Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre

The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.HN, AV were financed through the European Research Council (ERC-CoG Grant Nr 772923, project VORTEX). PDM was supported by NWO (VI.Veni.212.040)

Experimental design trade-offs for gene regulatory network inference: an in silico study of the yeast Saccharomyces cerevisiae cell cycle

Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that prescribe the minimal number of samples required to infer a reliable GRN model. We study the temporal resolution of data vs quality of GRN inference in order to ultimately overcome this deficit. The evolution of a Markovian jump process model for the Ras/cAMP/PKA pathway of proteins and metabolites in the G1 phase of the Saccharomyces cerevisiae cell cycle is sampled at a number of different rates. For each time-series we infer a linear regression model of the GRN using the LASSO method. The inferred network topology is evaluated in terms of the area under the precision-recall curve AUPR. By plotting the AUPR against the number of samples, we show that the trade-off has a, roughly speaking, sigmoid shape. An optimal number of samples corresponds to values on the ridge of the sigmoid

Gene-Based Modeling of Methane Oxidation in Coastal Sediments: Constraints on the Efficiency of the Microbial Methane Filter

Methane is a powerful greenhouse gas that is produced in large quantities in marine sediments. Microbially mediated oxidation of methane in sediments, when in balance with methane production, prevents the release of methane to the overlying water. Here, we present a gene-based reactive transport model that includes both microbial and geochemical dynamics and use it to investigate whether the rate of growth of methane oxidizers in sediments impacts the efficiency of the microbial methane filter. We focus on iron- and methane-rich coastal sediments and, with the model, show that at our site, up to 10% of all methane removed is oxidized by iron and manganese oxides, with the remainder accounted for by oxygen and sulfate. We demonstrate that the slow growth rate of anaerobic methane-oxidizing microbes limits their ability to respond to transient perturbations, resulting in periodic benthic release of methane. Eutrophication and deoxygenation decrease the efficiency of the microbial methane filter further, thereby enhancing the role of coastal environments as a source of methane to the atmosphere

Pathways of methane removal in the sediment and water column of a seasonally anoxic eutrophic marine basin

Methane (CH4) is a key greenhouse gas. Coastal areas account for a major proportion of marine CH4 emissions. Eutrophication and associated bottom water hypoxia enhance CH4 production in coastal sediments. Here, we assess the fate of CH4 produced in sediments at a site in a seasonally anoxic eutrophic coastal marine basin (Scharendijke, Lake Grevelingen, the Netherlands) in spring (March) and late summer (September) in 2020. Removal of CH4 in the sediment through anaerobic oxidation with sulfate (Formula presented.) is known to be incomplete in this system, as confirmed here by only slightly higher values of δ13C-CH4 and δD-CH4 in the porewater in the shallow sulfate-methane-transition zone (~5-15 cm sediment depth) when compared to deeper sediment layers. In March 2020, when the water column was fully oxygenated, CH4 that escaped from the sediment was at least partially removed in the bottom water through aerobic oxidation. In September 2020, when the water column was anoxic below ~35 m water depth, CH4 accumulated to high concentrations (up to 73 µmol L-1) in the waters below the oxycline. The sharp counter gradient in oxygen and CH4 concentrations at ~35 m depth and increase in δ13C-CH4 and δD-CH4 above the oxycline indicate mostly aerobic water column removal of CH4. Water column profiles of particulate and dissolved Fe and Mn suggest redox cycling of both metals at the oxycline, pointing towards a potential role of metal oxides in CH4 removal. Water column profiles of (Formula presented.) and (Formula presented.) indicate removal of both solutes near the oxycline. Analyses of 16S rRNA gene sequences retrieved from the water column reveal the presence of aerobic CH4 oxidizing bacteria (Methylomonadaceae) and anaerobic methanotrophic archaea (Methanoperedenaceae), with the latter potentially capable of (Formula presented.) and/or metal-oxide dependent CH4 oxidation, near the oxycline. Overall, our results indicate sediment and water column removal of CH4 through a combination of aerobic and anaerobic pathways, which vary seasonally. Some of the CH4 appears to escape from the surface waters to the atmosphere, however. We conclude that eutrophication may make coastal waters a more important source of CH4 to the atmosphere than commonly assumed

Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin

The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin

Analysis of species distribution, enterotoxin genes prevalence and antibiotic resistance profile of coagulase positive staphylococci isolated from frozen and chilled chicken meat

Estafilococos Coagulase Positivos são os agentes etiológicos da Intoxicação Alimentar Estafilocócica, uma das Doenças Transmitidas por Alimentos de maior ocorrência no mundo, que está frequentemente associada a alimentos de origem animal. Essa intoxicação ocorre devido à ingestão de Enterotoxinas Estafilocócicas, as quais são proteínas termorresistentes que apresentam atividade superantigênica, causando vômito, dor abdominal e disenteria. Estas bactérias também causam uma vasta gama de outras doenças, incluindo infecções hospitalares. Sua resistência a muitos antimicrobianos é motivo de preocupação, especialmente quanto aos Staphylococcus aureus Resistentes à Meticilina. Este estudo objetivou identificar os isolados em nível de espécie e avaliar a prevalência de genes de enterotoxinas e o perfil de resistência a antimicrobianos de estafilococos coagulase positivos isolados de carne de frango congelada e resfriada. Trinta carcaças de frango foram amostradas e, os estafilococos, quantificados. Os isolados foram identificados através de testes bioquímicos e submetidos à Reação em Cadeia da Polimerase para a identificação de genes de enterotoxinas clássicas (sea, seb, sec, sed e see). O perfil de resistência frente a onze antimicrobianos foi avaliado. Ao todo, 50 isolados foram identificados. S. aureus foi a espécie mais prevalente (62%), seguida de S. hyicus, S. intermedius, S. delphini e S. schleiferi subsp. coagulans. Genes de enterotoxinas foram encontrados em 70% dos isolados, e sea (68%) e sed (26%) mostraram-se os mais prevalentes. Oitenta por cento dos isolados apresentaram resistência a pelo menos um dos antimicrobianos testados e 40% demonstraram multirresistência. Os índices mais elevados de resistência foram aqueles à penicilina, teicoplanina, oxacilina e clindamicina. S. aureus Resistentes à Vancomicina e S. intermedius Resistentes à Vancomicina foram isolados e apresentaram Concentrações Inibitórias Mínimas de 512 e 54 μg/mL, respectivamente. Conclui-se que tais isolados de carne de frango podem representar riscos à segurança alimentar em nível de saúde pública, uma vez que genes de enterotoxinas e resistência a antimicrobianos foram amplamente encontrados. Além disso, estes achados, somados à detecção de estafilococos resistentes à vancomicina, podem indicar a disseminação de micro-organismos potencialmente patogênicos e de genes de resistência à vancomicina fora das barreiras clínicas.Coagulase-Positive Staphylococci are the causative agents of Staphylococcal Food Poisoning, one of the most common foodborne diseases, which are frequently related to foods of animal origin. This food poisoning occurs due to the ingestion of Staphylococcal Enterotoxins, which are thermo-resistant proteins that display superantigen activity, causing vomit, abdominal pain and diarrhea. These bacteria also cause a wide range of other diseases, including nosocomial infections. Their resistance to innumerous antimicrobials has been reason of concern, especially regarding Methicillin-Resistant Staphylococcus aureus. This study aimed to identify the isolates at species level and to evaluate enterotoxin genes prevalence and antimicrobials resistance profile of Coagulase-Positive Staphylococci isolated from chilled and frozen raw chicken meat. Thirty chicken carcasses were sampled and staphylococci were quantified. The isolates were identified by biochemical tests and submitted to Polymerase Chain Reaction identification of classical enterotoxin genes (sea, seb, sec, sed and see). The resistance to 11 antimicrobials was assessed. Fifty isolates were identified. S. aureus was the most prevalent species (62%), followed by S. hyicus, S. intermedius, S. delphini and S. schleiferi coagulans. Enterotoxin genes were found in 70% of isolates, and sea (68%) sed (26%) were most encountered genes. Eighty percent of the isolates were resistant at least to one antimicrobial and 40% were multiresistant. The highest resistance rates were those to penicillin, teicoplanin, oxacillin and clindamycin. Vancomycin-Resistant S. aureus and Vancomycin-Resistant S. intermedius were isolated and they presented Minimum Inhibitory Concentrations of 512 and 54 μg/mL, respectively. In conclusion, such isolates from raw chicken meat may represent food safety hazards regarding public health, since staphylococcal enterotoxin genes and antibiotic resistance were abundantly encountered. Moreover, these findings, summed to vancomycin-resistant staphylococci detection, may point out the dissemination of potentially pathogenic microorganisms and vancomycin resistance genes outside clinical boundaries