Biomass Spectra Research Articles

Nematodes as biological indicators of urban heat island effects in the Chongqing area urban green spaces

The urban heat island effect (UHIE) is defined as the tendency of urban regions to have higher temperatures than suburbs in their immediate vicinity. A better understanding of UHIE and its biological indicators facilitates the prediction of ecological changes, which is particularly important due to ongoing global warming. To determine whether soil nematodes may serve as biological indicators of UHIE, we compared soil nematode communities under three urban green spaces, namely, urban cold islands (CI), urban heat island transition regions (HIT), and urban heat islands (HI). Distinct soil nematodes characteristics were found in the 3 urban green spaces. In addition, seasonal variations in community composition were identified. Among the 30 nematode genera identified, Eucephalobus was the most dominant in CI and HIT, while Monhystera was the most dominant in HI. The mean nematode abundance significantly differed (p ≤ 0.01) between CI (322 ± 24 individuals/100 g dry soil), HIT (112 ± 9 individuals/100 g dry soil), and HI (107 ± 10 individuals/100 g dry soil). We found that UHIE had detrimental effects on the nematode community structure (i.e., abundance and Margalef, Shannon-Wiener, and Simpson diversity indices) and ecological function [Free-living Nematode Maturity Index (MI), Nematode Channel Ratio (NCR), Enrichment Index (EI), and Structure Index (SI)]. These detrimental effects were reflected in nematode community structure indices, which were all highest in CI and lowest in HI, as well as in MI and SI, which were lower in HI than in CI. Furthermore, nematodes found in HI were shorter (L = 502.15 μm), thinner (W = 38.42 μm), and exhibiting higher length-to-width ratios (L:W) (15.83) compared to nematodes found in CI (L = 986.13 μm, W = 83.58 μm, L:W: 12.24) and HIT (L = 786.80 μm, W = 58.88 μm, L:W: 14.82). Nematode biomass spectra (NBS) shifted towards smaller biomass classes in HI compared to CI, while nematodes of the HIT showed intermediary spectra, further confirming the detrimental effects of UHIE on the soil nematode community. Regarding the physicochemical properties of the 3 green spaces, CI was found to have the highest soil pH, moisture, organic carbon content, total nitrogen content, and available potassium content, while HI had the lowest. Soil physicochemical characteristics were inversely correlated with soil temperature, except for available soil phosphorus, which was positively corrected with temperature. We also found that soil characteristics were significantly correlated with nematode community structure and ecological function, suggesting that the effects of UHIE on soil nematodes could have been indirectly affected by changes in soil physicochemical characteristics.

Heavy Metal Tolerance of Microorganisms Isolated from Coastal Marine Sediments and Their Lead Removal Potential.

In this study, 338 microorganisms, comprising 271 bacteria and 67 fungi, were isolated from sediment samples collected from underexplored Pacific and Caribbean regions of Colombia. Screening trials were conducted on selected strains (n = 276) to assess their tolerance to cadmium (Cd2+), lead (Pb2+), and zinc (Zn2+), leading to the identification of six bacteria capable of withstanding 750 mg·L-1 of each heavy metal ion. Three promising microorganisms, identified as Enterobacter sp. INV PRT213, Pseudomonas sp. INV PRT215, and Stenotrophomonas sp. INV PRT216 were selected for lead removal experiments using LB broth medium supplemented with 400 mg·L-1 Pb2+. Among these, Pseudomonas sp. INV PRT215 exhibited significant potential, removing 49% of initial Pb2+ after 240 min of exposure (16.7 g wet biomass·L-1, pH 5, 30 °C). Infrared spectra of Pb-exposed biomass showed changes in functional groups, including carbonyl groups of amides, carboxylate, phosphate, hydroxyl, and amine groups, compared to the not-exposed control. These changes suggested interactions between the metal and functional groups in the biomass. The findings of this study highlight the potential of microorganisms derived from coastal marine environments as promising candidates for future applications in bioremediation of polluted environments contaminated with heavy metals.

Textile wastewater phytoremediation using Spirodela polyrhiza (L.) Schleid. assisted by novel bacterial consortium in a two-step remediation system

The study aims at developing a phyto-microremediation system for textile wastewater treatment using Spirodela polyrhiza (L.) Schleid. and a consortium of bacterial strains isolated from textile wastewater-contaminated matrices and rhizosphere of S. polyrhiza. The sequential phyto-microremediation of textile wastewater was carried out utilizing two-stage phyto-microremediation systems I [phytoremediation system (Stage 1) preceded microremediation system (Stage 2)] and II [microremediation system (Stage 1) preceded phytoremediation system (Stage 2)]. Pseudomonas stutzeri, Janibacter anophelis, Bacillus safensis, Bacillus pumilus, Bacillus thuringiensis, and Bacillus cereus constituted the bacterial consortium that was involved in the microremediation of textile wastewater. Biochemical characterization of Spirodela on exposure to untreated textile wastewater showed cadmium and nickel uptake as 26.03 and 22.99 mg g−1 dw−1. S. polyrhiza exhibited anatomical changes like distortion in the structure of the xylem, phloem, lower epidermis, and increased aerenchyma formation when remediating textile wastewater. The textile wastewater bioremediation in phyto-microremediation system I gives final reduction of COD 77.36%, color 91.70%, calcium 61.65%, iron 69.41%, nickel 89.30%, cadmium 88.37%, nitrate 70.83%, phosphate 73.11%, and sulfate 75.49%. Further, LC-MS analysis of treated wastewater from phyto-microremediation system I have shown biotransformation of metabolites into simpler compounds like 2-{Bis [4-(2-cyanophenoxy)phenyl]methyl}benzoic acid (C34H22N2O4). The FTIR spectrum of bacterial biomass exposed to textile wastewater exhibits substantial shifts of various bands in the IR region for functional groups such as alcohol, alkene, esters, azide, and amine as compared to non-exposed biomass.

Effect of enzymes adsorption on enzymatic hydrolysis of coffee silverskin: Kinetic characterization and validation

The use of waste lignocellulose feedstock for sugar-based biorefineries is attracting the interest of the scientific and industrial communities. The aim is to develop efficient sustainable processes to produce fuels and chemicals via the biotechnological route. However, the rational design of processes aimed at fermentable sugar recovery from lignocellulosic wastes asks for reliable quantitative data of a wide spectrum of biomass. Waste biomasses from food industries are among the most studied potential carbon sources. In the present study, the kinetics of enzymatic hydrolysis of coffee silverskin has been characterized. Coffee silverskin is one of the most abundant fractions of the coffee industry waste and it has been already used for saccharification purposes. The experimental investigation provided kinetic parameters of a semi-mechanistic model of glucose production rate from coffee silverskin catalyzed by a commercial cellulase cocktail. In addition, the adsorption of the enzymes on the solid biomass substrate has been characterized according to a Langmuir type model. The effect of enzymes adsorption on cellulose conversion and the process dynamics have been highlighted by validation tests. The optimization of biocatalyst use has been provided via a two-step hydrolysis procedure. The developed procedure can be successfully applied in the future to several biomasses to describe a wide range of possible substrates.

Assessment of benthic environmental disturbance in the Ba Lai estuary using the nematode biomass spectra

The researchs on the biomass spectra - a functional characteristic of biotic communities is still limited. In this study, the nematode biomass spectra in the bottom of Ba Lai estuary was investigated at six subtidal stations from the sea toward the upstream. The result showed that nematode biomass spectra ranged between -8 and 1 being significantly different between stations, and the lowest biomass of those spectras was in station BL4 (< 2 µg) which is upwardly closed to the Ba Lai dam. BL4 was also characterized by the lowest nematode abundance in the studied area. In addition, station BL3 downwardly closed to the dam exhibited low number of individuals. The heterogeneity in the nematode biomass spectra of BL3 and BL4 might due to the disturbance in the sedimentary environment of Ba Lai estuary related to the dam impact. This research again supports the important role of biomass spectra as bioindicator tool for biomonitoring and environmental quality assessment. Therefore, applying nematode biomass spectra is recommended for environmental assessment due to their advantages such as timesaving, not taxonomical expertise-requirement.

High Dynamic Range in Entomological Scheimpflug Lidars

Minimizing insecticide use, preventing vector diseases and facilitating biodiversity assessments are suitable applications of recent advances in photonic insect surveillance and entomological lidar. The tools also comprise a new window into fundamental aspect of the fascinating life and ecology of insects and their predators in situ. At the same time, it is evident that lidars are subject to finite detection range given by the instrument noise and saturation levels, and therefore, intervals of the biomass spectra are sectioned at different ranges. The Scheimpflug lidar allows an interesting trade-off between high sample rate and low pulse energy for retrieving wing beat harmonics and slow sample rates with high pulse energy for detecting small species far away. In this paper, we review and revise calibration, sizing and associated deficiencies, and report count rates to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> insects/minute up to 2 km range. We investigate if and how high dynamic range can be exploited in entomological lidar and also how fast and slow sample rates could complement each other and capture a wider span of the biomass spectrum. We demonstrate that smaller insect can be detected further away by long exposures and show consistency between the captured biomass size spectra. However, we find unexpected discrepancies between short and long exposures in the range distributions. We found that vertebrates as well as specular insects can saturate signals. Error sources and limitations are elaborated on.

Microalgal consortia technology: A novel and sustainable approach of resource reutilization, waste management and lipid production

The present study was conducted to assess the efficiency of naturally growing competent microalgal consortia (Chlorella vulgaris, Chlorococcum humicola and Nannochloropsis sp.) in the waste remediation of sewage water and lipid production. Results showed that microalgal consortia during wastewater (WW) treatment efficiently utilized the inorganic nutrients (N and P) and exhibited higher growth, biomass and photosystem II activity (Fv/Fo, Fv/Fm, Mo, ETo/RC and PiAbs) as compared to respective individual algal species. SEM data showed clumped morphology and 16.21% increases in the cell size treated with WW. The wastewater treated with microalgal consortia showed reduction in physicochemical parameters viz., conductivity (19.24%), NO3−1 (68.55%), PO4−3 (55.99%), TS (41.31%), TSS (35.48%), TDS (53.32%) and BOD (66.85%) after 15d of treatment. The FTIR spectra (4000–3400 cm −1) of algal biomass generated in BG-11 nutrient solution (NS) and wastewater showed higher absorption representing –OH compounds as compared to tap water. Further, the high IR spectral peak length ratio of L/C in microalgal consortia treated with WW exhibited greater lipid accumulation which could be used in the bioenergy production in sustainable way. Thus, species richness and complementary association of algae may be a better solution with multiple benefits of waste reutilization, phycoremediation and lipid yield.

A modified niche model for generating food webs with stage-structured consumers: The stabilizing effects of life-history stages on complex food webs.

Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life‐history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life‐history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies.We extended the niche model developed by Williams and Martinez (Nature, 2000, 404, 180–183) to generate food webs that included trophic species with a life‐history stage structure. Our method aggregated trophic species based on niche overlap to form a life‐history structured population; therefore, it largely preserved the topological structure of food webs generated by the niche model. We applied the theory of allometric predator–prey body mass ratio and parameterized an allometric bioenergetic model augmented with biomass flow between stages via growth and reproduction to study the effects of a stage structure on the stability of food webs.When life‐history stages were linked via growth and reproduction, more food webs persisted, and persisting food webs tended to retain more trophic species. Topological differences between persisting linked and unlinked food webs were small to modest. The slopes of biomass spectra were lower, and weak interaction links were more prevalent in the linked food webs than the unlinked ones, suggesting that a life‐history stage structure promotes characteristics that can enhance stability of complex food webs.Our results suggest a positive relationship between the complexity and stability of complex food webs. A life‐history stage structure in food webs may play important roles in dynamics of and diversity in food webs.

Biodegradation of low-density polyethylene (LDPE) using the mixed culture of Aspergillus carbonarius and A. fumigates

Low-density polyethylene (LDPE) possesses various applications in several industries owing to its durability, low-cost, and many mechano-thermal properties. Unfortunately, LDPE waste creates an environmental threat. The level of biodegradation of black LDPE sheets with fungi isolated from different landfills sites in Sharqiyah Governorate, Egypt, was evaluated. LDPE sheets, the only source of carbon, along with minimal salt medium were incubated on a rotary shaker at 30 °C and 120 rpm for 16 weeks. Aspergillus carbonarius MH 856457.1 and A. fumigatus MF 276893 confirmed to be good candidates for LDPE biodegradation. A mixed culture of two strains showed the excellent weight loss% of sheets as compared to single isolate. Further efforts to improve the degrading capacity through physical and chemical treatments were performed. The biodegradation was significantly stimulated by 39.1% (thermal treatment), 17.76% (HNO3 treatment), and 5.79% (Gamma-irradiation treatment). Laccases and manganese peroxidases activities were assayed. LDPE biodegradation was analyzed by scanning electronic microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and gas chromatography–mass spectrometry (GC–MS). FTIR spectra showed the appearance of new functional groups assigned to hydrocarbon biodegradation and confirmed the role of manganese peroxidase in process. The changes in the FTIR spectra of the mixed culture biomass before and after the biodegradation (Δ73 cm−1) and the surface changes in the biodegraded LDPE (as indicated from SEM) confirmed the depolymerization of LDPE. From GC–MS analysis, the plasticizers bis(2-ethylhexyl) phthalate, Diisssctyl phthalate, 1,2-benzenedicarboxylic acid diisooctyl ester, and tributyl acetylcitrate completely biodegraded. Moreover, several antioxidants, antimicrobial, and anticancer compounds, and methyl esters of fatty acids were produced.

Features of iron accumulation at high concentration in pulcherrimin-producing Metschnikowia yeast biomass.

In previous studies it was found that the antimicrobial properties of pulcherrimin-producing Metschnikowia species are related to the formation of a red pigment-pulcherrimin and sequestration of free iron from their growth medium. For strains of Metschnikowia pulcherrima, M. sinensis, M. shaxiensis, and M. fructicola, at a high, ≈80mg/kg, elemental Fe concentration in agar growth media we observed the essentially different (metal luster, non-glossy rust like, and colored) yeast biomass coatings. For the studied strains the optical and scanning electron microscopies showed the increased formation of chlamydospores that accumulate a red pigment-insoluble pulcherrimin rich in iron. The chlamydospore formation and decay depended on the iron concentration. In this study pulcherrimin in biomass of the selected Metschnikowia strains was detected by Mössbauer spectroscopy. At ≈80mg/kg elemental Fe concentration the Mössbauer spectra of biomass of the studied strains were almost identical to these of purified pulcherrimin. Iron in pulcherrimin reached ≈1% of biomass by weight which is very high in comparison with elemental Fe percentage in growth medium and is not necessary for yeast growth. The pulcherrimin in biomass was also observed by Mössbauer spectroscopy at lower, ≈5mg/kg, elemental Fe concentration. Through chemical binding of iron pulcherrimin sequestrates the soluble Fe in the growth media. However, at high Fe concentrations, the chemical and biochemical processes lead to the pulcherrimin accumulation in biomass chlamydospores. When soluble iron is sequestrated or removed from the growth media in this way, it becomes inaccessible for other microorganisms.

Characterization of biomass produced by Candida tropicalis ASY2 grown using sago processing wastewater for bioenergy applications and its fuel properties

The cost of biodiesel production and the requirement of raw ingredients are the primary constraints that need to be addressed while searching for viable alternative fuels to petrol and diesel. Oleaginous yeasts are gaining wider acceptance as biofuel candidates among oil-rich crops/microbes. The present investigation aimed to integrate the agro-industrial wastewater stream as a nutrient source for the cultivation of oleaginous yeast and to use the resultant biomass and lipid as a feedstock for biofuel synthesis. The yeast biomass grown in sago processing wastewater contained 7.21% moisture content, 69.01% volatile matter, 12.61% fixed carbon, and 11.16% ash content. The ultimate analysis determined the contents of carbon (40.43%), nitrogen (5.14%), hydrogen (4.62%), sulfur (0.54%), and oxygen (49.27%). The heating value of yeast biomass was 16.54 MJ kg−1. The thermal behavior of yeast biomass also suggests its potential use as an energy source. The FTIR spectrum of biomass had major lipid (3030–2800 cm−1 and 1500–1350 cm−1) and carbohydrate (1250 cm−1 and 1000 cm−1) functional peaks. Further FAME profiling revealed that the yeast biomass is primarily composed of stearic, oleic, linoleic, and linolenic acids, similar to the vegetable oils. The fuel characteristics of yeast biodiesel (SV, 168.87 mg KOH g−1; IV, 120 mg I2 100 g−1; CN, 61.79; and KV, 3.16 mm2 s−1) are also within the ASTM standard limits, suggesting that yeast biomass could be a sustainable and economically viable feedstock for both solid and liquid biofuel production.

Effect of ultrasonic vibration-assisted pelleting of biomass on biochar properties

The objective of this research was to investigate the potential of ultrasonic vibration-assisted (UV-A) pelleting as pretreatment method to produce biochar with desired properties. In this study, poplar (PP), switchgrass (SG), and wheat straw (WS) were pretreated with UV-A pelleting process, then the biochar were produced in a muffle at atmosphere condition with a highest temperature treatment (HTT) at 300, 500, and 700 °C, respectively. Ultrasonic power had an obvious effect on the biochar yield and pH, a higher biochar yield and biochar pH were obtained from PP00, SG50, and WS50 and PP50, SG50, and WS00, respectively. The FTIR spectra showed that O–H stretching, C–H stretching, carbonyl bonds/CO stretching, C–H stretching, C–O–C, and C–C stretching were found in spectra of UV-A pretreated biomass, while disappeared in spectra of biochar, indicating the changes of functional groups. Although UV-A pelleting pretreatment did not show considerable effect on the C, H, N, and S content of biochar (less than 2%) under the same HTT, the formation of multi-layer and porous structure was observed on biochar surface. The specific surface area, micropore surface area, and total pore volume of biochar from UV-A pelleting increased with increasing of ultrasonic power. In addition, HTT and type of biomass also had different functions on the biochar properties. The results of this study showed that UV-A pelleting pretreatment has a great potential to produce biochar with desired chemical structures and physical properties.

Lithium Biosorption by Arthrospira (Spirulina) Platensis Biomass

Abstract The biosorption of lithium from batch systems by Arthrospira (Spirulina) platensis biomass was studied. Adsorption capacity of the biosorbent was investigated as a function of contact time, initial metals concentration and pH values. Lithium content in biomass was determined using Proton Induced Gamma Emission technique. The ability of spirulina biomass for lithium biosorption showed a maximum at the pH = 11. Equilibrium data fitted well with the Langmuir model with maximum adsorption capacity of 1.75 mg/g, while the kinetic data were best described using the pseudo second-order kinetic model. The IR spectrum of the Li-loaded biomass revealed that lithium ions could be primarily bind to –OH, –COOH, –NH, –NH2, and –NH3 groups present on biosorbent surface. Arthrospira platensis biomass could be applied as environmentally friendly sorbent for lithium removal from wastewater.

Thermal degradation and pyrolysis kinetics of two Indian rice husk varieties using thermogravimetric analysis

ABSTRACT Agricultural crop residues are making significant inroads in the broad spectrum of lignocellulosic biomass for energy recovery and in realizing prospective potential of bio-based economy. In the present work, comprehensive physicochemical characterization of two rice husk varieties (RH-B and RH-P) of Indian origin, their thermal degradation behavior, and pyrolysis kinetics were studied via thermogravimetric analysis. Thermogravimetric experiments were conducted at five heating rates, viz. 2, 5, 10, 15 and 20°C/min. The activation energy for the thermal decomposition was calculated using Coats–Redfern and Distributed Activation Energy Model (DAEM) method. The ash content was found to be significantly less in RH-P (10.17 wt%) vis-a-vis RH-B (20.07 wt%) which infers that there will be fewer residues left after pyrolysis as compared to RH-B. The cellulose and hemicellulose contents put together was high in RH-P (60.1 wt%) as compared to RH-P (56.92 wt%), which was reflected in terms of average weight loss of 55.15% and 41.863% for RH-P and RH-B, respectively, just above 230ºC due to rapid decomposition. The maxima of the f(E) curve was found to appear at 192.77 kJ/mol and 229.12 kJ/mol for the RH-B and RH-P, respectively. The experimental data for the pyrolysis of RH-B and RH-P were found to fit well with the Ginstling–Brounshtein diffusion model from amongst various solid-state kinetic models.

Detrital food chain as a possible mechanism to support the trophic structure of the planktonic community in the photic zone of a tropical reservoir

espanolEn la zona fotica de los ecosistemas acuaticos, donde coexisten diferentes componentes de la comunidad con diferentes estrategias para acceder a uno o diferentes recursos, el espectro de biomasa puede describir las transferencias alimenticias y sus eficiencias. El proposito de este trabajo es describir el espectro de biomasa y la eficiencia de transferencia, desde los productores primarios hasta los principales depredadores de la red trofica, en la zona fotica del embalse de Riogrande II. Los datos utilizados en el modelo del espectro de biomasa se tomaron de varias investigaciones realizadas en este embalse entre 2010 y 2013. El analisis de los resultados de la pendiente del espectro de biomasa, de las eficiencias de transferencias, y de los indices omnivoria, sugieren que la mayoria de la produccion primaria en la zona fotica del embalse Riogrande II es escasamente utilizada directamente por los consumidores primarios, y parece que los flujos de masa detriticos son una forma indirecta de canalizar esta produccion hacia el zooplankton. De acuerdo con esto, las eficiencias optimas en la transferencia de masa entre productores y consumidores reflejadas por la pendiente del espectro de biomasa (cercana a -1), no se deben necesariamente a la cadena de pastoreo, sino que pueden ser el resultado del acoplamiento entre varias rutas alimenticias (detritica y pastoreo) que comienzan con la produccion primaria EnglishIn the photic zone of aquatic ecosystems, where different communities coexist showing different strategies to access one or different resources, the biomass spectra can describe the food transfers and their efficiencies. The purpose of this work is to describe the biomass spectrum and the transfer efficiency, from the primary producers to the top predators of the trophic network, in the photic zone of the Riogrande II reservoir. Data used in the model of the biomass spectrum were taken from several studies carried out between 2010 and 2013 in the reservoir. The analysis of the slope of a biomass spectrum, of the transfer efficiencies, and the omnivory indexes, suggest that most primary production in the photic zone of the Riogrande II reservoir is not directly used by primary consumers, and it appears that detritic mass flows are an indirect way of channeling this production towards zooplankton. Accordingly, the optimal efficiencies in mass transfer between producers and consumers reflected by the slope of the biomass spectrum (close to -1), are not necessarily linked to the grazing chains, but may be the result of the coupling between several food routes (detritic and grazing) that start with primary production

Targeting GRP78-dependent AR-V7 protein degradation overcomes castration-resistance in prostate cancer therapy.

Rationale: Androgen receptor splice variant 7 (AR-V7) is a leading cause of the development of castration-resistant prostate cancer (CRPC). However, the regulation and function of AR-V7 at levels of post-translational modifications in prostate cancer therapy remain poorly understood. Here, we conducted a library screen of natural products to identify potential small molecules responsible for AR-V7 protein degradation in human prostate cancer cell lines.Methods: A natural product library was used to screen the inhibitor of AR-V7. Co-IP and biomass spectrum assays were used to identify the AR-V7-interacting proteins, whereas western blot, confocal microscopy, RNA interfering, and gene transfection were used to validate these interactions. Cell viability, EDU staining, and colony formation assays were employed to detect cell growth and proliferation. Flowcytometry assays were used to detect the distribution of cell cycle. Mouse xenograft models were used to study the anti-CRPC effects in vivo.Results: This screen identified rutaecarpine, one of the major components of the Chinese medicine Evodia rutaecarpa, as a novel chemical that selectively induces AR-V7 protein degradation via K48-linked ubiquitination. Mechanically, this effect relies on rutaecarpine inducing the formation of a GRP78-AR-V7 protein complex, which further recruits the E3 ligase SIAH2 to directly promote the ubiquitination of AR-V7. Consequently, the genetic and pharmacological activation of the GRP78-dependent AR-V7 protein degradation restores the sensitivity of castration-resistant prostate cancer to anti-androgen therapy in cell culture and animal models.Conclusions: These findings not only provide a new approach for overcoming castration-resistance in prostate cancer therapy, but also increase our understanding about the interplay between molecular chaperones and ubiquitin ligase in shaping protein stability.

Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5.

In skin, Cutibacterium acnes (former Propionibacterium acnes) can behave as an opportunistic pathogen, depending on the strain and environmental conditions. Acneic strains of C. acnes form biofilms inside skin–gland hollows, inducing inflammation and skin disorders. The essential exogenous products of C. acnes accumulate in the extracellular matrix of the biofilm, conferring essential bacterial functions to this structure. However, little is known about the actual composition of the biofilm matrix of C. acnes. Here, we developed a new technique for the extraction of the biofilm matrix of Gram-positive bacteria without the use of chemical or enzymatic digestion, known to be a source of artifacts. Our method is based on the physical separation of the cells and matrix of sonicated biofilms by ultracentrifugation through a CsCl gradient. Biofilms were grown on the surface of cellulose acetate filters, and the biomass was collected without contamination by the growth medium. The biofilm matrix of the acneic C. acnes RT5 strain appears to consist mainly of polysaccharides. The following is the ratio of the main matrix components: 62.6% polysaccharides, 9.6% proteins, 4.0% DNA, and 23.8% other compounds (porphyrins precursors and other). The chemical structure of the major polysaccharide was determined using a nuclear magnetic resonance technique, the formula being →6)-α-D-Galp-(1→4)-β-D-ManpNAc3NAcA-(1→6)-α-D-Glcp-(1→4)-β-D-ManpNAc3NAcA-(1→3)-β-GalpNAc-(1→. We detected 447 proteins in the matrix, of which the most abundant were the chaperonin GroL, the elongation factors EF-Tu and EF-G, several enzymes of glycolysis, and proteins of unknown function. The matrix also contained more than 20 hydrolases of various substrata, pathogenicity factors, and many intracellular proteins and enzymes. We also performed surface-enhanced Raman spectroscopy analysis of the C. acnes RT5 matrix for the first time, providing the surface-enhanced Raman scattering (SERS) profiles of the C. acnes RT5 biofilm matrix and biofilm biomass. The difference between the matrix and biofilm biomass spectra showed successful matrix extraction rather than simply the presence of cell debris after sonication. These data show the complexity of the biofilm matrix composition and should be essential for the development of new anti-C. acnes biofilms and potential antibiofilm drugs.

Fitting methods and seasonality effects on the assessment of pelagic fish communities in Daya Bay, China

Abstract The general relationship indicating that biomass decreases with individual body size is referred to as size spectra. This is consistent with the power law that characterizes size frequency distributions. While many previous studies have used the estimated exponent in size spectra as a metric to assess external perturbations, limited empirical studies have focused on the fitting methods. Here, we compared the effects caused by fitting methods and distribution models based on one-year pelagic fish data from Daya Bay, China. Our empirical results showed that maximum likelihood estimation (MLE) is more suitable than traditional normalized biomass spectra (NBS), and that a power law is not always the best model when using MLE. Moreover, we found significant size structure variation in different seasons. Principal component analysis (PCA) and linear mixed effects model (LMM) results showed that temperature was the major factor in seasonal environmental variation, and fish migration might be the essential response strategy causing size structure changes. The estimated exponents and nonlinear structure indicated that the Daya Bay is under intensive human impact. Our results suggest that MLE methods are recommended in future size-based studies, and that environmental variation and migration patterns are crucial in understanding seasonal community structure changes.

Comprehensive Kinetic Study on the Pyrolysis and Combustion Behaviours of Five Oil Palm Biomass by Thermogravimetric-Mass Spectrometry (TG-MS) Analyses

Thermochemical conversion process is one of the most promising routes to harness the potential of oil palm biomass as renewable energy alternative in Malaysia. Despite this potential, there is a lack of comprehensive study that characterises the complete spectrum of oil palm biomass. In this work, thermogravimetric-mass spectrometry (TG-MS) results of five oil palm biomass, i.e., oil palm trunk (OPT), palm kernel shell (PKS), oil palm frond (OPF), mesocarp fibre (MF) and empty fruit bunch (EFB), in pyrolysis and combustion conditions are presented and analysed. Kinetic studies on the TG data of these biomass were performed using Coats–Redfern integral method and Sestak–Berggren function to determine the activation energy and the reaction mechanism at different thermal decomposition stages. Pyrolysis of hemicellulose, cellulose, and lignin occurs at 140–331, 235–435, and 380–600 °C, respectively, while combustion of hemicellulose, cellulose, and lignin took place at 140–313, 225–395, and 372–600 °C, respectively. The activation energy was the highest for cellulose decomposition in both pyrolysis and combustion cases. Phase boundary reaction dominated during hemicellulose and cellulose decompositions, while nucleation dominated during lignin decomposition and char oxidation. MS results show that majority of the gases came out between 250 and 600 °C, mainly from CH4 and H2O in pyrolysis case and from CH4, CO2 and H2O in combustion case. Other than these major gases, NO, NO2 and SO2 were also generated although in much lower proportion compared to these gases. Based on TG-MS results, the best potential application for each biomass was also identified where OPT and OPF are suggested for gasification and fermentation, PKS for bio-char production and combustion, MF for bio-oil production, combustion, and bio-char production and EFB for bio-oil and bio-char production.

Metabolic response of bacteria to elevated concentrations of glyphosate-based herbicide

Glyphosate-based herbicides (GBHs) are the most widespread commonly used broad-spectrum herbicides that contaminate soils and waters, are toxic to bacteria, plants and animals, and have been classified as ‘probably carcinogenic to humans’ by the International Agency for Research on Cancer in 2015. Particular soil bacteria and fungi can degrade GBHs, hence, search for new GBH-degrading strains or microbial consortia, effective under specific growth conditions and local environment, seems to be a promising solution for bio-remediation of glyphosate-contaminated environment. Consequently, there is a need for rapid and informative methods to evaluate the GBH-induced changes of the metabolic pathways in cells, that may serve as indicators of GBH-degrading potential.Three new GBH-degrading bacterial strains, Pseudomonas sp., Actinobacteria and Serratia sp. were isolated from sludge of municipal waste water treatment plant (Daugavgriva, Riga, Latvia), agricultural soil and plant tissue, respectively. This study examined the response of these isolates to elevated concentrations of glyphosate (GLP) (100 and 500 mg/L) in GBH Klinik® 360 SL. The GBH-induced shift of metabolic activity in cells of Pseudomonas sp. was shown by tests on EcoPlates™. Fourier transform infrared (FTIR) spectroscopy analyses were used to evaluate the metabolomic response of bacteria to elevated concentrations of GBH in the growth environment. The spectra of Pseudomonas sp. and Serratia sp., incubated with and without GBH, were similar, thus indicating their GBH-resistance. The absorption at 1736 cm−1, assigned to ester carbonyl stretch vibrations, was detected in spectra of all three bacteria. The highest ester content was detected in Actinobacteria grown in medium with 1.0% molasses and 100 or 500 mg/L GLP in GBH Klinik®. An increase of cellular amounts of esters, either those of phospholipids or poly-β-hydroxybutyrates, indicates degradation of GLP. Therefore, monitoring the ester carbonyl stretch vibration band in FTIR spectra of bacterial biomass may speed up the search GBH-degrading strains. Microbiological tests and cell metabolic response studies by FTIR spectroscopy showed that the three new isolates of Pseudomonas sp., Actinobacteria and Serratia sp. were resistant to elevated concentrations of GBH Klinik® in growth environment and exhibited the potential for GBH degradation.