scholarly journals An integrated metagenomic and metabolite profiling study of hydrocarbon biodegradation and corrosion in navy ships

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Christopher R. Marks ◽  
Kathleen E. Duncan ◽  
Mark A. Nanny ◽  
Brian H. Harriman ◽  
Recep Avci ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolite Profiling ◽  
Gene Activity ◽  
The Other ◽  
Hydrocarbon Degradation ◽  
Hydrocarbon Biodegradation ◽  
Residence Times ◽  
Ballast Tank ◽  
Ballast Tanks ◽  
Marine Microbial Communities

AbstractNaval vessels regularly mix fuel and seawater as ballast, a practice that might exacerbate fuel biodegradation and metal biocorrosion. To investigate, a metagenomic characterization and metabolite profiling of ballast from U.S. Navy vessels with residence times of 1-, ~20-, and 31 weeks was conducted and compared with the seawater used to fill the tanks. Aerobic Gammaproteobacteria differentially proliferated in the youngest ballast tank and aerobic-specific hydrocarbon degradation genes were quantitatively more important compared to seawater or the other ballast tanks. In contrast, the anaerobic Deltaproteobacteria dominated in the eldest ballast fluid with anaerobic-specific hydrocarbon activation genes being far more prominent. Gene activity was corroborated by detection of diagnostic metabolites and corrosion was evident by elevated levels of Fe, Mn, Ni and Cu in all ballast samples relative to seawater. The findings argue that marine microbial communities rapidly shift from aerobic to anaerobic hydrocarbonoclastic-dominated assemblages that accelerate fuel and infrastructure deterioration.

scholarly journals Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
John I. Miller ◽  
Stephen Techtmann ◽  
Dominique Joyner ◽  
Nagissa Mahmoudi ◽  
Julian Fortney ◽  
...  
Keyword(s):  
Decision Making ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Taxonomic Composition ◽  
Hydrocarbon Biodegradation ◽  
Decision Making Process ◽  
Degrading Bacteria ◽  
Vital Component ◽  
Marine Microbial Communities ◽  
Marine Basins

ABSTRACT The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins. IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.

Enhanced CO2 concentrations change the structure of Antarctic marine microbial communities

2016 ◽  
Vol 552 ◽  
pp. 93-113 ◽  
Author(s):  
AT Davidson ◽  
J McKinlay ◽  
K Westwood ◽  
PG Thomson ◽  
R van den Enden ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Co2 Concentrations ◽  
Antarctic Marine ◽  
Marine Microbial Communities

UV ability to inactivate microorganisms combined with factors affecting radiation

1997 ◽  
Vol 35 (11-12) ◽  
pp. 107-112 ◽  
Author(s):  
A. M. Shaban ◽  
G. E. El-Taweel ◽  
G. H. Ali
Keyword(s):  
Microbial Communities ◽  
Uv Radiation ◽  
Contact Time ◽  
Tap Water ◽  
Scenedesmus Obliquus ◽  
Morphological Characters ◽  
The Other ◽  
Bacterial Cells ◽  
Dark Repair ◽  
Nile Water

In the present study, the effect of UV radiation on the inactivation of a range of microorganisms was studied. Each organism was seeded into sterile tap water and exposed to UV in batch experiments with changing turbidities. In addition, the effect of UV on microbial communities in river Nile water was examined. It was found that 1min contact time (0.5L/min flow rate) was effective against vegetative cells levels almost reaching zero (except with Staphylococcus aureus). On the other hand, spore-forming bacteria, Candida albicans and coliphage were more resistant to UV. This contact time caused coenobia cells in single form with Scenedesmus obliquus while for Microcystis aeruginosa colonies broke into smaller groups. Exposure of Nile water microbial communities to UV showed that yeasts and Aeromonas survived better than the other organisms while in the phytoplankton partial fragmentation occurred in some algal groups. The protective effect of turbidity differed between organisms, with increased contact time under conditions of stable turbidity having no effect on the organisms. At 20 NTU the UV radiation had no effect on the morphological characters of algal cells. In reactivation experiments, it is clear that photoreactivation, and not dark repair, takes place with bacterial cells. Only coliphage had no photoreactivation and dark repair responses although with coliphage and host, both reactivation processes worked well. Moreover, the irradiated algae regained their normal shape after 3 days in suitable media and enough light.

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

scholarly journals Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

2020 ◽  
Author(s):  
Zexin Li ◽  
Donald Pan ◽  
Guangshan Wei ◽  
Weiling Pi ◽  
Jiang-Hai Wang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
Cold Seep ◽  
Hydrocarbon Biodegradation ◽  
Viral Diversity ◽  
Cold Seeps ◽  
Host Interaction ◽  
Deep Sea Sediments ◽  
Subsurface Reservoir ◽  
Network Comparisons

AbstractIn marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

scholarly journals The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0142690 ◽  
Author(s):  
Zilian Zhang ◽  
Yi Chen ◽  
Rui Wang ◽  
Ruanhong Cai ◽  
Yingnan Fu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Exopolysaccharide ◽  
Marine Microbial Communities

A Study into the Coating Thickness of Ship Ballast Tanks

2020 ◽  
Vol 162 (A3) ◽  
Author(s):  
B Khan ◽  
F Khan ◽  
B Veitch
Keyword(s):  
Coating Thickness ◽  
Performance Standard ◽  
Coating System ◽  
Ballast Tank ◽  
Coating Performance ◽  
Coating Application ◽  
Flat Surfaces ◽  
Ballast Tanks ◽  
Dry Film Thickness

Ballast tanks are expected to be coated according to the IMO Performance Standard for Protective Coating regulations (PSPC15), in addition to the paint application requirements of the paint producer. In general, a coating system should consist of minimum two spray coats of light-colored epoxy coating on flat surfaces with a Nominal total Dry Film Thickness (NDFT) of 320 μm and 90% of all thickness measurements greater than, or equal to the NDFT and none of the remaining measurements below 0.9 x NDFT (the “90/10 rule”). Allegedly, the value of 320 μm in this PSPC15 rule may be misconstrued as a benchmark for coating application on flat surfaces, eventually leading to a non-PSPC15 compliance due to the resulting variation in coating thickness violating this 90/10 rule. This study indicates that over the years, the arithmetic mean in-situ DFT appears to be 498±18 μm and that too high and low thicknesses, below 288 μm and above 800 μm, were noted in the field. Analysis of a survey of ballast tank coating performance of ships indicates that too low thicknesses appear to be negatively impacting the average theoretical ballast tank performance. However, when an application mean DFT benchmark of 525 μm is used, the coating will almost surely comply to the 90/10 rule and the risk of falling below the 288 μm threshold is small, less than 2% in most cases. Consequently, using 320 μm as a mean DFT benchmark could result in a non-PSPC15 compliance with the in-situ ascertained coating thickness variation as this does not exclude coating thicknesses below 288 μm, which may then result in a significantly less than average theoretical coating performance. If the coating application is performed very evenly, the benchmark may be reduced to 429 μm with a probability of falling below 288 μm reduced to 0.1%. It should therefore be emphasized that the PSPC15 requirement is a coating system framework description, and that the requirement should be broadened to include a mean DFT as a coating applicator benchmark together with a clearly specified minimum and maximum DFT, in order to avoid any misinterpretations.

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