Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment.

Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron-sulphur clusters coordinated by different numbers of cysteine residues in the enzyme's small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme's small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases.

Ocean acidification reduces the crystallographic control in juvenile mussel shells.

Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000µatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000µatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750µatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification.

Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell-cell approach.

Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell-cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 µm. Moreover, the motile response displays spatial sensitivity with greater cell-cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation.

A field and modeling study of fractured rock permeability reduction using microbially induced calcite precipitation.

Microbially induced calcite precipitation (MICP) offers an attractive alternative to traditional grouting technologies for creating barriers to groundwater flow and containing subsurface contamination, but has only thus far been successfully demonstrated at the laboratory scale and predominantly in porous media. We present results of the first field experiments applying MICP to reduce fractured rock permeability in the subsurface. Initially, the ureolytic bacterium, Sporosarcina pasteurii, was fixed in the fractured rock. Subsequent injection of cementing fluid comprising calcium chloride and urea resulted in precipitation of large quantities (approximately 750 g) of calcite; significant reduction in the transmissivity of a single fracture over an area of several m(2) was achieved in around 17 h of treatment. A novel numerical model is also presented which simulates the field data well by coupling flow and bacterial and solute reactive transport processes including feedback due to aperture reduction via calcite precipitation. The results show that MICP can be successfully manipulated under field conditions to reduce the permeability of fractured rock and suggest that an MICP-based technique, informed by numerical models, may form the basis of viable solutions to aid pollution mitigation.

Magnetic resonance imaging of mass transport and structure inside a phototrophic biofilm.

The aim of this study was to utilize magnetic resonance imaging (MRI) to image structural heterogeneity and mass transport inside a biofilm which was too thick for photon based imaging. MRI was used to map water diffusion and image the transport of the paramagnetically tagged macromolecule, Gd-DTPA, inside a 2.5 mm thick cyanobacterial biofilm. The structural heterogeneity of the biofilm was imaged at resolutions down to 22 × 22 µm, enabling the impact of biofilm architecture on the mass transport of both water and Gd-DTPA to be investigated. Higher density areas of the biofilm correlated with areas exhibiting lower relative water diffusion coefficients and slower transport of Gd-DTPA, highlighting the impact of biofilm structure on mass transport phenomena. This approach has potential for shedding light on heterogeneous mass transport of a range of molecular mass molecules in biofilms.

Impact of growth environment and physiological state on metal immobilization by Pseudomonas aeruginosa PAO1.

Environmental growth conditions and cell physiology have the potential to influence bacterial surface-metal interactions in both planktonic and biofilm systems. Here, Pseudomonas aeruginosa was studied to determine the influence of these factors (pH, redox potential, and active respiration) on surface electrostatics and metal immobilization. Acid-base titrations revealed a decrease in ionizable ligands at pKa 5 (putative carboxyls) in cells grown below pH 6.2 and in cells grown anaerobically relative to cells grown under oxic and circumneutral pH conditions. This observation correlates with Western immunoblotting assays that revealed a reduction in carboxylated B-band lipopolysaccharide in these cells. Furthermore, spectrophotometric analysis revealed a decrease in zinc, copper, and iron immobilization in these cells, suggesting that lipopolysaccharide modification in response to environmental stimuli influences metal binding. The effect of active versus inactive metabolism on metal adsorption was also examined using respiration inhibitors carbonyl cyanide m-chlorophenylhydrazone and sodium azide. Cells treated with these compounds bound more zinc, copper, and iron than untreated controls, suggesting proton extrusion through respiration competes with metal cations for reactive groups on the cell surface. Accumulation of gold did not show the same trend, and transmission electron microscopy studies confirmed it was not a surface-mediated process. These results suggest that variations in growth environment and cell physiology influence metal accumulation by bacterial cell surfaces and may help to explain discontinuous accumulation of metal observed throughout microbial communities.

Examination of the ocean as a source for atmospheric microplastics.

Global plastic litter pollution has been increasing alongside demand since plastic products gained commercial popularity in the 1930's. Current plastic pollutant research has generally assumed that once plastics enter the ocean they are there to stay, retained permanently within the ocean currents, biota or sediment until eventual deposition on the sea floor or become washed up onto the beach. In contrast to this, we suggest it appears that some plastic particles could be leaving the sea and entering the atmosphere along with sea salt, bacteria, virus' and algae. This occurs via the process of bubble burst ejection and wave action, for example from strong wind or sea state turbulence. In this manuscript we review evidence from the existing literature which is relevant to this theory and follow this with a pilot study which analyses microplastics (MP) in sea spray. Here we show first evidence of MP particles, analysed by µRaman, in marine boundary layer air samples on the French Atlantic coast during both onshore (average of 2.9MP/m3) and offshore (average of 9.6MP/m3) winds. Notably, during sampling, the convergence of sea breeze meant our samples were dominated by sea spray, increasing our capacity to sample MPs if they were released from the sea. Our results indicate a potential for MPs to be released from the marine environment into the atmosphere by sea-spray giving a globally extrapolated figure of 136000 ton/yr blowing on shore.

Microscopy and elemental analysis characterisation of microplastics in sediment of a freshwater urban river in Scotland, UK.

Understanding of the sources, fate, and impact of microplastics (MPs, < 5 mm) remains limited, particularly in freshwater environments, while limited comparability across available surveys hinders adequate monitoring and risk assessment of these contaminants. Here, the distribution of microscopic debris in an urban river close to the marine environment in the West of Scotland was investigated to assess concentration and distribution of primary and secondary MPs. Also, the efficiency of light and scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS) was evaluated for characterisation and quantification of MPs sized 2.8 mm-11 µm. Bank sediment samples were collected twice from the River Kelvin in Glasgow and were size-fractionated and processed for extraction of MPs by density separation. Sample MPs spiking and use of procedural blanks allowed the influence of processing on field data quality to be considered. Total abundances were 161-432 MPs kg-1 dry sediment, with fibres as the dominant type, comprising > 88% of total counts. Nevertheless, fibres in blanks suggest potential contributions from atmospheric contamination. Moreover, fibres concentrated mainly in fractions < 0.09 mm suggesting that their fate may be influenced by drivers of fine sediment dynamics in rivers. While no primary MPs were observed, metallic and glass pellets were present in high abundances in settled material and could be easily misidentified by visual inspection, demonstrating that compositional analysis is needed to avoid analytical errors from MP misidentification and overestimation. SEM-EDS allowed for a quick screening of plastic vs non-plastic pellets and improved identification of smaller fragments, whereas more advanced techniques are needed for proper identification of fibres. This study is the first to report on MPs in freshwater rivers in Scotland and suggests that diffuse sources of pollution may be delivering secondary MPs to the river. Their sources, fate, and risk in these systems will thus warrant further attention.

Accurate phase-shift velocimetry in rock.

Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

Biomineral shell formation under ocean acidification: a shift from order to chaos.

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 µatm pCO2) compared to present day conditions (380 µatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Ocean acidification and temperature increase impact mussel shell shape and thickness: problematic for protection?

Ocean acidification threatens organisms that produce calcium carbonate shells by potentially generating an under-saturated carbonate environment. Resultant reduced calcification and growth, and subsequent dissolution of exoskeletons, would raise concerns over the ability of the shell to provide protection for the marine organism under ocean acidification and increased temperatures. We examined the impact of combined ocean acidification and temperature increase on shell formation of the economically important edible mussel Mytilus edulis. Shell growth and thickness along with a shell thickness index and shape analysis were determined. The ability of M. edulis to produce a functional protective shell after 9 months of experimental culture under ocean acidification and increasing temperatures (380, 550, 750, 1000 µatm pCO 2, and 750, 1000 µatm pCO 2 + 2°C) was assessed. Mussel shells grown under ocean acidification conditions displayed significant reductions in shell aragonite thickness, shell thickness index, and changes to shell shape (750, 1000 µatm pCO 2) compared to those shells grown under ambient conditions (380 µatm pCO 2). Ocean acidification resulted in rounder, flatter mussel shells with thinner aragonite layers likely to be more vulnerable to fracture under changing environments and predation. The changes in shape presented here could present a compensatory mechanism to enhance protection against predators and changing environments under ocean acidification when mussels are unable to grow thicker shells. Here, we present the first assessment of mussel shell shape to determine implications for functional protection under ocean acidification.

Ocean acidification alters the material properties of Mytilus edulis shells.

Ocean acidification (OA) and the resultant changing carbonate saturation states is threatening the formation of calcium carbonate shells and exoskeletons of marine organisms. The production of biominerals in such organisms relies on the availability of carbonate and the ability of the organism to biomineralize in changing environments. To understand how biomineralizers will respond to OA the common blue mussel, Mytilus edulis, was cultured at projected levels of pCO2 (380, 550, 750, 1000 µatm) and increased temperatures (ambient, ambient plus 2°C). Nanoindentation (a single mussel shell) and microhardness testing were used to assess the material properties of the shells. Young's modulus (E), hardness (H) and toughness (KIC) were measured in mussel shells grown in multiple stressor conditions. OA caused mussels to produce shell calcite that is stiffer (higher modulus of elasticity) and harder than shells grown in control conditions. The outer shell (calcite) is more brittle in OA conditions while the inner shell (aragonite) is softer and less stiff in shells grown under OA conditions. Combining increasing ocean pCO2 and temperatures as projected for future global ocean appears to reduce the impact of increasing pCO2 on the material properties of the mussel shell. OA may cause changes in shell material properties that could prove problematic under predation scenarios for the mussels; however, this may be partially mitigated by increasing temperature.

The microbial role in hot spring silicification.

Recent experimental studies indicate that microorganisms play a passive role in silicification. The organic functional groups that comprise the outer cell surfaces simply serve as heterogeneous nucleation sites for the adsorption of polymeric and/or colloidal silica, and because different microorganisms have different cell ultrastructural chemistry, species-specific patterns of silicification arise. Despite their templating role, they do not appear to increase the kinetics of silicification, and at the very most, they contribute only marginally to the magnitude of silicification. Instead, silicification is due to the polymerization of silica-supersaturated hydrothermal fluids upon discharge at the surface of the hot spring. Microorganisms do, however, impart an influence on the fabric of the siliceous sinters that form around hot spring vents. Different microorganisms have different growth patterns, that in turn, affect the style of laminations, the primary porosity of the sinter and the distribution of later-stage diagenetic cementation.

Ocean acidification impacts mussel control on biomineralisation.

Ocean acidification is altering the oceanic carbonate saturation state and threatening the survival of marine calcifying organisms. Production of their calcium carbonate exoskeletons is dependent not only on the environmental seawater carbonate chemistry but also the ability to produce biominerals through proteins. We present shell growth and structural responses by the economically important marine calcifier Mytilus edulis to ocean acidification scenarios (380, 550, 750, 1000 µatm pCO2). After six months of incubation at 750 µatm pCO2, reduced carbonic anhydrase protein activity and shell growth occurs in M. edulis. Beyond that, at 1000 µatm pCO2, biomineralisation continued but with compensated metabolism of proteins and increased calcite growth. Mussel growth occurs at a cost to the structural integrity of the shell due to structural disorientation of calcite crystals. This loss of structural integrity could impact mussel shell strength and reduce protection from predators and changing environments.

Influence of lipopolysaccharide on the surface proton-binding behavior of Shewanella spp.

This study investigates the potentiometric properties of several strains of Shewanella spp. and determines whether these properties can be correlated with lipopolysaccharide (LPS) type. The LPS of eight Shewanella strains was characterized using silver-stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and their potentiometric properties determined using high-resolution acid-base titrations. Titrations showed that total ligand concentrations (L(T)) ranged from 0.903 +/- 0.007 micromol/mg (S. baltica 63) to 1.387 +/- 0.007 micromol/mg (S. amazonensis SB2B). Smooth strains (possessing O-side chains) exhibited higher mean L(T) values than rough strains (no O-side chain). A Tukey's honestly significantly different (HSD) test revealed, smooth strains exhibited significantly higher L(T) values than rough strains in 69% of comparisons. Comparison of individual pK(a) concentrations revealed that smooth LPS strains of Shewanella were relatively enriched in reactive groups at pK(a) 5, suggesting their LPS O-side chains contained detectable carboxyl groups. Combined pKa spectra from all eight Shewanella strains produced a common trend indicating that the way in which the surface proton-buffering capacity changes with pH is similar for the species studied here.

Characterization of metal-cyanobacteria sorption reactions: a combined macroscopic and infrared spectroscopic investigation.

In this study, we conducted synchrotron radiation Fourier transform infrared (IR) spectroscopy, potentiometric titration, and metal sorption experiments to characterize metal-cyanobacteria sorption reactions. Infrared spectra were collected with samples in solution for intact cyanobacterial filaments and separated exopolymeric sheath material to examine the deprotonation reactions of cell surface functional groups. The infrared spectra of intact cells sequentially titrated from pH 3.2 to 6.5 display an increase in peak intensity and area at 1400 cm(-1) corresponding to vibrational COO- frequencies from the formation of deprotonated carboxyl surface sites. Similarly, bulk acid-base titration of cyanobacterial filaments and sheath material indicates that the concentration of proton-active surface sites is higher on the cell wall compared to the overlying sheath. A three-site model provides an excellent fit to the titration curves of both intact cells and sheath material with corresponding pKa values of 4.7 +/- 0.4, 6.6 +/- 0.2, 9.2 +/- 0.3 and 4.8 +/- 0.3, 6.5 +/- 0.1, 8.7 +/- 0.2, respectively. Finally, Cu2+, Cd2+, and Pb2+ sorption experiments were conducted as a function of pH, and a site-specific surface complexation model was used to describe the metal sorption data. The modeling indicates that metal ions are partitioned between the exopolymer sheath and cell wall and that the carboxyl groups on the cyanobacterial cell wall are the dominant sink for metals at near neutral pH. These results demonstrate that the cyanobacterial surfaces are complex structures which contain distinct surface layers, each with unique molecular functional groups and metal binding properties.