young’ sediment ages of Desulfobacteraceaemembers, correlated positively with sulfate reduction rates, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such asDesulfatiglans, AtribacteriaandChloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.Contribution to the Field StatementIn most coastal marine sediments organic matter turnover and total energy flux are highest at the surface and decrease significantly with increasing sediment depth, causing depth-dependent changes in the microbial community composition. Glacial runoff in arctic and subarctic fjords alters the composition of the microbial community at the surface, mainly due to different availabilities of organic matter and metals. Here we show that glacial runoff also modifies microbial community assembly with sediment depth. Sediment age was a key driver of microbial community composition in six-meter-long marine sediment cores from the Godthåbsfjord region, south-western Greenland. High sedimentation rates at glacier-influenced sediment stations enabled a complex community of sulfur-cycling-associated microorganisms to continuously thrive at high relative abundances from the surface into the sediment subsurface. These communities consisted of putative fermenters, sulfate reducers and sulfur oxidizers, which likely depended on high metal concentrations in the relatively young, glacier-influenced sediments. In non-glacier-influenced sediments with lower sedimentation rates, these sulfur-cycling-associated microorganisms were only present near the surface. With increasing sediment depth these surface microorganisms were largely replaced by other surface microorganisms that positively correlated with sediment age and belong to known taxa of the energy-limited, marine deep biosphere.

We investigated the colonization dynamics of different microplastic (MP) pellets, namely, polyethylene (PE), polyethylene terephthalate (PET), polystyrene (PS), polypropylene (PP) and polyvinyl chloride (PVC), either pristine or contaminated with polychlorinated biphenyls (PCBs), by an organohalide respiring marine microbial community and its biotransformation activity towards PCBs sorbed on MPs, in anaerobic laboratory microcosms of a marine sediment. All MPs were rapidly colonized by the microbial community within 2 weeks of incubation, when approximately 1010 16S rRNA gene copies cm−2 were detected on PVC, 109 copies cm−2 on PE, and 108 copies cm−2 on PET, PP and PS. A greater biofilm growth on PVC pellets than other MPs was confirmed by quantification of the reducing sugars of the EPS and biofilm staining with crystal violet. Illumina sequencing of the 16S rRNA genes and Principal Coordinate Analysis (PCoA) revealed that the biofilm community on MPs significantly differed from the sediment community, being enriched of chemoorganotrophic fermenting species, and was significantly affected by the type of polymer. The presence of sorbed PCBs did not significantly affect the overall community composition, and mainly resulted in the enrichment of Dehalococcoidia, i.e., of the organohalide respiring members of the community. Reductive dechlorination of PCBs sorbed to MPs was observed after 2 weeks of incubation, when the average number of chlorines per biphenyl molecule was reduced from 5.2 to 4.8–4.3, and was faster (35.2 ± 1.9 to 61.2 ± 5.8 μmol of Cl removed kgMP−1 week−1) than that of sediment-sorbed ones (33.9 ± 9.1 μmol of Cl removed kgsediment−1 week−1), which started only after 10 weeks of incubation. These data suggest that microbial colonization of contaminated MPs might change the composition of sorbed PCB mixtures and therefore the toxicity associated to PCB-polluted MPs.

Methane (CH4) in marine sediments has the potential to contribute to changes in the ocean and climate system. Physical and biochemical processes that are difficult to quantify with current standard methods such as acoustic surveys and discrete sampling govern the distribution of dissolved CH4 in oceans and lakes. Detailed observations of aquatic CH4 concentrations are required for a better understanding of CH4 dynamics in the water column, how it can affect lake and ocean acidification, the chemosynthetic ecosystem, and mixing ratios of atmospheric climate gases. Here we present pioneering high-resolution in situ measurements of dissolved CH4 throughout the water column over a 400 m deep CH4 seepage area at the continental slope west of Svalbard. A new fast-response underwater membrane-inlet laser spectrometer sensor demonstrates technological advances and breakthroughs for ocean measurements. We reveal decametre-scale variations in dissolved CH4 concentrations over the CH4 seepage zone. Previous studies could not resolve such heterogeneity in the area, assumed a smoother distribution, and therefore lacked both details on and insights into ongoing processes. We show good repeatability of the instrument measurements, which are also in agreement with discrete sampling. New numerical models, based on acoustically evidenced free gas emissions from the seafloor, support the observed heterogeneity and CH4 inventory. We identified sources of CH4, undetectable with echo sounder, and rapid diffusion of dissolved CH4 away from the sources. Results from the continuous ocean laser-spectrometer measurements, supported by modelling, improve our understanding of CH4 fluxes and related physical processes over Arctic CH4 degassing regions.

Terrosamycins A (1) and B (2), two polycyclic polyether natural products, were purified from the fermentation broth of Streptomyces sp. RKND004 isolated from Prince Edward Island sediment. The one strain-many compounds (OSMAC) approach coupled with UPLC-HRMS-based metabolomics screening led to the identification of these compounds. The structure of 1 was determined from analysis of NMR, HRMS, and X-ray diffraction data. NMR experiments performed on 2 revealed the presence of two methoxy groups replacing two hydroxy groups in 1. Like other polyether ionophores, 1 and 2 exhibited excellent antibiotic activity against Gram-positive pathogens. Interestingly, the terrosamycins also exhibited activity against two breast cancer cell lines.

Sediment color reflectance contains important information on paleoenvironmental changes. Such data are routinely measured on sediment cores from the Southern Ocean. Their usefulness, however, is undervalued. Here for the first time, color reflectance of an ~520-kyr sediment core retrieved off Prydz Bay (East Antarctica) was intensively investigated to correlate sediment color changes to changes in sediment compositions. Total carbon, total organic carbon, X-ray fluorescence-derived Fe/Ti and Br/Ti ratios, water content and mineral composition of sediment from this core, and color reflectance of another two sediment cores retrieved nearby were analyzed in this study. The raw reflectance data were transformed into their first-order derivatives and subjected to factor analysis algorithms. A four-factor model was selected to unmix the data set, explaining >80% of the total data variance. Its robustness is supported by similar factor analysis results from the other two cores. The four factors represent (from Factors 1–4) pulses of sedimentary Mn enrichment and Fe3+/Fe2+ changes in clay minerals, relative content changes of colorless components, hematite and goethite, and water, respectively. Scores of Factor 1 show high spikes at glacial terminations, recording enhanced deglacial ventilation in the abyssal Southern Ocean. Scores of Factor 2 mainly reflect biogenic components and chlorite but are further complicated by refractory terrigenous organic carbon and Mn-oxides/-hydroxides. Higher Scores of Factor 3 occur mainly at peak interglacial intervals, associated with enhanced transport of sediment of Antarctic origin by oceanic currents. Water content (Factor 4) in the core sediment was significantly influenced by opal content and sediment grain size compositions.

Discovery of environmentally safe anti-fouling agent is currently of considerable interest, due to the continuous impact of biofoulers on the marine habitats and the adverse effects of biocides on the environment. This study reports the anti-adhesion effect of marine living Actinobacteria against fouling strains isolated from submerged panels in marine environments of Iran. The extract of Glycomyces sediminimaris UTMC 2460 affected the biofilm formation of Kocuria sp. and Mesorhizobium sp., as the dominant fouling agents in this ecosystem, up to 93.2% and 71.4%, respectively. The metabolic activity of the fouler bacteria was reduced by the extract up to 17 and 9%, respectively. This indicated the bactericidal potency of the extract on cells in the biofilm state that enables the compound to be effective even once the biofilms are established in addition to the inhibition of biofilm initiation. Moreover, extra polymeric substance (EPS) production by fouling bacteria was reduced by 60–70%. The absence of activities against fouling bacteria in suspension and also the absence of toxic effect on Artemia salina showed the harmless ecological effect of the anti-microfouling extract on the prokaryotic and eukaryotic microflora of the studied Iran marine ecosystem. Metabolic profiling of G. sediminimaris UTMC 2460 revealed the presence of compounds with molecular formulae matching those of known anti-fouling diketopiperazines as major components of the extract. These results suggest that the extract of Glycomyces sediminimaris UTMC 2460 could be used as a potentially eco-friendly viable candidate in comparison to the synthetic common commercial anti-microfouling material to prevent the fouling process in marine habitats of Iran.

Microbial Fuel Cells (MFCs) remedial technology was used for the degradation of Polycyclic Aromatic Hydrocarbons (PAHs) in marine sediments taken in front of the brownfleld steelwork facility of Bagnoli, Gulf of Pozzuoli, South Western Italy. PAHs levels were quite high and up to 30 mu g/g for fluoranthene and 0.21 mu g/g d.w. L of sediments for acenaphthene. Heavy PAHs prevailed vs light PAHs in the sediment samples before, during and after the treatment by MFCs. Different degradation rates were measured according to the complexity of each PAH, as expected. Among all PAHs, naphthalene showed after four weeks the highest degradation rate (86%), while just the 10% of Indenol[1,2,3-c,d]pyrene was degraded. MFCs achieved their highest performance in terms of Power Density (PD) after two weeks, with values ranging between 20.4 mW/m(2) and 3.17 mW/m(2) of anodic surface. CD values were normalized to the anodic surface as well, falling within a maximum of 204.8 mA/m(2) and a minimum of 9.5 mA/m(2). Even though the dynamics of PAHs degradation in MFCs and the influence of other pollutants (like metals) on MFCs performance as well as the potential mobilization of pollutants in consequence of microbial activity have to be ascertained, our preliminary results prove the high potentialities of MFCs for in-situ marine sediments remediation. (C) 2019 Elsevier Ltd. All rights reserved.

19 páginas, 2 figuras, 4 tablas, During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T, S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strain S2901T, S2903, and S2904 showed the highest similarity (99.2%) with the type strain of Micromonospora halophytica DSM 43171T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with gyrB gene and MLSA phylogenies. Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the isolates should be assigned to a new species within the genus Micromonospora for which the name Micromonospora globispora sp. nov. (S2901T, S2903 and S2904) is proposed., This project was supported by Ondokuz Mayis University (project PYO. FEN. 1901.12.014) and the School of Biology (Newcastle University).

A total of 114 moderately halophilic bacteria were isolated from marine sediment environments. The isolates are belonged to 23 species based on the 16S rRNA sequence analysis. 63, 52, 47, 57, 74, 15 and 4 isolates are able to produce protease, amylase, lipase, pectinase, pulluanase, xylanase, cellulase, respectively. Combined hydrolytic enzyme activity analysis show that 15 strains present 1 hydrolytic activity, 32 strains present 2 hydrolytic activities, 21 strains present 3 hydrolytic activities, 26 strains present 4 hydrolytic activities, 11 strains present 5 hydrolytic activities and 2 strains present 6 hydrolytic activities. Hydrolase activities are widely distributed in a variety of species. The highest rates for production of protease, amylase, lipase, pectinase, pullanase, xylanase and cellulase were observed in species of B. baekryungensis, Hallobacillus sp., B. pumilus, B. megaterium or P. chungwhensis, B. amyloliquefaciens, B. pumilus, B. baekryungensis, respectively. However, the higher activities of protease, pectinase and pulluanase are frequently produced by the species of Halomonas sp. B. amyloliquefaciens or P. chungwhensis, and Vibrio sp. respectively. This investigation show that the diversity of halophilic bacteria from marine sediments could serve as a potential source of hydrolytic enzymes for industrial applications. Um total de 114 bactérias moderadamente halofílicas foram isoladas de ambientes de sedimentos marinhos. Os isolados pertencem a 23 espécies com base na análise da sequência 16S rRNA. 63, 52, 47, 57, 74, 15 e 4 isolados são capazes de produzir protease, amilase, lipase, pectinase, pululanase, xilanase, celulase, respectivamente. A análise da atividade enzimática hidrolítica combinada mostra que 15 cepas apresentam 1 atividade hidrolítica, 32 cepas apresentam 2 atividades hidrolíticas, 21 cepas apresentam 3 atividades hidrolíticas, 26 cepas apresentam 4 atividades hidrolíticas, 11 cepas apresentam 5 atividades hidrolíticas e 2 cepas apresentam 6 atividades hidrolíticas. Atividades de hidrolase são amplamente distribuídas em uma variedade de espécies. As maiores taxas de produção de protease, amilase, lipase, pectinase, pululanase, xilanase e celulase foram observadas em espécies de B. baekryungensis, Hallobacillus sp., B. pumilus, B. megaterium ou P. chungwhensis, B. amyloliquefaciens, B. pumilus, B. baekryungensis, respectivamente. Noentanto, as atividades mais elevadas de protease, pectinase e pululanase são freqüentemente produzidas pelas espécies de Halomonas sp. B. amyloliquefaciens ou P. chungwhensis e Vibrio sp. respectivamente. Esta investigação mostra que a diversidade de bactérias halofílicas de sedimentos marinhos pode servir como uma fonte potencial de enzimas hidrolíticas para aplicações industriais.

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment–water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic–pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0–4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5–10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5–33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters ( n -alkanes, n -alkanoic acids, n -alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning’.

Redox-sensitive trace metals have been used extensively as geochemical proxies to infer the redox-status of marine sediments at the time of their deposition, and by extension, the concentration of oxygen in the overlying water and atmosphere. However, to reliably apply these paleoredox proxies in ancient sediment samples we must calibrate their geochemical behavior in modern sedimentary environments with known redox-status. Here we report a new compilation and analysis of modern trace-metal enrichment data for a range of marine depositional environments, including euxinic basins, continental margin upwelling settings, and normal oxic settings. The enrichments (i.e., concentrations normalized to aluminum content) of vanadium, uranium, molybdenum and rhenium (the VUMoRe database) in the various depositional categories were analyzed using receiver operating characteristic (ROC) curve analysis to systematically identify threshold values that differentiate the various settings. The enrichment of both Mo (> 5 μg g−1/%) and V (> 23 μg g−1/%), but with V not exceeding 46 μg g−1/%, provides strong evidence for a euxinic basin-type depositional environment. Furthermore, the enrichment of V (> 46 μg g−1/%), U (> 5 μg g−1/%) and Mo (> 5 μg g−1/%) is strong evidence for sediments depositing within the anoxic core of perennial OMZ environments, whereas the enrichment of U (> 1 μg g−1/%) coinciding with a low enrichment of V (< 23 μg g−1/%) and Mo (< 5 μg g−1/%) is strong evidence of sediment deposition in the oxic water beneath the core of a perennial OMZ environment. The new method we describe here for determining enrichment thresholds of trace metal-based redox proxies will support the reliable classification of ancient depositional environments and the ongoing development of trace metals as paleoredox proxies.

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin’s history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program at three locations in the South China Sea with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the South China Sea are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

Polyketides (PKs) and nonribosomal peptides (NRPs) are widely applied as drugs in use today, and one potential source for novel PKs and NRPs is the marine sediment microbes. However, the diversities of microbes and their PKs and NRPs biosynthetic genes in the marine sediment are rarely reported. In this study, 16S rRNA gene fragments of the Yellow Sea sediment were analyzed, demonstrating that Proteobacteria and Bacteroidetes accounted for 62% of all the bacterial species and Actinobacteria bacteria which were seen as the typical PKs and NRPs producers only accounted for 0.82% of all the bacterial species. At the same time, PKs and NRPs diversities were evaluated based on the diversity of gene fragments of type I polyketide synthase (PKS) ketosynthase domain (KS), nonribosomal peptide synthetase (NRPS) adenylation domain (AD), and dTDP-glucose-4,6-dehydratase (dTGD). The results showed that AD genes and dTGD genes were abundant and some of them had less than 50% identities with known ones; By contrast, only few KS genes were identified and most of them had more than 60% identities with known KS genes. Moreover, one 70,000-fosmid clone library was further constructed to screen for fosmid clones harboring PKS or NRPS gene clusters of the Yellow Sea sediment. Nine selected fosmid clones harboring KS or AD were sequenced, and three of the clones were assigned to Proteobacteria. Though only few Actinobacteria 16S rRNA gene sequences were detected in the microbial community, five of the screened fosmid clones were assigned to Actinobacteria. Further assembly of the 9 fosmid clones resulted in 11 contigs harboring PKS, NRPS or hybrid NPRS-PKS gene clusters. These gene clusters showed less than 60% identities with the known ones and might synthesize novel natural products. Taken together, we revealed the diversity of microbes in the Yellow Sea sediments and found that most of the microbes were uncultured. Besides, evaluation of PKS and NRPS biosynthetic gene clusters suggested that the marine sediment might have the ability to synthesize novel natural products and more NRPS gene clusters than PKS gene clusters distributed in this environment.

The degradation of organic matter in the anoxic seabed proceeds through a complex microbial network in which the terminal steps are dominated by oxidation with sulfate or conversion into methane and CO2. The controls on pathway and rate of the degradation process in different geochemical zones remain elusive. Radiotracer techniques were used to perform measurements of sulfate reduction, methanogenesis, and acetate oxidation with unprecedented sensitivity throughout Holocene sediment columns from the Baltic Sea. We found that degradation rates transition continuously from the sulfate to the methane zone, thereby demonstrating that terminal steps do not exert feedback control on upstream hydrolytic and fermentative processes, as previously suspected. Acetate was a key intermediate for carbon mineralization in both zones. However, acetate was not directly converted into methane. Instead, an additional subterminal step converted acetate to CO2 and reducing equivalents, such as H-2, which then fed autotrophic reduction of CO2 to methane.

Sediment samples from three coastal sites - two beach resorts (Beach 1 and Beach 2 sites) and an area lying between an oil refinery and a river estuary (Estuarine site) - were analyzed for antibiotic- and heavy metal (HM)-resistant enterococci. A total of 123 enterococci, 36 E. faecium, 34 E. casseliflavus, 33 E. hirae, 5 E. faecalis, 3 E. durans, 3 E. gallinarum, and 9 Enterococcus spp, were recovered. Strains resistant to erythromycin, tetracycline and quinupristin/dalfopristin (Q/D) were recovered from all sites, whereas multidrug-resistant isolates were recovered only from “Beach 2” (14%) and “Estuarine” (3.7%). As regards HM resistance, the strains showed a high frequency (68%) of cadmium and/or copper resistance and uniform susceptibility to mercury. The prevalence of cadmium-resistant strains was significantly higher among erythromycin-resistant than among erythromycin-susceptible strains. A significant association between cadmium or copper resistance and Q/D resistance was also observed at “Estuarine” site. The levels of the two HMs in sediment from all sites were fairly low, ranging from 0.070 to 0.126 μg/g, for cadmium and from 1.00 to 7.64 μg/g for copper. Mercury was always undetectable. These findings are consistent with reports that low HM concentrations may contribute to co-selection of antibiotic-resistant bacterial strains, including enterococci.

Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.

High-pressure (HP) environments represent the largest volumetric majority of habitable space for microorganisms on the planet, including the deep-sea and subsurface biosphere. However, the importance of pressure as an environmental variable affecting deep microbial life and their biogeochemical functions in carbon cycling still remains poorly understood. Here, we designed a new high-volume HP-sediment core sampler that is deployable on the payload of a remotely operated vehicle and can maintain in situ HP conditions throughout multi-month enrichment incubations including daily amendments with liquid media and gases and daily effluent sampling for geochemical or microbiological analysis. Using the HP core device, we incubated sediment and overlying water associated with methane hydrate-exposed on the seafloor of the Joetsu Knoll, Japan, at 10 MPa and 4°C for 45 days in the laboratory. Diversity analyses based on 16S rRNA and methane-related functional genes, as well as carbon isotopic analysis of methane and bicarbonate, indicated the stimulation of both aerobic and anaerobic methanotrophy driven by members of the Methylococcales, and ANME, respectively: i.e., aerobic methanotrophy was observed upon addition of oxygen whereas anaerobic processes subsequently occurred after oxygen consumption. These laboratory-measured rates at 10 MPa were generally in agreement with previously reported rates of methane oxidation in other oceanographic locations.

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.

Methylated amines and sulfides are ubiquitous organic nitrogen and sulfur compounds in the marine environment and could serve as important energy substrates to methanogens inhabiting anoxic sediments. However, their abundance and isotopic values remain largely unconstrained in marine sediments. In this study, we investigated the distribution of trimethylamine (TMA), dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) in Aarhus Bay, Denmark and provided the first report for their stable carbon isotopic composition. Simultaneous measurement of those two compounds in small volumes of pore waters and sediments was accomplished with gas chromatography in combination with either a purge and trap system for quantification or a headspace method for carbon isotopic analysis. TMA in the solid phase (exchangeable pool, 0.3-6.6 mu mol kg(-1) wet sediment; base-extractable pool, 2-18 mu mol kg(-1)) was much more abundant than the dissolved pool (

The composition and metabolic traits of the microbial communities acting in an innovative bioelectrochemical system were here investigated. The system, known as Oil Spill Snorkel, was recently developed to stimulate the oxidative biodegradation of petroleum hydrocarbons in anoxic marine sediments. Next Generation Sequencing was used to describe the microbiome of the bulk sediment and of the biofilm growing attached to the surface of the electrode. The analysis revealed that sulfur cycling primarily drives the microbial metabolic activities occurring in the bioelectrochemical system. In the anoxic zone of the contaminated marine sediment, petroleum hydrocarbon degradation occurred under sulfate-reducing conditions and was lead by different families of Desulfobacterales (46% of total OTUs). Remarkably, the occurrence of filamentous Desulfubulbaceae, known to be capable to vehicle electrons deriving from sulfide oxidation to oxygen serving as a spatially distant electron acceptor, was demonstrated. Differently from the sediment, which was mostly colonized by Deltaproteobacteria, the biofilm at the anode hosted, at high extent, members of Alphaproteobacteria (59%) mostly affiliated to Rhodospirillaceae family (33%) and including several known sulfur- and sulfide-oxidizing genera. Overall, we showed the occurrence in the system of a variety of electroactive microorganisms able to sustain the contaminant biodegradation alone or by means of an external conductive support through the establishment of a bioelectrochemical connection between two spatially separated redox zones and the preservation of an efficient sulfur cycling.

Sodium azide (NaN3) was evaluated as inhibitor of microbial growth and activity in marine sediment resuspensions by monitoring the abundance of free-living and sessile bacteria using both flow cytometry and qPCR methods. Results show that 50 mM of NaN3 strongly inhibits bacterial growth under natural and enriched resource conditions.

Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide reme-diation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as nontoxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety. (C) 2016 Elsevier Ltd. All rights reserved. This study was supported by the European Commission [grant number 266473] (MIXES Project).

A tropical mangrove forest in Northern Peru was studied to determine if physical and biogeochemical characteristics of creek water and subtidal sediments are related to the seasonal hydrological regimes. The results showed that during the dry season, there were greater reducing conditions (Eh) and greater fine particle content (silt and clay) in the subtidal sediments. In contrast, the wet season showed greater dissolved oxygen concentrations in creek water as well as lower total organic matter and chlorophyll-a contents in the subtidal sediments. Carbohydrate and protein concentrations indicated remobilization and degradation of sedimentary organic matter, which were higher during the dry season than in the wet season. The results presented here indicate that changes in the hydrological regime affect the biogeochemical dynamics of mangroves, modulating the sediment redistribution as well as the organic matter deposition and degradation. This research provides insight to the biogeochemical dynamics in Peruvian mangrove sediments which are sensitive to extreme El Nino-Southern Oscillation events and the potential effects of climate change.