Inherent Negative Refraction on Acoustic Branch of Two Dimensional Phononic Crystals

Guided by theoretical predictions, we have demonstrated experimentally the existence of negative refraction on the lowest two (acoustic) passbands (shear and longitudinal modes) of a simple two dimensional phononic crystal consisting of an isotropic stiff (aluminum) matrix and square- patterned isotropic compliant (PMMA) circular inclusions. At frequencies and wave vectors where the refraction is negative, the effective mass density and the effective stiffness tensors of the crystal can be positive-defnite, and that, this is an inherent property of phononic crystals with an isotropic stiff matrix containing periodically distributed isotropic compliant inclusions. The equi-frequency contours and energy ux vectors as fuctions of the phase-vector components, reveal a rich body of refractive properties that can be exploited to realize, for example, beam splitting, focusing, and frequency filtration on the lowest passbands of the crystal where the dissipation is the least. By proper selection of material and geometric parameters these phenomena can be realized at remarkably low frequencies (large wave lengths) using rather small simple two-phase unit cells. Keywords: Doubly periodic phononic crystals, acoustic branch negative refraction, beam splitting, focusing, imaging, frequency filtration at large wave length

Virus-like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries

Viruses are recognized as ubiquitous components of marine ecosystems; however, there has been limited study of viral abundance and its ecological role in sediments. Viral abundance was determined in both the water column and sediments of a eutrophic (Brisbane River/Moreton Bay; 27°25′S, 153°5′E) and oligotrophic (Noosa River; 26°15′S, 153°0′E) estuary in subtropical Queensland, Australia. Viruses, bacteria, and microalgae from both water column and extracted sediment samples were enumerated using SYBR Green I staining and epifluorescence microscopy. Sediment viral abundance ranged from 10 to 10 particles cm of sediment, bacterial abundance ranged from 10 to 10 cells cm of sediment, and microalgal abundance ranged from 10 to 10 cells cm sediment. Pelagic abundances for all microorganisms were 10-1,000-fold lower than sediment abundances. Correlations between viral abundances and suspended solids suggest that viruses sorbed to suspended material in the water column may settle out and contribute to the benthic viral population. Virus production was measured by a time course increase of viral abundance in seawater using a dilution technique. Virus production was highest in eutrophic waters of the Brisbane River, and addition of inorganic nutrients (NO + NH + PO + SiO) stimulated viral production rates at all stations by 14-52% above ambient, suggesting that inorganic nutrient availability may play a key role in aquatic viral abundance

Symbiotic UCYN-A Strains Co-occurred with El Niño, Relaxed Upwelling, and Varied Eukaryotes Over 10 Years Off Southern California

Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This “open ocean ecotype” was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics

Distribution of extracellular flavins in a coastal marine basin and their relationship to redox gradients and microbial community members

The flavins (including flavin mononucleotide (FMN) and riboflavin (RF)) are a class of organic compounds synthesized by organisms to assist in critical redox reactions. While known to be secreted extracellularly by some species in laboratory-based cultures, flavin concentrations are largely unreported in the natural environment. Here, we present pore water and water column profiles of extracellular flavins (FMN and RF) and two degradation products (lumiflavin and lumichrome) from a coastal marine basin in the Southern California Bight alongside ancillary geochemical and 16S rRNA microbial community data. Flavins were detectable at picomolar concentrations in the water column (93–300 pM FMN, 14–40 pM RF) and low nanomolar concentrations in pore waters (250–2070 pM FMN, 11–210 pM RF). Elevated pore water flavin concentrations displayed an increasing trend with sediment depth and were significantly correlated with the total dissolved Fe (negative) and Mn (positive) concentrations. Network analysis revealed a positive relationship between flavins and the relative abundance of Dehalococcoidia and the MSBL9 clade of Planctomycetes, indicating possible secretion by members of these lineages. These results suggest that flavins are a common component of the so-called shared extracellular metabolite pool, especially in anoxic marine sediments where they exist at physiologically relevant concentrations for metal oxide reduction

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Systems Biology 5 Suppl 2 (2011): S15, doi:10.1186/1752-0509-5-S2-S15.The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsaThis research is partially supported by the National Science Foundation (NSF) DMS-1043075 and OCE 1136818