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In this paper, we study two configurations of a full-Stokes polarimeter that measures three wavelengths simultaneously. A recently developed fitting calibration process is used to reduce the error in the final Stokes vector. The first configuration uses an optimized setup for the central wavelength that fixes the non-optimized setups for the other two wavelengths. The second configuration is the result of a search for the best simultaneous setups for all three wavelengths. It is found that this second setup gives smaller errors in the measured Stokes parameters before calibration, but the first configuration gives smaller errors after calibration. These results demonstrate the need for a method of finding the best polarimeter configuration for this type of measurement. It seems clear that the condition number by itself is not a metric that provides sufficient information to determine whether a particular configuration is better by giving smaller errors. It is also important to point out that the results presented here are for the particular calibration scheme used. Additionally, it may be that a different calibration method is required to give better results, but that is outside the scope of the present work.

Liquid crystal variable retarders (LCVRs) are often used in Stokes polarimeters as they allow the measurement of different polarization components by applying an electric field that manipulates the induced retardance. However, the optical retardance introduced by these devices is in general not homogenous across the aperture. Another problem with this type of devices is that the fast-axis orientation is not homogenous, and it changes with the applied voltage. For the optimization of polarimeters, in terms of the noise amplification from the intensity measurements to the polarimetric data, the condition number (CN) is often used, but the effects of LCVR spatial variations are not considered. This paper analyzes the impact of errors in LCVRs in a set of optimized Stokes polarimeters simulated by adding errors in the induced retardance and fast-axis orientation. Then, the CN is calculated to observe the effect of these errors on the optimization. We show how errors in the LCVRs lead to different impacts in the polarimetric measurements for different optimized polarimeters, depending on their experimental parameters. Furthermore, we present the propagation error theory to choose the best experimental parameters to reduce the nonideal effects in optimized polarimeters.

Background Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), synthesised by endosymbionts living in specialised shipworm cells called bacteriocytes and located in the animal’s gills, play an important role in wood digestion in shipworms. However, the main site of lignocellulose digestion within these wood-boring molluscs, which contains both endogenous lignocellulolytic enzymes and prokaryotic enzymes, is the caecum, and the mechanism by which bacterial enzymes reach the distant caecum lumen has remained so far mysterious. Here, we provide a characterisation of the path through which bacterial CAZymes produced in the gills of the shipworm Lyrodus pedicellatus reach the distant caecum to contribute to the digestion of wood. Results Through a combination of transcriptomics, proteomics, X-ray microtomography, electron microscopy studies and in vitro biochemical characterisation, we show that wood-digesting enzymes produced by symbiotic bacteria are localised not only in the gills, but also in the lumen of the food groove, a stream of mucus secreted by gill cells that carries food particles trapped by filter feeding to the mouth. Bacterial CAZymes are also present in the crystalline style and in the caecum of their shipworm host, suggesting a unique pathway by which enzymes involved in a symbiotic interaction are transported to their site of action. Finally, we characterise in vitro four new bacterial glycosyl hydrolases and a lytic polysaccharide monooxygenase identified in our transcriptomic and proteomic analyses as some of the major bacterial enzymes involved in this unusual biological system. Conclusion Based on our data, we propose that bacteria and their enzymes are transported from the gills along the food groove to the shipworm’s mouth and digestive tract, where they aid in wood digestion.

Spectrally modulated Stokes polarimeters use a pair of high-order crystal retarders to generate a spectrally dependent modulation of the polarization of light. In these systems, the detected intensity versus wavenumber spectrum is usually referred to as a channeled spectrum, and the Fourier inversion of this spectrum allows the determination of Stokes parameters of light without needing any other mechanical or active device for polarization control. This work proposes a spectrally modulated polarimeter beyond the concept of a channeled wavenumber spectrum, so effectively detaching the spectral modulation from the Fourier analysis technique. The wavelength domain analysis we use is best suited for dispersive spectrometers offering intensity versus wavelength measurements. The technique is illustrated with the measurement of very small optical rotations produced by sucrose solutions. The proposed technique is easily extendable to spectrally modulated Mueller polarimeters.

Potato pectin falls to Phytophthora Phytophthora infestans is a plant oomycete pathogen that drove the potato famines of the 1800s and continues to afflict potato fields today. The polysaccharide pectin makes up about a third of the cell wall in potatoes. Sabbadin et al . identified a family of lytic polysaccharide monooxygenases (LMPOs) that cleave pectin and are upregulated in P. infestans during infection. Silencing the relevant LMPO gene successfully inhibited P. infestans infections. These findings open doors for disease intervention targets and for biotech applications. —PJH

There is an urgent need to replace petroleum-based plastic with bio-based and biodegradable alternatives. Polyhydroxyalkanoates (PHAs) are attractive prospective replacements that exhibit desirable mechanical properties and are recyclable and biodegradable in terrestrial and marine environments. However, the production costs today still limit the economic sustainability of the PHA industry. Seaweed cultivation represents an opportunity for carbon capture, while also supplying a sustainable photosynthetic feedstock for PHA production. We mined existing gene and protein databases to identify bacteria able to grow and produce PHAs using seaweed-derived carbohydrates as substrates. There were no significant relationships between the genes involved in the deconstruction of algae polysaccharides and PHA production, with poor to negative correlations and diffused clustering suggesting evolutionary compartmentalism. We identified 2 987 bacterial candidates spanning 40 taxonomic families predominantly within Alphaproteobacteria, Gammaproteobacteria and Burkholderiales with enriched seaweed-degrading capacity that also harbour PHA synthesis potential. These included highly promising candidates with specialist and generalist specificities, including Alteromonas , Aquisphaera , Azotobacter , Bacillus , Caulobacter , Cellvibrionaceae , Duganella , Janthinobacterium , Massilia , Oxalobacteraceae , Parvularcula , Pirellulaceae , Pseudomonas , Rhizobacter , Rhodanobacter , Simiduia , Sphingobium , Sphingomonadaceae , Sphingomonas , Stieleria , Vibrio and Xanthomonas . In this enriched subset, the family-level densities of genes targeting green macroalgae polysaccharides were considerably higher (n=231.6±68.5) than enzymes targeting brown (n=65.34±13.12) and red (n=30.5±10.72) polysaccharides. Within these organisms, an abundance of FabG genes was observed, suggesting that the fatty acid de novo synthesis pathway supplies (R)−3-hydroxyacyl-CoA or 3-hydroxybutyryl-CoA from core metabolic processes and is the predominant mechanism of PHA production in these organisms. Our results facilitate extending seaweed biomass valorization in the context of consolidated biorefining for the production of bioplastics.

Of the many topics generally taught in undergraduate or graduate optics courses, the propagation of light through crystals with electrical anisotropy is one of the most difficult topics for students and for teachers who do not work in this field. In particular, the mathematics and equations are complex vectorial equations, and this complicates the visualization of the implications of the theory. Also, the standard textbooks and papers on the subject have led to some misconceptions on this problem by presenting results only for specific cases of the theory in graphical form. For example, it is a general belief that after refraction of an incident wave on the crystal, the polarization state of the two waves propagating inside the crystal, given by their displacement vectors D, are always orthogonal to each other. However, this is not the case, as explained and illustrated for uniaxial crystals by Aleman-Castaneda and Rosete-Aguilar [J. Opt. Soc. Am. A 33(4), 677–682 (2016)]. The purpose of this paper is to help students and teachers visualize the solution to Maxwell's equations in electrical anisotropic crystals. An algorithm has been written in mathematica so the reader can use it to visualize the normal surface in uniaxial and biaxial crystals. This algorithm can be used as the basis of computational projects for students to better understand the equations involved, or as a visualization tool for teachers in class.

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a major component of munitions, is used extensively on military training ranges. As a result, widespread RDX pollution in groundwater and aquifers in the United States is now well documented. RDX is toxic, but its removal from training ranges is logistically challenging, lacking cost-effective and sustainable solutions. Previously, we have shown that thale cress (Arabidopsis thaliana) engineered to express two genes, xplA and xplB, encoding RDX-degrading enzymes from the soil bacterium Rhodococcus rhodochrous 11Y can break down this xenobiotic in laboratory studies. Here, we report the results of a 3-year field trial of XplA/XplB-expressing switchgrass (Panicum virgatum) conducted on three locations in a military site. Our data suggest that XplA/XplB switchgrass has in situ efficacy, with potential utility for detoxifying RDX on live-fire training ranges, munitions dumps and minefields. Switchgrass engineered to express two enzymes that degrade the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) detoxifies military sites contaminated with the munition when grown on these plots in a 3-year field trial.

Engineered plants can clean up pollution and recover technology-critical metals

The transmission properties of a photonic crystal immersed in several different oils have been characterized using terahertz time domain spectroscopy in the spectral range of 0.3–1.5 THz. As in previous works, oil samples can be distinguished using terahertz transmission measurements. When the same oils are introduced into a photonic crystal, we find that the effective refractive index of the photonic crystal is sensitive to the properties of the oils and shows differences not seen in bulk measurements. These effects are described in detail and have potential applications in both the sensing of very small volumes of oils and in the fine control of the refractive indices of photonic crystals.

Woody biomass represents an important source of carbon on earth, and its global recycling is highly dependent on Agaricomycetes fungi. White-rot Basidiomycetes are a very important group in this regard, as they possess a large and diverse enzymatic repertoire for biomass decomposition. Among these enzymes, the recently discovered lytic polysaccharide monooxygenases (LPMOs) have revolutionized biomass processing with their novel oxidative mechanism of action. The strikingly high representation of LPMOs in fungal genomes raises the question of their functional versatility. In this work, we studied an AA9 LPMO from the white-rot basidiomycete Pycnoporus sanguineus, PsAA9A. Successfully produced as a recombinant secreted protein in Pichia pastoris, PsAA9A was found to be a C1-specific LPMO active on cellulosic substrates, generating native and oxidized cello-oligosaccharides in the presence of an external electron donor. PsAA9A boosted cellulolytic activity of glysoside hydrolases from families GH1, GH5, and GH6.This study serves as a starting point towards understanding the functional versatility and biotechnological potential of this enzymatic family, highly represented in wood decay fungi, in Pycnoporus genus. KEY POINTS: • PsAA9A is the first AA9 from P. sanguineus to be characterized. • PsAA9A has activity on cellulose, producing C1-oxidized cello-oligosaccharides. • Boosting activity with GH1, GH5, and GH6 was proven.

To date, there is sparse information for the genus Robertkochia with Robertkochia marina CC-AMO-30DT as the only described member. We report here a new species isolated from mangrove soil collected at Malaysia Tanjung Piai National Park and perform polyphasic characterization to determine its taxonomic position. Strain CL23T is a Gram-negative, yellow-pigmented, strictly aerobic, catalase-positive and oxidase-positive bacterium. The optimal growth conditions were determined to be at pH 7.0, 30–37 °C and in 1–2 % (w/v) NaCl. The major respiratory quinone was menaquinone-6 (MK-6) and the highly abundant polar lipids were four unidentified lipids, a phosphatidylethanolamine and two unidentified aminolipids. The 16S rRNA gene similarity between strain CL23T and R. marina CC-AMO-30DT is 96.67 %. Strain CL23T and R. marina CC-AMO-30DT clustered together and were distinguished from taxa of closely related genera in 16S rRNA gene phylogenetic analysis. Genome sequencing revealed that strain CL23T has a genome size of 4.4 Mbp and a G+C content of 40.72 mol%. Overall genome related indexes including digital DNA–DNA hybridization value and average nucleotide identity are 17.70 % and approximately 70%, below the cutoffs of 70 and 95%, respectively, indicated that strain CL23T is a distinct species from R. marina CC-AMO-30DT. Collectively, based on the phenotypic, chemotaxonomic, phylogenetic and genomic evidences presented here, strain CL23T is proposed to represent a new species with the name Robertkochia solimangrovi sp. nov. (KCTC 72252T=LMG 31418T). An emended description of the genus Robertkochia is also proposed.

Background Efficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable manner is a prerequisite for its global acceptance as a feedstock in bioethanol production. This is achieved in nature by suites of enzymes with the capability of efficiently depolymerizing all the components of lignocellulose. Here, we provide detailed insight into the repertoire of enzymes produced by microorganisms enriched from the gut of the crop pathogen rice yellow stem borer (Scirpophaga incertulas). Results A microbial community was enriched from the gut of the rice yellow stem borer for enhanced rice straw degradation by sub-culturing every 10 days, for 1 year, in minimal medium with rice straw as the main carbon source. The enriched culture demonstrated high cellulolytic and xylanolytic activity in the culture supernatant. Metatranscriptomic and metaexoproteomic analysis revealed a large array of enzymes potentially involved in rice straw deconstruction. The consortium was found to encode genes ascribed to all five classes of carbohydrate-active enzymes (GHs, GTs, CEs, PLs, and AAs), including carbohydrate-binding modules (CBMs), categorized in the carbohydrate-active enzymes (CAZy) database. The GHs were the most abundant class of CAZymes. Predicted enzymes from these CAZy classes have the potential to digest each cell-wall components of rice straw, i.e., cellulose, hemicellulose, pectin, callose, and lignin. Several identified CAZy proteins appeared novel, having an unknown or hypothetical catalytic counterpart with a known class of CBM. To validate the findings, one of the identified enzymes that belong to the GH10 family was functionally characterized. The enzyme expressed in E. coli efficiently hydrolyzed beechwood xylan, and pretreated and untreated rice straw. Conclusions This is the first report describing the enrichment of lignocellulose degrading bacteria from the gut of the rice yellow stem borer to deconstruct rice straw, identifying a plethora of enzymes secreted by the microbial community when growing on rice straw as a carbon source. These enzymes could be important candidates for biorefineries to overcome the current bottlenecks in biomass processing.

Plasmonic photothermal therapy (PPTT), as an increasingly studied treatment alternative, has been widely regarded mostly as a surface tissue treatment choice. Although some techniques have been implemented for interstitial tumors, these involve some grade of invasiveness, as the outer skin is usually broken to introduce light-delivering optical fibers or even catheters. In this work, we present a potential non-invasive strategy using the stereotactic approach, long employed in radiosurgery, by converging multiple near infrared laser beams for PPTT in tissue-equivalent optical phantoms that enclose small gel spheres and simulate interstitial tissue impregnated with plasmonic nanoparticles. The real-time in-depth monitoring of temperature increase is realized by an infrared camera face-on mounted over the phantom. Our results show that a significant reduction in the surface heating can be achieved with this configuration while remarkably increasing the interstitial reach of PPTT, assuring a ∼ 6 ∘ C temperature increase for the simulated tumors at 10 mm depth and ∼ 4 ∘ C at 15 mm depth and opening up new possibilities for future clinical applications.

This work analyzes the effect of experimental errors and measurement noise on Mueller matrix channeled spectropolarimeters. The main advantage of this type of polarimeter is the independence on temporal resolution, as it can be used as a snapshot polarimeter. The simulation of the polarimeters with experimental errors and two published extraction methods of the sample Mueller matrix are also presented. The Mueller matrix channeled spectropolarimeter (MMCS) setup consists of a mirrored Stokes channeled spectropolarimeter (SCS) as the polarization states generator (PSG) and a SCS as the polarization states analyzer (PSA). The SCS setup comprises two thick birefringent retarders followed by a horizontal linear polarizer. The effects of the thickness ratio of the retarders, the global retardance factor, retardance errors, axes alignment errors, and additive Gaussian noise are further studied to optimize the MMCS setups. In this work, we do not include a calibration procedure to improve the measured Mueller matrix parameters, but we study the sensitivity of the polarimeter to different configurations and error sources.

We present a method for calibration and data extraction for a Stokes polarimeter working with three different wavelengths simultaneously. In the Stokes polarimeter considered in this work, we use two liquid crystal variable retarders (LCVRs) combined with a Glan–Thompson linear polarizer. A recently developed fitting calibration procedure is used. We use the same calibration samples and LCVR voltages for all three wavelengths, giving simultaneous measurement and calibration. We compare the performance of the polarimeter, after calibration, using four or six calibration samples in our experiment. To generate the four known calibration beams, we use a linear polarizer oriented at 130° and 30° with respect to the horizontal, a horizontal linear polarizer followed by a half-wave plate (at 632 nm) with its fast axis at 30°, and a horizontal linear polarizer followed by a quarter-wave plate (at 632 nm) with its fast axis at 30°. For calibration with six reference beams, we add two known calibration beams by setting the fast axis of the half- and quarter-wave plates at 130°. Experimental results show good agreement with the expected results, with the fitting calibration procedure giving an approximately 50% reduction in total RMS error with four calibration samples. There is a negligible reduction in the error when six calibration samples are used compared to the case with four samples.

Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. Here, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.

Background The quest for novel enzymes for cellulosic biomass-degradation has recently been focussed on lytic polysaccharide monooxygenases (LPMOs/PMOs), Cu-containing proteins that catalyse the oxidative degradation of otherwise recalcitrant polysaccharides using O2 or H2O2 as a co-substrate. Results Although classical saprotrophic fungi and bacteria have been a rich source of lytic polysaccharide monooxygenases (LPMOs), we were interested to see if LPMOs from less evident bio-environments could be discovered and assessed for their cellulolytic activity in a biofuel context. In this regard, the marine shipworm Lyrodus pedicellatus represents an interesting source of new enzymes, since it must digest wood particles ingested during its natural tunnel boring behaviour and plays host to a symbiotic bacterium, Teredinibacter turnerae, the genome of which has revealed a multitude of enzymes dedicated to biomass deconstruction. Here, we show that T. turnerae encodes a cellulose-active AA10 LPMO. The 3D structure, at 1.4 Å resolution, along with its EPR spectrum is distinct from other AA10 polysaccharide monooxygenases insofar as it displays a “histidine-brace” catalytic apparatus with changes to the surrounding coordination sphere of the copper. Furthermore, TtAA10A possesses a second, surface accessible, Cu site 14 Å from the classical catalytic centre. Activity measurements show that the LPMO oxidises cellulose and thereby significantly augments the rate of degradation of cellulosic biomass by classical glycoside hydrolases. Conclusion Shipworms are wood-boring marine molluscs that can live on a diet of lignocellulose. Bacterial symbionts of shipworms provide many of the enzymes needed for wood digestion. The shipworm symbiont T. turnerae produces one of the few LPMOs yet described from the marine environment, notably adding to the capability of shipworms to digest recalcitrant polysaccharides.

While the immediate effect of explosives in armed conflicts is frequently in the public eye, until recently, the insidious, longer-term corollaries of these toxic compounds in the environment have gone largely unnoticed. Now, increased public awareness and concern are factors behind calls for more effective remediation solutions to these global pollutants. Scientists have been working on bioremediation projects in this area for several decades, characterizing genes, biochemical detoxification pathways, and field-applicable plant species. This review covers the progress made in understanding the fundamental biochemistry behind the detoxification of explosives, including new shock-insensitive explosive compounds; how field-relevant plant species have been characterized and genetically engineered; and the major roles that endophytic and rhizospheric microorganisms play in the detoxification of organic pollutants such as explosives.

We present a new method to calculate the complex refractive index of spherical scatterers in a novel optical phantom developed by using homemade monodisperse silica nanospheres embedded into a polyester resin matrix and an ethanol–water mixture for applications in diffuse imaging. The spherical geometry of these nanoparticles makes them suitable for direct comparison between the values of the absorption and reduced scattering coefficients ( μ a and μ s ′ , respectively) obtained by the diffusion approximation solution to the transport equation from scattering measurements and those obtained by the Mie solution to Maxwell’s equations. The values of the optical properties can be obtained by measuring, using an ultrafast detector, the time-resolved intensity distribution profiles of diffuse light transmitted through a thick slab of the silica nanosphere phantom, and by fitting them to the time-dependent diffusion approximation solution to the transport equation. These values can also be obtained by Mie solutions for spherical particles when their physical properties and size are known. By using scanning electron microscopy, we measured the size of these nanospheres, and the numerical results of μ a and μ s ′ can then be inferred by calculating the absorption and scattering efficiencies. Then we propose a numerical interval for the imaginary part of the complex refractive index of S i O 2 nanospheres, n s , which is estimated by fixing the fitted values of μ a and μ s ′ , using the known value of the real part of n s , and finding the corresponding value of I m ( n s ) that matches the optical parameters obtained by both methods finding values close to those reported for silica glass. This opens the possibility of producing optical phantoms with scattering and absorption properties that can be predicted and designed from precise knowledge of the physical characteristics of their constituents from a microscopic point of view.

The use of refractometers to investigate the nature of liquids is very common. Here it is shown that surface relief diffraction gratings can be used to measure the refractive index of liquids. Calibration plots showing the relation between first order intensity as a function of refractive index are shown. We also developed a microfluidic device behaving as a grating which is used as refractometer where a very small amount of liquid (microliters) is used.

Variations of the induced retardance in the aperture of liquid-crystal variable retarders LCVR and spatial light modulators LC-SLM are measured. It is found that the induced retardance, in LCVR, shows variations over the aperture which depend on the wavelength of the light used and the voltage applied. Larger retardance variations appear near to the edges of the cell. There are also larger variations in the maximum and minimum unwrapped retardances in the retardance versus voltage curves. These voltage values and the edges positions of the cells should be avoided in applications of these devices. On the other hand, the induced retardance is calculated pixel by pixel in LC-SLM. For the same gray level over the entire LC-SLM screen, there are differences in the induced retardance between pixels located in a central area and pixels located in the edges. For correct calibration of the LC-SLM, the retardance value as a function of gray level was determined, pixel by pixel.

The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, &beta, xylosidase, and &beta, glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.

The eco-evolutionary dynamics of microbial communities are predicted to affect both the tempo and trajectory of evolution in constituent species [1]. While community composition determines available niche space, species sorting dynamically alters composition, changing over time the distribution of vacant niches to which species adapt [2], altering evolutionary trajectories [3, 4]. Competition for the same niche can limit evolutionary potential if population size and mutation supply are reduced [5, 6] but, alternatively, could stimulate evolutionary divergence to exploit vacant niches if character displacement results from the coevolution of competitors [7, 8]. Under more complex ecological scenarios, species can create new niches through their exploitation of complex resources, enabling others to adapt to occupy these newly formed niches [9, 10]. Disentangling the drivers of natural selection within such communities is extremely challenging, and it is thus unclear how eco-evolutionary dynamics drive the evolution of constituent taxa. We tracked the metabolic evolution of a focal species during adaptation to wheat straw as a resource both in monoculture and in polycultures wherein on-going eco-evolutionary community dynamics were either permitted or prevented. Species interactions accelerated metabolic evolution. Eco-evolutionary dynamics drove increased use of recalcitrant substrates by the focal species, whereas greater exploitation of readily digested substrate niches created by other species evolved if on-going eco-evolutionary dynamics were prevented. Increased use of recalcitrant substrates was associated with parallel evolution of tctE, encoding a carbon metabolism regulator. Species interactions and species sorting set, respectively, the tempo and trajectory of evolutionary divergence among communities, selecting distinct ecological functions in otherwise equivalent ecosystems.

The World Health Organization reported that “an estimated 12.6 million people died as a result of living or working in an unhealthy environment in 2012, nearly 1 in 4 of total global deaths”. Air, water and soil pollution were the significant risk factors, and there is an urgent need for effective remediation strategies. But tackling this problem is not easy; there are many different types of pollutants, often widely dispersed, difficult to locate and identify, and in many cases cost-effective clean-up techniques are lacking. Biology offers enormous potential as a tool to develop microbial and plant-based solutions to remediate and restore our environment. Advances in synthetic biology are unlocking this potential enabling the design of tailor-made organisms for bioremediation. In this article, we showcase examples of xenobiotic clean-up to illustrate current achievements and discuss the limitations to advancing this promising technology to make real-world improvements in the remediation of global pollution.

We developed two versions of refractometers to measure the refractive index of liquids. One refractometer comprises a glass cell with a surface relief grating on the inner face of one of its walls, while the other one is a microfluidic channel in the form of serpentine that behaves as a grating. Measurements of the liquid refractive index were performed by sensing the first order intensity. Several liquids have been used including an organic one. Calibration plots are shown.

We present a method for using liquid-crystal variable retarders (LCVRs) with continually varying voltage to measure, both, the Stokes vector of a light beam and the complete Mueller matrix of a general sample.

Background Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify novel biocatalysts that could improve industrial lignocellulose conversion. Results In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. Conclusions This study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation. Electronic supplementary material The online version of this article (10.1186/s13068-017-0944-4) contains supplementary material, which is available to authorized users.