Jeremy Shaw

Low Pore Connectivity Increases Bacterial Diversity in Soil

ABSTRACT One of soil microbiologys most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P < 0.012), but they were not affected by texture (P > 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P < 0.001) and was correlated with WFPS (sum of squared correlations [δ2] = 0.88, P < 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.

Marine Plastic Pollution in Waters around Australia: Characteristics, Concentrations, and Pathways

Plastics represent the vast majority of human-made debris present in the oceans. However, their characteristics, accumulation zones, and transport pathways remain poorly assessed. We characterised and estimated the concentration of marine plastics in waters around Australia using surface net tows, and inferred their potential pathways using particle-tracking models and real drifter trajectories. The 839 marine plastics recorded were predominantly small fragments (“microplastics”, median length = 2.8 mm, mean length = 4.9 mm) resulting from the breakdown of larger objects made of polyethylene and polypropylene (e.g. packaging and fishing items). Mean sea surface plastic concentration was 4256.4 pieces km−2, and after incorporating the effect of vertical wind mixing, this value increased to 8966.3 pieces km−2. These plastics appear to be associated with a wide range of ocean currents that connect the sampled sites to their international and domestic sources, including populated areas of Australias east coast. This study shows that plastic contamination levels in surface waters of Australia are similar to those in the Caribbean Sea and Gulf of Maine, but considerably lower than those found in the subtropical gyres and Mediterranean Sea. Microplastics such as the ones described here have the potential to affect organisms ranging from megafauna to small fish and zooplankton.

Clusters of iron-rich cells in the upper beak of pigeons are macrophages not magnetosensitive neurons

Understanding the molecular and cellular mechanisms that mediate magnetosensation in vertebrates is a formidable scientific problem. One hypothesis is that magnetic information is transduced into neuronal impulses by using a magnetite-based magnetoreceptor. Previous studies claim to have identified a magnetic sense system in the pigeon, common to avian species, which consists of magnetite-containing trigeminal afferents located at six specific loci in the rostral subepidermis of the beak. These studies have been widely accepted in the field and heavily relied upon by both behavioural biologists and physicists. Here we show that clusters of iron-rich cells in the rostro-medial upper beak of the pigeon Columbia livia are macrophages, not magnetosensitive neurons. Our systematic characterization of the pigeon upper beak identified iron-rich cells in the stratum laxum of the subepidermis, the basal region of the respiratory epithelium and the apex of feather follicles. Using a three-dimensional blueprint of the pigeon beak created by magnetic resonance imaging and computed tomography, we mapped the location of iron-rich cells, revealing unexpected variation in their distribution and number—an observation that is inconsistent with a role in magnetic sensation. Ultrastructure analysis of these cells, which are not unique to the beak, showed that their subcellular architecture includes ferritin-like granules, siderosomes, haemosiderin and filopodia, characteristics of iron-rich macrophages. Our conclusion that these cells are macrophages and not magnetosensitive neurons is supported by immunohistological studies showing co-localization with the antigen-presenting molecule major histocompatibility complex class II. Our work necessitates a renewed search for the true magnetite-dependent magnetoreceptor in birds.

Millimeter-sized marine plastics: a new pelagic habitat for microorganisms and invertebrates.

Millimeter-sized plastics are abundant in most marine surface waters, and known to carry fouling organisms that potentially play key roles in the fate and ecological impacts of plastic pollution. In this study we used scanning electron microscopy to characterize biodiversity of organisms on the surface of 68 small floating plastics (length range = 1.7–24.3 mm, median = 3.2 mm) from Australia-wide coastal and oceanic, tropical to temperate sample collections. Diatoms were the most diverse group of plastic colonizers, represented by 14 genera. We also recorded ‘epiplastic’ coccolithophores (7 genera), bryozoans, barnacles (Lepas spp.), a dinoflagellate (Ceratium), an isopod (Asellota), a marine worm, marine insect eggs (Halobates sp.), as well as rounded, elongated, and spiral cells putatively identified as bacteria, cyanobacteria, and fungi. Furthermore, we observed a variety of plastic surface microtextures, including pits and grooves conforming to the shape of microorganisms, suggesting that biota may play an important role in plastic degradation. This study highlights how anthropogenic millimeter-sized polymers have created a new pelagic habitat for microorganisms and invertebrates. The ecological ramifications of this phenomenon for marine organism dispersal, ocean productivity, and biotransfer of plastic-associated pollutants, remains to be elucidated.

Multimodal analysis of PEI-mediated endocytosis of nanoparticles in neural cells.

Polymer nanoparticles are widely used as a highly generalizable tool to entrap a range of different drugs for controlled or site-specific release. However, despite numerous studies examining the kinetics of controlled release, the biological behavior of such nanoparticles remains poorly understood, particularly with respect to endocytosis and intracellular trafficking. We synthesized polyethylenimine-decorated polymer nanospheres (ca. 100-250 nm) of the type commonly used for drug release and used correlated electron microscopy, fluorescence spectroscopy and microscopy, and relaxometry to track endocytosis in neural cells. These capabilities provide insight into how polyethylenimine mediates the entry of nanoparticles into neural cells and show that polymer nanosphere uptake involves three distinct steps, namely, plasma membrane attachment, fluid-phase as well as clathrin- and caveolin-independent endocytosis, and progressive accumulation in membrane-bound intracellular vesicles. These findings provide detailed insight into how the intracellular delivery of nanoparticles is mediated by polyethylenimine, which is presently the most commonly used nonviral gene transfer agent. This fundamental knowledge may also assist in the preparation of next-generation nonviral vectors.

NanoSIMS multi-element imaging reveals internalisation and nucleolar targeting for a highly-charged polynuclear platinum compound

Simultaneous multi-element imaging using NanoSIMS (nano-scale secondary ion mass spectrometry), exploiting the novel combination of (195)Pt and (15)N in platinum-am(m)ine antitumour drugs, provides information on the internalisation and subcellular localisation of both metal and ligands, and allows identification of ligand exchange.

Characterization of biominerals in the radula teeth of the chiton, Acanthopleura hirtosa

Understanding biomineralization processes provides a route to the formation of novel biomimetic materials with potential applications in fields from medicine to materials engineering. The teeth of chitons (marine molluscs) represent an excellent example of a composite biomineralized structure, comprising variable layers of iron oxide, iron oxyhydroxide and apatite. Previous studies of fully mineralized teeth using X-ray diffraction, Raman spectroscopy and scanning electron microscopy (SEM) have hinted at the underlying microstructure, but have lacked the resolution to provide vital information on fine scale structure, particularly at interfaces. While transmission electron microscopy (TEM) is capable of providing this information, difficulties in producing suitable samples from the hard, complex biocomposite have hindered progress. To overcome this problem we have used focused ion beam (FIB) processing to prepare precisely oriented sections across interfaces in fully mineralized teeth. In particular, the composite structure is found to be more complex than previously reported, with additional phases (goethite and amorphous apatite) and interface detail observed. This combination of FIB processing and TEM analysis has enabled us to investigate the structural and compositional properties of this complex biocomposite at higher resolution than previously reported and has the potential to significantly enhance future studies of biomineralization in these animals.

No evidence for intracellular magnetite in putative vertebrate magnetoreceptors identified by magnetic screening

Significance The list of animals that use the Earth’s magnetic field as a navigation tool is long and diverse; however, the cells responsible for transducing magnetic information into a neuronal impulse have not been discovered. One hypothesis argues that these cells use an iron oxide called magnetite (Fe3O4). Here, we use a “magnetoscope” coupled with single-cell correlative light and electron microscopy to identify candidate magnetoreceptors in the pigeon and trout. We report that a small percentage of cells in both species appear to have large magnetic moments, but they do not contain biogenic magnetite. Our work illustrates the need for technological innovation if the true magnetoreceptors are to be found. The cellular basis of the magnetic sense remains an unsolved scientific mystery. One theory that aims to explain how animals detect the magnetic field is the magnetite hypothesis. It argues that intracellular crystals of the iron oxide magnetite (Fe3O4) are coupled to mechanosensitive channels that elicit neuronal activity in specialized sensory cells. Attempts to find these primary sensors have largely relied on the Prussian Blue stain that labels cells rich in ferric iron. This method has proved problematic as it has led investigators to conflate iron-rich macrophages with magnetoreceptors. An alternative approach developed by Eder et al. [Eder SH, et al. (2012) Proc Natl Acad Sci USA 109(30):12022–12027] is to identify candidate magnetoreceptive cells based on their magnetic moment. Here, we explore the utility of this method by undertaking a screen for magnetic cells in the pigeon. We report the identification of a small number of cells (1 in 476,000) with large magnetic moments (8–106 fAm2) from various tissues. The development of single-cell correlative light and electron microscopy (CLEM) coupled with electron energy loss spectroscopy (EELS) and energy-filtered transmission electron microscopy (EFTEM) permitted subcellular analysis of magnetic cells. This revealed the presence of extracellular structures composed of iron, titanium, and chromium accounting for the magnetic properties of these cells. Application of single-cell CLEM to magnetic cells from the trout failed to identify any intracellular structures consistent with biogenically derived magnetite. Our work illustrates the need for new methods to test the magnetite hypothesis of magnetosensation.

Polydorid species (Polychaeta: Spionidae) in south-western Australian waters with special reference to Polydora uncinata and Boccardia knoxi

Eight species of polydorid polychaetes were found to inhabit mollusc shells from south-western Australian waters. Numerous individuals of Polydora uncinata were extracted for the first time from the shells of both land-based cultured abalone Haliotis laevigata and H. roei, as well as from natural subtidal H. roei and Chlamys australis. Shells of the oyster Saccostrea commercialis cultured in sea-based systems were infested by Boccardia knoxi which was first recorded in these waters. Polydora aura, Dipolydora giardi, D. armata, D. aciculata and Boccardia proboscidea were common among shells of various natural intertidal and subtidal molluscs. A small number of P. haswelli were extracted from their self-excavated burrows in shells of cultured oysters. Boccardia knoxi and D. aciculata were redescribed based on the newly collected materials. Polydora uncinata and B. knoxi exhibited similar larval development patterns (exolecithotrophy and adelphophagy), iteroparity and longer life span, suggesting a high reproductive potential. This study suggests that further monitoring of polydorid species is needed not only from the viewpoint of marine biology but also to survey the risk invasive species pose to commercially important molluscs in this region and worldwide.

An Iron-Rich Organelle in the Cuticular Plate of Avian Hair Cells

Hair cells reside in specialized epithelia in the inner ear of vertebrates, mediating the detection of sound, motion, and gravity. The transduction of these stimuli into a neuronal impulse requires the deflection of stereocilia, which are stabilized by the actin-rich cuticular plate. Recent electrophysiological studies have implicated the vestibular system in pigeon magnetosensation. Here we report the discovery of a single iron-rich organelle that resides in the cuticular plate of cochlear and vestibular hair cells in the pigeon. Transmission electron microscopy, coupled with elemental analysis, has shown that this structure is composed of ferritin-like granules, is approximately 300-600 nm in diameter, is spherical, and in some instances is membrane-bound and/or organized in a paracrystalline array. This organelle is found in hair cells in a wide variety of avian species, but not in rodents or in humans. This structure may function as (1) a store of excess iron, (2) a stabilizer of stereocilia, or (3) a mediator of magnetic detection. Given the specific subcellular location, elemental composition, and evolutionary conservation, we propose that this structure is an integral component of the sensory apparatus in birds.