Host dispersal relaxes selective pressures in rafting microbiomes and triggers successional changes.

What little we know about how microbiomes change over the course of host dispersal has been gleaned from simulations or snapshot sampling of microbiomes of hosts undertaking regular, cyclical migrations. These studies suggest that major changes in both microbiome richness and turnover occur in response to long-distance movements, but we do not yet know how rare or sporadic dispersal events for non-migratory organisms might affect the microbiomes of their hosts. Here we directly examine the microbiomes of rafting seaweed, leveraging host genomic analyses, amplicon sequencing, and oceanographic modelling to study the impacts of ecological dispersal of hosts on their microbiomes.

A cry for kelp: Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae.

Genomic resources have yielded unprecedented insights into ecological and evolutionary processes, not to mention their importance in economic and conservation management of specific organisms. However, the field of macroalgal genomics is hampered by difficulties in the isolation of suitable DNA. Even when DNA that appears high quality by standard metrics has been isolated, such samples may not perform well during the sequencing process.

Long-distance movement dynamics shape host microbiome richness and turnover.

Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change.

Host population crashes disrupt the diversity of associated marine microbiomes.

Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems.

Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance.

Background And Aims: Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation.

Southern Hemisphere coasts are biologically connected by frequent, long-distance rafting events.

Globally, species distributions are shifting in response to environmental change, and those that cannot disperse risk extinction. Many taxa, including marine species, are showing poleward range shifts as the climate warms. In the Southern Hemisphere, however, circumpolar oceanic fronts can present barriers to dispersal.

Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data.

Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across the genome of an organism. The dominant class of RRS approaches assay loci associated with restriction sites within the genome (restriction site associated DNA sequencing, or RADseq). RADseq is frequently applied to non-model organisms since it enables population genetic studies without relying on well-characterized reference genomes.

Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod.

Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda species in multiple lineages have atypical and rearranged mitochondrial genomes.

Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod.

Population genetic structure in the marine environment can be influenced by life-history traits such as developmental mode (biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults) or habitat specificity, as well as geography and selection. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, this prediction can be complicated by the presence of geophysical barriers to dispersal.

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding.

The use of DNA metabarcoding to characterise the biodiversity of environmental and community samples has exploded in recent years. However, taxonomic inferences from these studies are contingent on the quality and completeness of the sequence reference database used to characterise sample species-composition. In response, studies often develop custom reference databases to improve species assignment.

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads.

Background: The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data.

Characterization of the Ag mediated surface-enhanced Raman spectroscopy of saxitoxin.

The rapid detection and quantification of saxitoxin (STX) is reported using surface-enhanced Raman spectroscopy (SERS) with a colloidal hydrosol of silver nanoparticles. Under the conditions of our experiments, the limit of detection (LD) for STX using SERS is 3 nM, with a limit of quantification (LQ) of 20 nM. It is shown that the SERS method is rapid, with spectra being collected in as little as 5 seconds total integration time for a 40 nM STX sample.

Quantitative measurements of CO2 and CH4 using a multipass Raman capillary cell.

Raman measurements of two common gases are made using a simple multipass capillary Raman cell (MCC) coupled to an unfiltered 18 around 1 fiber-optic Raman probe. The MCC, which is fabricated by chemical deposition of silver on the inner walls of a 2 mm inner diameter glass capillary tube, gives up to 20-fold signal enhancements for nonabsorbing gases. The device is relatively small and suitable for remote and in situ Raman measurements with optical fibers.

Multipass capillary cell for enhanced Raman measurements of gases.

A simple Raman multipass capillary cell (MCC) is described that gives 12- to 30-fold signal enhancements for non-absorbing gases. The cell is made by coating the inside of 2-mm inner diameter silica capillary tubes with silver. The device is very small and suitable for remote and in situ Raman measurements with optical fibers.

Surface-enhanced Raman spectroscopy for in situ measurements of signaling molecules (autoinducers) relevant to bacteria quorum sensing.

Autoinducer (AI) molecules are used by quorum sensing (QS) bacteria to communicate information about their environment and are critical to their ability to coordinate certain physiological activities. Studying how these organisms react to environmental stresses could provide insight into methods to control these activities. To this end, we are investigating spectroscopic methods of analysis that allow in situ measurements of these AI molecules under different environmental conditions.

Classification of chemical and biological warfare agent simulants by surface-enhanced Raman spectroscopy and multivariate statistical techniques.

Initial results demonstrating the ability to classify surface-enhanced Raman (SERS) spectra of chemical and biological warfare agent simulants are presented. The spectra of two endospores (B. subtilis and B.

Temporal dependence of the enhancement of material removal in femtosecond-nanosecond dual-pulse laser-induced breakdown spectroscopy.

Despite the large neutral atomic and ionic emission enhancements that have been noted in collinear and orthogonal dual-pulse laser-induced breakdown spectroscopy, the source or sources of these significant signal and signal-to-noise ratio improvements have yet to be explained. In the research reported herein, the combination of a femtosecond preablative air spark and a nanosecond ablative pulse yields eightfold and tenfold material removal improvement for brass and aluminum, respectively, but neutral atomic emission is enhanced by only a factor of 3-4. Additionally, temporal correlation between enhancement of material removal and of atomic emission is quite poor, suggesting that the atomic-emission enhancements noted in the femtosecond-nanosecond pulse configuration result in large part from some source other than simple improvement in material removal.

Spatial and temporal dependence of interspark interactions in femtosecond-nanosecond dual-pulse laser-induced breakdown spectroscopy.

A femtosecond air spark has recently been combined with a nanosecond ablative pulse in order to map the spatial and temporal interactions of the two plasmas in femtosecond-nanosecond orthogonal preablation spark dual-pulse laser-induced breakdown spectroscopy (LIBS). Good spatial and temporal correlation was found for reduced atomic emission from atmospheric species (nitrogen and oxygen) and increased atomic emission from ablated species (copper and aluminum) in the femtosecond-nanosecond plasma, suggesting a potential role for atmospheric pressure or nitrogen/oxygen concentration reduction following air spark formation in generating atomic emission enhancements in dual-pulse LIBS.

Effects of sample temperature in femtosecond single-pulse laser-induced breakdown spectroscopy.

As much as tenfold atomic emission enhancements have been observed in experiments combining nanosecond (ns) and femtosecond (fs) laser pulses in an orthogonal dual-pulse configuration for laser-induced breakdown spectroscopy (ns-fs orthogonal dual-pulse LIBS). In the examination of one of several potential sources of these atomic emission enhancements (sample heating by a ns air spark), minor reductions in atomic emission and as much as 15-fold improvements in mass removal have been observed for fs single-pulse LIBS of heated brass and aluminum samples. These results suggest that, although material removal with a high-powered, ultrashort fs pulse is temperature dependent, sample heating by the ns air spark is not the source of the atomic emission enhancements observed in ns-fs orthogonal dual-pulse LIBS.

Dual-pulse laser-induced breakdown spectroscopy with combinations of femtosecond and nanosecond laser pulses.

Nanosecond and femtosecond laser pulses were combined in an orthogonal preablation spark dual-pulse laser-induced breakdown spectroscopy (LIBS) configuration. Even without full optimization of interpulse alignment, ablation focus, large signal, signal-to-noise ratio, and signal-to-background ratio enhancements were observed for both copper and aluminum targets. Despite the preliminary nature of this study, these results have significant implications in the attempt to explain the sources of dual-pulse LIBS enhancements.

Dual-pulse laser-induced breakdown spectroscopy in bulk aqueous solution with an orthogonal beam geometry.

Use of dual-pulse laser-induced breakdown spectroscopy with an orthogonal spark orientation is presented as a technique for trace metal analysis in bulk aqueous solutions. Two separate Q-switched Nd:YAG lasers operating at their fundamental wavelengths are used to form a subsurface, laser-induced plasma in a bulk aqueous solution that is spectroscopically analyzed for the in situ detection of Ca, Cr, and Zn. Optimizing the key experimental parameters of proper spark alignment, gate delay (td), gate width (tb), and interpulse timing (deltaT) allowed experimentally determined detection limits of the order of micrograms per milliliter and submicrograms per milliliter.