Practical applications of small-angle neutron scattering.

Recent improvements in beam-line accessibility and technology have led to small-angle neutron scattering (SANS) becoming more frequently applied to materials problems. SANS has been used to study the assembly, dispersion, alignment and mixing of nanoscale condensed matter, as well as to characterise the internal structure of organic thin films, porous structures and inclusions within steel. Using time-resolved SANS, growth mechanisms in materials systems and soft matter phase transitions can also be explored. This review is intended for newcomers to SANS as well as experts. Therefore, the basic knowledge required for its use is first summarised. After this introduction, various examples are given of the types of soft and hard matter that have been studied by SANS. The information that can be extracted from the data is highlighted, alongside the methods used to obtain it. In addition to presenting the findings, explanations are provided on how the SANS measurements were optimised, such as the use of contrast variation to highlight specific parts of a structure. Emphasis is placed on the use of complementary techniques to improve data quality (e.g. using other scattering methods) and the accuracy of data analysis (e.g. using microscopy to separately determine shape and size). This is done with a view to providing guidance on how best to design and analyse future SANS measurements on materials not listed below

Leaf Area and Structural Changes after Thinning in Even-Aged Picea rubens and Abies balsamea Stands in Maine, USA

We tested the hypothesis that changes in leaf area index (LAI m2 m−2) and mean stand diameter following thinning are due to thinning type and residual density. The ratios of pre- to postthinning diameter and LAI were used to assess structural changes between replicated crown, dominant, and low thinning treatments to 33% and 50% residual density in even-aged Picea rubens and Abies balsamea stands with and without a precommercial thinning history in Maine, USA. Diameter ratios varied predictably by thinning type: low thinnings were 0.7 but 1.0 . LAI change was affected by type and intensity of thinning. On average, 33% density reduction removed 50% of LAI. Overall reduction of LAI was generally greatest in dominant thinnings (54%), intermediate in crown thinnings (46%), and lowest in low thinnings (35%). Upon closer examination by crown classes, the postthinning distribution of LAI between upper and lower crown classes varied by thinning history, thinning method, and amount of density reduction

Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo

Marine bacteria exhibit positive chemotactic responses to the extracellular exudates of the toxic phytoplankton Heterosigma akashiwo. In the environment, this will support bacteria–algae associations with potential implications for harmful algal bloom dynamics.National Science Foundation (U.S.) (OCE-0526241)National Science Foundation (U.S.) (OCE-0744641 CAREER)Australian Research Council (Discovery Grant)Massachusetts Institute of Technology. Energy Initiative (Martin Family Society of Fellows for Sustainability Fellowship

Microscale patchiness of virioplankton

The microscale spatial distributions of viruses were investigated in three contrasting environments including oligotrophic open ocean, eutrophic coastal and estuarine habitats. The abundances of two discrete populations of both viruses and heterotrophic bacteria were measured at spatial resolutions of between 1 and 5 cm using purpose-designed microscale sampling equipment and flow cytometric sample analysis. Within open water samples, virus distributions were characterized by non-normal distributions and by 'hotspots' in abundance where concentrations varied by up to 17-fold. In contrast to patterns generally observed at larger spatiotemporal scales, there was no correlation between bacterial and viral abundance or correspondence between bacteria and virus hotspots within these samples. Consequently, strong hotspots and gradients in the virus:bacteria ratio (VBR) were also apparent within samples. Within vertical profiles taken from above the sediment-water interface within a temperate mangrove estuary, distributions of planktonic viruses were characterized by gradients in abundance, with highest concentrations observed within the 1-2 cm immediately above the sediment surface, and virus distributions were correlated to bacterial abundance (P<0.01). The patterns observed in these contrasting habitats indicate that microscale patchiness of virus abundance may be a common feature of the marine environment. This form of heterogeneity may have important implications for virus-host dynamics and subsequently influence microbial trophodynamics and nutrient cycling in the ocean

Spatiotemporal dynamics of Vibrio spp. within the Sydney Harbour estuary

© 2016 Siboni, Balaraju, Carney, Labbate and Seymour. Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.Human Frontier Science Program (Strasbourg, France) (Grant RGY0089/2011

Elevated estuary water temperature drives fish gut dysbiosis and increased loads of pathogenic vibrionaceae

Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of coastal waters is increasing the abundance and virulence of pathogenic members of the Vibrionaceae, posing a significant health risk to both humans and aquatic organisms. Fish disease, notably outbreaks of emerging pathogens in response to environmental perturbations such as heatwaves, have been recognised in aquaculture settings. Considerably less is known about how rising sea surface temperatures will impact the microbiology of wild fish populations, particularly those within estuarine systems that are more vulnerable to warming. We used a combination of Vibrio-specific quantitative PCR and amplicon sequencing of the 16S rRNA and hsp60 genes to examine seawater and fish (Pelates sexlineatus) gut microbial communities across a quasi-natural experimental system, where thermal pollution from coal-fired power stations creates a temperature gradient of up to 6 °C, compatible with future predicted temperature increases. At the warmest site, fish hindgut microbial communities were in a state of dysbiosis characterised by shifts in beta diversity and a proliferation (71.5% relative abundance) of the potential fish pathogen Photobacterium damselae subsp. damselae. Comparable patterns were not identified in the surrounding seawater, indicating opportunistic proliferation within estuarine fish guts under thermal stress. A subsequent evaluation of predicted future warming-related risk due to pathogenic Vibrionaceae in temperate estuarine fish demonstrated that warming is likely to drive opportunistic pathogen increases in the upper latitudinal range of this estuarine fish, potentially impacting adaptations to future warming. These findings represent a breakthrough in our understanding of the dynamics of emerging pathogens in populations of wild aquatic organisms within environments likely to experience rapid warming under future climate change

Mucospheres produced by a mixotrophic protist impact ocean carbon cycling

Mixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)-are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich 'mucospheres' that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17-1.24 mg m-2 d-1 of particulate organic carbon, or 0.02-0.15 Gt to the biological pump annually, which represents 0.1-0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean

Bacteria-mediated aggregation of the marine phytoplankton Thalassiosira weissflogii and Nannochloropsis oceanica

Funder: Australian Government Research Training Program ScholarshipFunder: University of Technology Sydney Climate Change Cluster (C3)Abstract: The ecological relationships between heterotrophic bacteria and marine phytoplankton are complex and multifaceted, and in some instances include the bacteria-mediated aggregation of phytoplankton cells. It is not known to what extent bacteria stimulate aggregation of marine phytoplankton, the variability in aggregation capacity across different bacterial taxa or the potential role of algogenic exopolymers in this process. Here we screened twenty bacterial isolates, spanning nine orders, for their capacity to stimulate aggregation of two marine phytoplankters, Thalassiosira weissflogii and Nannochloropsis oceanica. In addition to phytoplankton aggregation efficiency, the production of exopolymers was measured using Alcian Blue. Bacterial isolates from the Rhodobacterales, Flavobacteriales and Sphingomonadales orders stimulated the highest levels of cell aggregation in phytoplankton cultures. When co-cultured with bacteria, exopolymer concentration accounted for 34.1% of the aggregation observed in T. weissflogii and 27.7% of the aggregation observed in N. oceanica. Bacteria-mediated aggregation of phytoplankton has potentially important implications for mediating vertical carbon flux in the ocean and in extracting phytoplankton cells from suspension for biotechnological applications

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites.

Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site