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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A comparative genome analysis of the Bacillota ( Firmicutes ) class Dehalobacteriia

Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparative genomics of pyrophilous fungi reveals a link between fire events and developmental genes

Forest fires generate a large amount of carbon that remains resident on the site as dead and partially ‘pyrolysed’ (i.e. burnt) material that has long residency times and constitutes a significant pool in fire–prone ecosystems. In addition, fire–induced hydrophobic soil layers, caused by condensation of pyrolysed waxes and lipids, increase post–fire erosion and can lead to long–term productivity losses. A small set of pyrophilous fungi dominate post–fire soils and are likely to be involved with the degradation of all these compounds, yet almost nothing is currently known about what these fungi do or the metabolic processes they employ. In this study, we sequenced and analyzed genomes from fungi isolated after Rim fire near Yosemite National Park in 2013 and showed the enrichment/expansion of CAZymes and families known to be involved in fruiting body initiation when compared to other basidiomycete fungi. We found gene families potentially involved in the degradation of the hydrophobic layer and pyrolysed organic matter, such as hydrophobic surface binding proteins, laccases (AA1_1), xylanases (GH10, GH11), fatty acid desaturases and tannases. Furthermore, pyrophilous fungi are important actors to restate the soil's functional capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comparative study of GaN mesa etch characteristics in Cl{sub 2} based inductively coupled plasma with Ar and BCl{sub 3} as additive gases

GaN thin film etching is investigated and compared for mesa formation in inductively coupled plasma (ICP) of Cl{sub 2} with Ar and BCl{sub 3} gas additives using photoresist mask. Etch characteristics are studied as a function of ICP process parameters, viz., ICP power, radio frequency (RF) power, and chamber pressure at fixed total flow rate. The etch rate at each ICP/RF power is 0.1–0.2 μm/min higher for Cl{sub 2}/Ar mixture mainly due to higher Cl dissociation efficiency of Ar additive that readily provides Cl ion/radical for reaction in comparison to Cl{sub 2}/BCl{sub 3} mixture. Cl{sub 2}/Ar mixture also leads to better photoresist mask selectivity. The etch-induced roughness is investigated using atomic force microscopy. Cl{sub 2}/Ar etching has resulted in lower root-mean-square roughness of GaN etched surface in comparison to Cl{sub 2}/BCl{sub 3} etching due to increased Ar ion energy and flux with ICP/RF power that enhances the sputter removal of etch product. The GaN surface damage after etching is also evaluated using room temperature photoluminescence and found to be increasing with ICP/RF power for both the etch chemistries with higher degree of damage in Cl{sub 2}/BCl{sub 3} etching under same condition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

SU-E-T-545: A MLC-Equipped Robotic Radiosurgery-Radiotherapy Combined System in Treating Hepatic Lesions: Delivery Efficiency as Compared to a Standard Linac for Treating Hepatic Lesions

Purpose: The CyberKnife (CK) M6 Series introduced a mulitleaf collimator (MLC) beam for extending its capability to the conventional radiotherapy. This work is to investigate delivery efficiency of this system as compared to a standard Varian linac when treating hepatic lesions. Methods: Nine previously treated patients were divided into three groups with three patients in each. Group one: fractionated radiotherapy; Group two: SBRT-like treatments and Group three: fractionated radiotherapy targeting two PTVs. The clinically used plans were generated with the Eclipse treatment planning system (TPS). We re-planned these cases using a Mulitplan (MP) TPS for the CK M6 and normalized to the same PTV dose coverage. CK factors (CF) (defined as modulation scaling factor in this work), number of nodes (NN), number of MLC segments (NS) and beam delivery time (BT) with an estimated image interval of 60 seconds, were used for evaluation of delivery efficiency. Results: Generated plans from the MP and Eclipse TPS demonstrated the similar quality in terms of PTV confomality index, minimum and maximum PTV doses, and doses received by critical structures. Group one: CF ranged from 8.1 to 8.7, NN from 30 to 40, NS from 120 to 155 and BT from 20 to 23 minutes; group two: CF from 4.7 to 8.5, NN from 15 to 19, NS from 82 to 141 and BT from 18 to 24 minutes; and group three: CF from 7.9 to 10, NN from 47 to 49, NS from 110 to 113 and BT from 20 to 22 minutes. Conclusions: Delivery time is longer for the CK M6 than for the Varian linac (7.8 to 13.7 minutes). Further investigation will be necessary to determine if a PTV reduction from the tracking feature will shorten the delivery time without decreasing plan quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

WE-E-BRE-06: High-Dose Microbeam Radiation Induces Different Responses in Tumor Microenvironment Compared to Conventional Seamless Radiation in Window Chamber Tumor Models

Purpose: Microbeam radiation therapy and GRID therapy are different forms of Spatially-Fractioned Radiation Therapy (SFRT) that is fundamentally different from the conventional seamless and temporally fractionated radiation therapy. SFRT is characterized by a ultra-high dose (10s –100s Gy) dose single treatment with drastic inhomogeneity pattern of given spatial frequencies. Preclinical and limited clinical studies have shown that the SFRT treatments may offer significant improvements in reducing treatment toxicity, especially for those patients who have not benefited from the state-of-the-art radiation therapy approaches. This preliminary study aims to elucidate the underlying working mechanisms of SFRT, which currently remains poorly understood. Methods: A genetically engineered 4T1 murine mammary carcinoma cell line and nude mice skin fold window chamber were used. A nanotechnology-based 160kV x-ray irradiator delivered 50Gy (entrance dose) single treatments of microbeam or seamless radiation. Animals were in 3 groups: mock, seamless radiation, and 300μm microbeam radiation. The windows were imaged using a hyperspectral system to capture total hemoglobin/saturation, GFP fluorescence emission, RFP fluorescence emission, and vessel density at 9 time points up to 7 days post radiation. Results: We found unique physiologic changes in different tumor/normal tissue regions and differential effects between seamless and microbeam treatments. They include 1) compared to microbeam and mock radiation seamless radiation damaged more microvasculature in tumor-surrounding normal tissue, 2) a pronounced angiogenic effect was observed with vascular proliferation in the microbeam irradiated portion of the tumor days post treatment (no such effect observed in seamless and mock groups), and 3) a notable change in tumor vascular orientation was observed where vessels initially oriented parallel to the beam length were replaced by vessels running perpendicular to the irradiation portion of the tumor. Conclusion: Our preliminary study indicated that microbeam radiation modified tumor microenvironment in ways significantly different than of the conventional seamless radiation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists

Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as “leftover scavengers” and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Comparative analysis of the structural and morphological features of biogenic and synthesized goethite nanoparticles

A comparative analysis of the relationship between the morphological forms and magnetic properties of natural goethite particles from the crust of weathering of the Far East and Vietnam basalts and pure, chemically synthesized goethite particles was performed using Mössbauer spectroscopy, X-ray diffraction analysis, and scanning electron microscopy. It is shown how the shape of biogenic goethite particles affects their magnetic properties, which significantly differ from the magnetic properties of chemically synthesized samples.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Ternary fission of nuclei into comparable fragments

The problem of nuclear fission into three comparable fragments is considered. A mechanism of true ternary fission is proposed. In contrast to sequential fission, where the three fragments arise upon two sequential events of binary fission, the mechanism in question relies on a scenario that originally involves fission into three fragments. This mechanism is driven by a hexadecapole deformation of the fissioning nucleus, in contrast to binary fission associated with quadrupole vibrations of the nuclear surface. The fragment-mass ratios are estimated. The dynamics of formation of collinear fragments and their subsequent motion in opposite directions is traced. The calculated probability of true ternary fission complies with observed values.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Comparative analysis of the possibility of applying low-melting metals with the capillary-porous system in tokamak conditions

The use of capillary-porous systems (CPSs) with liquid Li, Ga, and Sn is considered as an alternative for solving the problem of creating plasma-facing elements (PFEs) of the fusion neutron source (FNS) and the DEMO-type reactor. The main advantages of CPSs with liquid metal compared with hard materials are their stability with respect to the degradation of properties in tokamak conditions and capability of surface self-restoration. The evaluation of applicability of liquid metals is performed on the basis of the analysis of their physical and chemical properties, the interaction with the tokamak plasma, and constructive and process features of in-vessel elements with CPSs implementing the application of these metals in a tokamak. It is shown that the upper limit of the PFE working temperature for all low-melting metals under consideration lies in the range of 550–600°Ð¡. The decisive factor for PFEs with Li is the limitation on the admissible atomic flux into plasma, while for those with Ga and Sn it is the corrosion resistance of construction materials. The upper limit of thermal loads in the steady-state operating mode for the considered promising PFE design with the use of Li, Ga, and Sn is close to 18–20 MW/m{sup 2}. It is seen from the analysis that the use of metals with a low equilibrium vapor pressure of (Ga, Sn) gives no gain in extension of the region of admissible working temperatures of PFEs. However, with respect to the totality of properties, the possibility of implementing the self-restoration and stabilization effect of the liquid surface, the influence on the plasma discharge parameters, and the ability to protect the PFE surface in conditions of plasma perturbations and disruption, lithium is the most attractive liquid metal to create CPS-based PFEs for the tokamak.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Comparative investigation of InGaP/GaAs pseudomorphic field-effect transistors with triple doped-channel profiles

In this article, the comparison of DC performance on InGaP/GaAs pseudomorphic field-effect transistors with tripe doped-channel profiles is demonstrated. As compared to the uniform and high-medium-low doped-channel devices, the low-medium-high doped-channel device exhibits the broadest gate voltage swing and the best device linearity because more twodimensional electron gases are formed in the heaviest doped channel to enhance the magnitude of negative threshold voltage. Experimentally, the transconductance within 50% of its maximum value for gate voltage swing is 4.62 V in the low-medium-high doped-channel device, which is greater than 3.58 (3.30) V in the uniform (high-medium-low) doped-channel device.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Comparative analysis of the effects of electron and hole capture on the power characteristics of a semiconductor quantum-well laser

The operating characteristics of a semiconductor quantum-well laser calculated using three models are compared. These models are (i) a model not taking into account differences between the electron and hole parameters and using the electron parameters for both types of charge carriers; (ii) a model, which does not take into account differences between the electron and hole parameters and uses the hole parameters for both types of charge carriers; and (iii) a model taking into account the asymmetry between the electron and hole parameters. It is shown that, at the same velocity of electron and hole capture into an unoccupied quantum well, the laser characteristics, obtained using the three models, differ considerably. These differences are due to a difference between the filling of the electron and hole subbands in a quantum well. The electron subband is more occupied than the hole subband. As a result, at the same velocities of electron and hole capture into an empty quantum well, the effective electron-capture velocity is lower than the effective hole-capture velocity. Specifically, it is shown that for the laser structure studied the hole-capture velocity of 5 × 10{sup 5} cm/s into an empty quantum well and the corresponding electron-capture velocity of 3 × 10{sup 6} cm/s into an empty quantum well describe the rapid capture of these carriers, at which the light–current characteristic of the laser remains virtually linear up to high pump-current densities. However, an electron-capture velocity of 5 × 10{sup 5} cm/s and a corresponding hole-capture velocity of 8.4 × 10{sup 4} cm/s describe the slow capture of these carriers, causing significant sublinearity in the light–current characteristic.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.

In this study, Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae . They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus , based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp. As a result, Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position. In conclusion, the present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

Background: Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Results: Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Conclusions: Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

Background: The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. Results: The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. Conclusions: The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Comparing Germany's and California's Interconnection Processes for PV Systems (White Paper)

Establishing interconnection to the grid is a recognized barrier to the deployment of distributed energy generation. This report compares interconnection processes for photovoltaic projects in California and Germany. This report summarizes the steps of the interconnection process for developers and utilities, the average length of time utilities take to process applications, and paperworkrequired of project developers. Based on a review of the available literature, this report finds that while the interconnection procedures and timelines are similar in California and Germany, differences in the legal and regulatory frameworks are substantial.

14 SOLAR ENERGY↗
DOE OSTI2013

Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria

L-rhamnose (L-Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L-Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and L-Rha-containing polymers. Large-scale regulon inference using bioinformatics revealed remarkable variations in transcriptional regulators for L-Rha utilization genes among bacteria. A novel bifunctional enzyme, L-rhamnulose-phosphate aldolase (RhaE) fused to L-lactaldehyde dehydrogenase (RhaW), which is not homologous to previously characterized L-Rha catabolic enzymes, was identified in diverse bacteria including Chloroflexi, Bacilli, and Alphaproteobacteria. By using in vitro biochemical assays we validated both enzymatic activities of the purified recombinant RhaEW proteins from Chloroflexus aurantiacus and Bacillus subtilis. Another novel enzyme of the L-Rha catabolism, L-lactaldehyde reductase (RhaZ), was identified in Gammaproteobacteria and experimentally validated by in vitro enzymatic assays using the recombinant protein from Salmonella typhimurium. C. aurantiacus induced transcription of the predicted L-Rha utilization genes when L-Rha was present in the growth medium and consumed L-Rha from the medium. This study provided comprehensive insights to L-Rha catabolism and its regulation in diverse Bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat

Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO 2 uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.

59 BASIC BIOLOGICAL SCIENCES↗