The effect of pressure on leucine and thymidine incorporation by free-living bacteria and by bacteria attached to sinking oceanic particles

The effect of pressure on upper ocean free-living bacteria and bacteria attached to rapidly sinking particles was investigated through studying their ability to synthesize DNA and protein by measuring their rate of 3H-thymidine and 3H-leucine incorporation. Studies were carried out on samples from the NE Atlantic under the range of pressures (1–430 atm) encountered by sinking aggregates during their journey to the deep-sea bed. Thymidine and leucine incorporation rates per bacterium attached to sinking particles from 200 m were about six and ten times higher, respectively, than the free-living bacterial assemblage. The ratio of leucine incorporation rate per cell to thymidine incorporation rate per cell was significantly different between the larger attached (18.9:1) and smaller free-living (10.4:1) assemblages. The rates of leucine and thymidine incorporation decreased exponentially with increasing pressure for the free-living and linearly for attached bacteria, while there was no significant influence of pressure on cell numbers. At 100 atm leucine and thymidine incorporation rate per free-living bacterium was reduced to 73 and 20%, respectively, relative to that measured at 1 atm. Pressure of 100 atm reduced leucine and thymidine incorporation per attached bacterium to 94 and 70%, and at 200 atm these rates were reduced to 34 and 51%, respectively, relative to those measured at 1 atm. There was no significant uncoupling of thymidine and leucine incorporation for either the free-living or attached bacterial assemblages with increasing pressure, indicating that the processess of DNA and protein synthesis may be equally affected by increasing pressure. It is therefore unlikely that bacteria, originating from surface waters, attached to rapidly sinking particles play a role in particle remineralization below approximately 1000–2000 m. These results may help to explain the occurrence of relatively fresh aggregates on the deep-sea bed that still contain sufficient organic carbon to fuel the rapid growth of benthic micro-organisms; they also indicate that the effect of pressure on microbial processes may be important in oceanic biogeochemical cycles.

Spatio-temporal variability in ammonia oxidation and ammonia oxidising bacteria and archaea in coastal sediments of the Western English Channel

The abundance of ammonia-oxidising bacterial (AOB) and ammonia-oxidising archaeal (AOA) (amoA) genes and ammonia oxidation rates were compared bimonthly from July 2008 to May 2011 in 4 contrasting coastal sediments in the western English Channel. Despite a higher abundance of AOA amoA genes within all sediments and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Sediment type was a major factor in determining both AOB amoA gene abundance and AOB community structure, possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation. Decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. PCR-DGGE of AOB amoA genes indicated that no seasonal changes to community composition occurred; however, a gradual movement in community composition occurred at 3 of the sites studied. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rates, or any other environmental variable measured, may be related to the higher spatial variation amongst measurements, obscuring temporal trends, or the bimonthly sampling, which may have been too infrequent to capture temporal variability in the deposition of fresh organic matter. Alternatively, AOA may respond to changing substrate concentrations by an increase or decrease in transcript rather than gene abundance.

Conceptual Ecological Modelling of Sublittoral Rock Habitats to Inform Indicator Selection

The purpose of this study is to produce a series of Conceptual Ecological Models (CEMs) that represent sublittoral rock habitats in the UK. CEMs are diagrammatic representations of the influences and processes that occur within an ecosystem. They can be used to identify critical aspects of an ecosystem that may be studied further, or serve as the basis for the selection of indicators for environmental monitoring purposes. The models produced by this project are control diagrams, representing the unimpacted state of the environment free from anthropogenic pressures. It is intended that the models produced by this project will be used to guide indicator selection for the monitoring of this habitat in UK waters. CEMs may eventually be produced for a range of habitat types defined under the UK Marine Biodiversity Monitoring R&D Programme (UKMBMP), which, along with stressor models, are designed to show the interactions within impacted habitats, would form the basis of a robust method for indicator selection. This project builds on the work to develop CEMs for shallow sublittoral coarse sediment habitats (Alexander et al 2014). The project scope included those habitats defined as ‘sublittoral rock’. This definition includes those habitats that fall into the EUNIS Level 3 classifications A3.1 Atlantic and Mediterranean high energy infralittoral rock, A3.2 Atlantic and Mediterranean moderate energy infralittoral rock, A3.3 Atlantic and Mediterranean low energy infralittoral rock, A4.1 Atlantic and Mediterranean high energy circalittoral rock, A4.2 Atlantic and Mediterranean moderate energy circalittoral rock, and A4.3 Atlantic and Mediterranean low energy circalittoral rock as well as the constituent Level 4 and 5 biotopes that are relevant to UK waters. A species list of characterising fauna to be included within the scope of the models was identified using an iterative process to refine the full list of species found within the relevant Level 5 biotopes. A literature review was conducted using a pragmatic and iterative approach to gather evidence regarding species traits and information that would be used to inform the models and characterise the interactions that occur within the sublittoral rock habitat. All information gathered during the literature review was entered into a data logging pro-forma spreadsheet that accompanies this report. Wherever possible, attempts were made to collect information from UK-specific peer-reviewed studies, although other sources were used where necessary. All data gathered was subject to a detailed confidence assessment. Expert judgement by the project team was utilised to provide information for aspects of the models for which references could not be sourced within the project timeframe. A multivariate analysis approach was adopted to assess ecologically similar groups (based on ecological and life history traits) of fauna from the identified species to form the basis of the models. A model hierarchy was developed based on these ecological groups. One general control model was produced that indicated the high-level drivers, inputs, biological assemblages, ecosystem processes and outputs that occur in sublittoral rock habitats. In addition to this, seven detailed sub-models were produced, which each focussed on a particular ecological group of fauna within the habitat: ‘macroalgae’, ‘temporarily or permanently attached active filter feeders’, ‘temporarily or permanently attached passive filter feeders’, ‘bivalves, brachiopods and other encrusting filter feeders’, ‘tube building fauna’, ‘scavengers and predatory fauna’, and ‘non-predatory mobile fauna’. Each sub-model is accompanied by an associated confidence model that presents confidence in the links between each model component. The models are split into seven levels and take spatial and temporal scale into account through their design, as well as magnitude and direction of influence. The seven levels include regional to global drivers, water column processes, local inputs/processes at the seabed, habitat and biological assemblage, output processes, local ecosystem functions, and regional to global ecosystem functions. The models indicate that whilst the high level drivers that affect each ecological group are largely similar, the output processes performed by the biota and the resulting ecosystem functions vary both in number and importance between groups. Confidence within the models as a whole is generally high, reflecting the level of information gathered during the literature review. Physical drivers which influence the ecosystem were found to be of high importance for the sublittoral rock habitat, with factors such as wave exposure, water depth and water currents noted to be crucial in defining the biological assemblages. Other important factors such as recruitment/propagule supply, and those which affect primary production, such as suspended sediments, light attenuation and water chemistry and temperature, were also noted to be key and act to influence the food sources consumed by the biological assemblages of the habitat, and the biological assemblages themselves. Output processes performed by the biological assemblages are variable between ecological groups depending on the specific flora and fauna present and the role they perform within the ecosystem. Of particular importance are the outputs performed by the macroalgae group, which are diverse in nature and exert influence over other ecological groups in the habitat. Important output processes from the habitat as a whole include primary and secondary production, bioengineering, biodeposition (in mixed sediment habitats) and the supply of propagules; these in turn influence ecosystem functions at the local scale such as nutrient and biogeochemical cycling, supply of food resources, sediment stability (in mixed sediment habitats), habitat provision and population and algae control. The export of biodiversity and organic matter, biodiversity enhancement and biotope stability are the resulting ecosystem functions that occur at the regional to global scale. Features within the models that are most useful for monitoring habitat status and change due to natural variation have been identified, as have those that may be useful for monitoring to identify anthropogenic causes of change within the ecosystem. Biological, physical and chemical features of the ecosystem have been identified as potential indicators to monitor natural variation, whereas biological factors and those physical /chemical factors most likely to affect primary production have predominantly been identified as most likely to indicate change due to anthropogenic pressures.

Bacterial symbiosis in Syssitomya pourtalesiana Oliver, 2012 (Galeommatoidea: Montacutidae), a bivalve commensal with the deep-sea echinoid Pourtalesia.

For the first time, bacterial symbiosis is recognized in the bivalve family Montacutidae of the superfamily Galeommatoidea. The ctenidial filaments of Syssitomya pourtalesiana Oliver, 2012 are extended abfrontally and a dense layer of bacteriocyte cells cover the entire surface behind a narrow ciliated frontal zone. The bacteria are extracellular and held within a matrix of epithelial extensions and microvilli. There is no cuticular layer (glycocalyx) covering the bacteria as in many thyasirid symbioses. The bacteriocytes hold more than one morphotype of bacteria, but bacilli, 1–3 μm in length, dominate. Scanning electron microscopy observations show a surface mat of filamentous bacteria over the extreme abfrontal surfaces. Filter feeding was confirmed by the presence of food particles in the stomach and the bivalve is presumed to be mixotrophic. Syssitomya is commensal and lives attached to the anal spines of the deep-sea echinoid Pourtalesia. In this position, echinoid feeding currents and echinoid faecal material may supply the bacteria with a variety of nutrient materials including dissolved organic matter.

A comparison between ultraviolet disinfection and copper alginate beads within a vortex bioreactor for the deactivation of bacteria in simulated waste streams with high levels of colour, humic acid and suspended solids

We show in this study that the combination of a swirl flow reactor and an antimicrobial agent (in this case copper alginate beads) is a promising technique for the remediation of contaminated water in waste streams recalcitrant to UV-C treatment. This is demonstrated by comparing the viability of both common and UV-C resistant organisms in operating conditions where UV-C proves ineffective - notably high levels of solids and compounds which deflect UV-C. The swirl flow reactor is easy to construct from commonly available plumbing parts and may prove a versatile and powerful tool in waste water treatment in developing countries.

Role of zooplankton dynamics for Southern Ocean phytoplankton biomass and global biogeochemical cycles

Global ocean biogeochemistry models currently employed in climate change projections use highly simplified representations of pelagic food webs. These food webs do not necessarily include critical pathways by which ecosystems interact with ocean biogeochemistry and climate. Here we present a global biogeochemical model which incorporates ecosystem dynamics based on the representation of ten plankton functional types (PFTs); six types of phytoplankton, three types of zooplankton, and heterotrophic bacteria. We improved the representation of zooplankton dynamics in our model through (a) the explicit inclusion of large, slow-growing zooplankton, and (b) the introduction of trophic cascades among the three zooplankton types. We use the model to quantitatively assess the relative roles of iron vs. grazing in determining phytoplankton biomass in the Southern Ocean High Nutrient Low Chlorophyll (HNLC) region during summer. When model simulations do not represent crustacean macrozooplankton grazing, they systematically overestimate Southern Ocean chlorophyll biomass during the summer, even when there was no iron deposition from dust. When model simulations included the developments of the zooplankton component, the simulation of phytoplankton biomass improved and the high chlorophyll summer bias in the Southern Ocean HNLC region largely disappeared. Our model results suggest that the observed low phytoplankton biomass in the Southern Ocean during summer is primarily explained by the dynamics of the Southern Ocean zooplankton community rather than iron limitation. This result has implications for the representation of global biogeochemical cycles in models as zooplankton faecal pellets sink rapidly and partly control the carbon export to the intermediate and deep ocean.

Microplastics Alter the Properties and Sinking Rates of Zooplankton Faecal Pellets

Plastic debris is a widespread contaminant, prevalent in aquatic ecosystems across the globe. Zooplankton readily ingest microscopic plastic (microplastic, < 1 mm), which are later egested within their faecal pellets. These pellets are a source of food for marine organisms, and contribute to the oceanic vertical flux of particulate organic matter as part of the biological pump. The effects of microplastics on faecal pellet properties are currently unknown. Here we test the hypotheses that (1) faecal pellets are a vector for transport of microplastics, (2) polystyrene microplastics can alter the properties and sinking rates of zooplankton egests and, (3) faecal pellets can facilitate the transfer of plastics to coprophagous biota. Following exposure to 20.6 μm polystyrene microplastics (1000 microplastics mL–1) and natural prey (∼1650 algae mL–1) the copepod Calanus helgolandicus egested faecal pellets with significantly (P < 0.001) reduced densities, a 2.25-fold reduction in sinking rates, and a higher propensity for fragmentation. We further show that microplastics, encapsulated within egests of the copepod Centropages typicus, could be transferred to C. helgolandicus via coprophagy. Our results support the proposal that sinking faecal matter represents a mechanism by which floating plastics can be vertically transported away from surface waters.

Biofilm formation by bacteria isolated from retrieved failed prosthetic hip implants in an in vitro model of hip arthroplasty antibiotic prophylaxis

Bacterial infection primarily with Staphylococcus spp. and Propionibacterium acnes remains a significant complication following total hip replacement. In this in vitro study, we investigated the efficacy of gentamicin loading of bone cement and pre- and postoperative administration of cefuroxime in the prevention of biofilm formation by clinical isolates. High and low initial inocula, representative of the number of bacteria that may be present at the operative site as a result of overt infection and skin contamination, respectively, were used. When a high initial inoculum was used, gentamicin loading of the cement did not prevent biofilm formation by the 10 Staphylococcus spp. and the 10 P. acnes isolates tested. Similarly, the use of cefuroxime in the fluid phase with gentamicin-loaded cement did not prevent biofilm formation by four Staphylococcus spp. and four P. acnes isolates tested. However, when a low bacterial inoculum was used, a combination of both gentamicin-loaded cement and cefuroxime prevented biofilm formation by these eight isolates. Our results indicate that this antibiotic combination may protect against infection after intra-operative challenge with bacteria present in low numbers as a result of contamination from the skin but would not protect against bacteria present in high numbers as a result of overt infection of an existing implant.

Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria

The largest biological fractionations of stable carbon isotopes observed in nature occur during production of methane by methanogenic archaea. These fractionations result in substantial (as much as 70) shifts in 13C relative to the initial substrate. We now report that a stable carbon isotopic fractionation of comparable magnitude (up to 70) occurs during oxidation of methyl halides by methylotrophic bacteria. We have demonstrated biological fractionation with whole cells of three methylotrophs (strain IMB-1, strain CC495, and strain MB2) and, to a lesser extent, with the purified cobalamin-dependent methyltransferase enzyme obtained from strain CC495. Thus, the genetic similarities recently reported between methylotrophs, and methanogens with respect to their pathways for C1-unit metabolism are also reflected in the carbon isotopic fractionations achieved by these organisms. We found that only part of the observed fractionation of carbon isotopes could be accounted for by the activity of the corrinoid methyltransferase enzyme, suggesting fractionation by enzymes further along the degradation pathway. These observations are of potential biogeochemical significance in the application of stable carbon isotope ratios to constrain the tropospheric budgets for the ozone-depleting halocarbons, methyl bromide and methyl chloride.