Biology subjects

Holm, J. B.

Publications and source records attributed to Holm, J. B..

4 recordsLinked to original sources

bioRxiv2018

Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform

Amplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300 bp paired-end reads of higher quality than produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-Step PCR amplification protocol is also described that allows for targeting of different amplicon regions, thus improving amplification success from low bacterial bioburden samples.\n\nImportanceAmplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high throughput sequencing have made it a widely-adopted approach, especially for projects which necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per sample cost relative to the Illumina MiSeq platform, without sacrificing amplicon length. To make this method more flexible to various amplicon targeted regions as well as improve amplification from low biomass samples, we also present and validate a 2-Step PCR library preparation method.

microbiology↗

bioRxiv2018

Bio-optical properties and radiative energy budgets in fed and starved scleractinian corals (Pocillopora damicornis) during thermal bleaching

Corals achieve outstanding photosynthetic quantum efficiencies approaching theoretical limits (i.e. 0.125 O2 photon-1) and it is unknown how such photosynthetic efficiency varies with environmental stress. In this study, we investigated the combined effects of thermal stress and active feeding on the radiative energy budget and photosynthetic efficiency of the symbiont-bearing coral Pocillopora damicornis by using fiber-optic and electrochemical microsensors in combination with variable chlorophyll fluorescence imaging. At normal temperature (25{degrees}C), the percentage of absorbed light energy used for photosynthesis was higher for fed (~5-6% under low light exposure) compared to unfed corals (4%). Corals from both feeding treatments responded equally to stress from high light exposure (2400 mol photons m-2 s-1), exhibiting a decrease in photosynthetic energy efficiency down to 0.5-0.6%. Fed corals showed increased resilience against thermal bleaching compared to unfed corals, as fed corals were able to uphold their high photosynthetic energy efficiency for 5 days longer during thermal stress, as compared to unfed corals, which decreased their photosynthetic energy efficiency almost immediately when exposed to thermal stress. We conclude that active feeding is beneficial to corals by prolonging coral health and resilience during thermal stress as a result of an overall healthier symbiont population.

biophysics↗

bioRxiv2018

Effect of feeding and thermal stress on photosynthesis, respiration and the carbon budget of the scleractinian coral Pocillopora damicornis

Studying carbon dynamics in the coral holobiont provides essential knowledge of nutritional strategies and is thus central to understanding coral ecophysiology. In this study, the first aim was to investigate the effect of daily feeding and thermal stress on oxygen (O2) rates measured at polyp-scale with microsensors and at whole fragment scale using incubation methods. The second aim was to assess the carbon budget of the symbiotic association using H13CO3, under the different conditions. Micro- and macro-scale measurements revealed enhanced O2 evolution rates for fed compared to unfed corals. However, gross O2 production in fed corals was increased at high temperature on a macroscale but not on a microscale basis, likely due to a heterogeneous distribution of photosynthesis over the coral surface. Starved corals always exhibited reduced photosynthetic activity at high temperature, which suggests that the nutritional status of the coral host is a key limiting factor for coral productivity under thermal stress. Quantification of photosynthate translocation and carbon budgets showed very low incorporation rates, for both symbionts and host (0.03 - 0.6 g C cm-2 h-1) equivalent to only 0.008 - 0.6 %, of the photosynthetically fixed carbon for P. damicornis, in all treatments. Carbon loss (via respiration and/or mucus release) was about 41 - 47 % and 52 - 76% of the fixed carbon for starved and fed corals, respectively. Such high loss of translocated carbon suggests that P. damicornis is nitrogen and/or phosphorus limited. Heterotrophy might thus cover a larger portion of the nutritional demand for P. damicornis than previously assumed. Our results suggest that active feeding plays a fundamental role in metabolic dynamics and bleaching susceptibility of corals.

ecology↗

bioRxiv2018

Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography

Coral reefs are highly productive photosynthetic systems and coral optics studies suggest that such high efficiency is due to optimised light scattering by coral tissue and skeleton. Here, we characterise the inherent optical properties, i.e., the scattering coefficient, s, and the anisotropy of scattering, g, of 8 intact coral species using optical coherence tomography (OCT). Specifically, we describe light scattering by coral skeletons, coenoarc tissues, polyp tentacles and areas covered by fluorescent pigments (FP). Our results reveal that light scattering between coral species ranges from s = 3 mm-1 (Stylophora pistillata) to s= 25 mm-1 (Echinopora lamelosa). For Platygyra pini, s was 10-fold higher for tissue vs skeleton, while in other corals (e.g. Hydnophora pilosa) no difference was found between tissue and skeletal scattering. Tissue scattering was 3-fold enhanced in coenosarc tissues (s = 24.6 mm-1) vs polyp tentacles (s = 8.3 mm-1) in Turbinaria reniformis. FP scattering was almost isotropic when FP were organized in granule chromatophores (g=0.34) but was forward directed when FP were distributed diffusely in the tissue (g=0.96). Our study provides detailed measurements of coral scattering and establishes a rapid approach for characterising optical properties of photosynthetic soft tissues via OCT in vivo.

biophysics↗