Investigating the Impact of Cerium Oxide Nanoparticles Upon the Ecologically Significant Marine Cyanobacterium Prochlorococcus

Cerium oxide nanoparticles (nCeO_{2}) are used at an ever-increasing rate, however, their impact within the aquatic environment remains uncertain. Here, we expose the ecologically significant marine cyanobacterium Prochlorococcus sp. MED4 to nCeO_{2} at a wide range of concentrations (1 μg L^{–1} to 100 mg L^{–1}) under simulated natural and nutrient rich growth conditions. Flow cytometric analysis of cyanobacterial populations displays the potential of nCeO_{2} (100 μg L^{–1}) to significantly reduce Prochlorococcus cell density in the short-term (72 h) by up to 68.8% under environmentally relevant conditions. However, following longer exposure (240 h) cyanobacterial populations are observed to recover under simulated natural conditions. In contrast, cell-dense cultures grown under optimal conditions appear more sensitive to exposure during extended incubation, likely as a result of increased rate of encounter between cyanobacteria and nanoparticles at high cell densities. Exposure to supra-environmental nCeO_{2} concentrations (i.e., 100 mg L^{–1}) resulted in significant declines in cell density up to 95.7 and 82.7% in natural oligotrophic seawater and nutrient enriched media, respectively. Observed cell decline is associated with extensive aggregation behaviour of nCeO_{2} upon entry into natural seawater, as observed by dynamic light scattering (DLS), and hetero-aggregation with cyanobacteria, confirmed by fluorescent microscopy. Hence, the reduction of planktonic cells is believed to result from physical removal due to co-aggregation and co-sedimentation with nCeO_{2} rather than by a toxicological and cell death effect. The observed recovery of the cyanobacterial population under simulated natural conditions, and likely reduction in nCeO_{2} bioavailability as nanoparticles aggregate and undergo sedimentation in saline media, means that the likely environmental risk of nCeO_{2} in the marine environment appears low

Environmentally relevant concentrations of titanium dioxide nanoparticles pose negligible risk to marine microbes

Nano-sized titanium dioxide (nTiO2) represents the highest produced nanomaterial by mass worldwide and, due to its prevalent industrial and commercial use, it inevitably reaches the natural environment. Previous work has revealed a negative impact of nTiO2 upon marine phytoplankton growth, however, studies are typically carried out at concentrations far exceeding those measured and predicted to occur in the environment currently. Here, a series of experiments were carried out to assess the effects of both research-grade nTiO2 and nTiO2 extracted from consumer products upon the marine dominant cyanobacterium, Prochlorococcus, and natural marine communities at environmentally relevant and supra-environmental concentrations (i.e., 1 μg L−1 to 100 mg L−1). Cell declines observed in Prochlorococcus cultures were associated with the extensive aggregation behaviour of nTiO2 in saline media and the subsequent entrapment of microbial cells. Hence, higher concentrations of nTiO2 particles exerted a stronger decline of cyanobacterial populations. However, within natural oligotrophic seawater, cultures were able to recover over time as the nanoparticles aggregated out of solution after 72 h. Subsequent shotgun proteomic analysis of Prochlorococcus cultures exposed to environmentally relevant concentrations confirmed minimal molecular features of toxicity, suggesting that direct physical effects are responsible for short-term microbial population decline. In an additional experiment, the diversity and structure of natural marine microbial communities showed negligible variations when exposed to environmentally relevant nTiO2 concentrations (i.e., 25 μg L−1). As such, the environmental risk of nTiO2 towards marine microbial species appears low, however the potential for adverse effects in hotspots of contamination exists. In future, research must be extended to consider any effect of other components of nano-enabled product formulations upon nanomaterial fate and impact within the natural environment

A Novel Ca2+ Signaling Pathway Coordinates Environmental Phosphorus Sensing and Nitrogen Metabolism in Marine Diatoms

Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients, including phosphorus (P) and nitrogen (N). Although it is well established that diatoms are common first responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here, we show that P-limited diatoms use a Ca2+-dependentsignaling pathway, notpreviouslydescribed ineukaryotes,tosenseandrespondto thecritical macronutrient P. We demonstrate that P-Ca2+ signaling is conserved between a representative pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom. Moreover, this pathway is ecologically relevant, being sensitive to sub-micromolar concentrations of inorganic phosphate and a range of environmentally abundant P forms. Notably, we show that diatom recovery from P limitation requires rapid and substantial increases in N assimilation and demonstrate that this process is dependent on P-Ca2+ signaling. P-Ca2+ signaling thus governs the capacity of diatoms to rapidly sense and respond to P resupply, mediating fundamental cross-talk between the vital nutrients P and N and maximizing diatom resource competition in regions of pulsed nutrient supply

Analysis and comparative genomics of R997, the first SXT/R391 integrative and conjugative element (ICE) of the Indian Sub-Continent

peer-reviewedThe aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located. The Hotspot regions of the element contains restriction digestion systems and insertion sequences. R997 is very closely related to the SXT-like elements from widely dispersed geographic areas. The sequencing of R997 increases the knowledge of the earliest isolated SXT/R391 elements and may provide insight on the emergence of these elements on the Indian sub-continent.PUBLISHEDpeer-reviewe

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

Horizontal gene transfer (HGT) between bacterial lineages is a fundamental evolutionary process that accelerates adaptation. Sequence analyses show that conjugative plasmids are principal agents of HGT in natural communities. However, we lack understanding of how the ecology of bacterial communities and their environments affect the dynamics of plasmid-mediated gene mobilization and transfer. Here we show, in simple experimental soil bacterial communities containing a conjugative mercury resistance plasmid, the repeated, independent mobilization of transposon-borne genes from chromosome to plasmid, plasmid to chromosome and, in the absence of mercury selection, interspecific gene transfers from the chromosome of one species to the other via the plasmid. By reducing conjugation, positive selection for plasmid-encoded traits, like mercury resistance, can consequently inhibit HGT. Our results suggest that interspecific plasmid-mediated gene mobilization is most likely to occur in environments where plasmids are infectious, parasitic elements rather than those where plasmids are positively selected, beneficial elements

Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics

Functionally important proteins at the interface of cell and soil are of potentially low abundance when compared with commonly recovered intracellular proteins. A novel approach was developed and used to extract the metaexoproteome, the subset of proteins found outside the cell, in the context of a soil enriched with the nitrogen-containing recalcitrant polymer chitin. The majority of proteins recovered was of bacterial origin and localized to the outer membrane or extracellular milieu. A wide variety of transporter proteins were identified, particularly those associated with amino-acid and phosphate uptake. The metaexoproteome extract retained chitinolytic activity and we were successful in detecting Nocardiopsis-like chitinases that correlated with the glycoside hydrolase family 18 (GH18) chi gene data and metataxonomic analysis. Nocardiopsis-like chitinases appeared to be solely responsible for chitinolytic activity in soil. This is the first study to detect and sequence bacterial exoenzymes with proven activity in the soil enzyme pool

Defining a pipeline for metaproteomic analyses

Metaproteomics is the analysis of the proteome of environmental samples. While proteomics has been established as a robust and reliable technique, the meta aspect of this omic approach is still in its infancy and subject to methodological and data analysis improvements over the next years. The need to define correct methods for such analyses is essential before hypothesis-driven projects can be addressed. Here we discuss the current state of metaproteomics and propose a protocol covering the three main steps to be implemented in any metaproteomics pipeline: (1) sample preparation, (2) high-throughput mass spectrometry analysis and (3) data search. We also detail current bottlenecks and alternatives to such pipeline