scholarly journals Assessing the Diversity and Metabolic Potential of Psychrotolerant Arsenic-Metabolizing Microorganisms From a Subarctic Peatland Used for Treatment of Mining-Affected Waters by Culture-Dependent and -Independent Techniques

2021 ◽  
Vol 12 ◽  
Author(s):  
Aileen Ziegelhöfer ◽  
Katharina Kujala
Keyword(s):  
Arsenic Removal ◽  
Physiological Activity ◽  
Cold Climate ◽  
Model Systems ◽  
Metabolic Potential ◽  
Rare Biosphere ◽  
Starting Point ◽  
Mine Effluent ◽  
Culture Dependent ◽  
Contaminated Waters

Arsenic contamination in water by natural causes or industrial activities is a major environmental concern, and treatment of contaminated waters is needed to protect water resources and minimize the risk for human health. In mining environments, treatment peatlands are used in the polishing phase of water treatment to remove arsenic (among other contaminants), and peat microorganisms play a crucial role in arsenic removal. The present study assessed culture-independent diversity obtained through metagenomic and metatranscriptomic sequencing and culture-dependent diversity obtained by isolating psychrotolerant arsenic-tolerant, arsenite-oxidizing, and arsenate-respiring microorganisms from a peatland treating mine effluent waters of a gold mine in Finnish Lapland using a dilution-to-extinction technique. Low diversity enrichments obtained after several transfers were dominated by the genera Pseudomonas, Polaromonas, Aeromonas, Brevundimonas, Ancylobacter, and Rhodoferax. Even though maximal growth and physiological activity (i.e., arsenite oxidation or arsenate reduction) were observed at temperatures between 20 and 28°C, most enrichments also showed substantial growth/activity at 2–5°C, indicating the successful enrichments of psychrotolerant microorganisms. After additional purification, eight arsenic-tolerant, five arsenite-oxidizing, and three arsenate-respiring strains were obtained in pure culture and identified as Pseudomonas, Rhodococcus, Microbacterium, and Cadophora. Some of the enriched and isolated genera are not known to metabolize arsenic, and valuable insights on arsenic turnover pathways may be gained by their further characterization. Comparison with phylogenetic and functional data from the metagenome indicated that the enriched and isolated strains did not belong to the most abundant genera, indicating that culture-dependent and -independent methods capture different fractions of the microbial community involved in arsenic turnover. Rare biosphere microorganisms that are present in low abundance often play an important role in ecosystem functioning, and the enriched/isolated strains might thus contribute substantially to arsenic turnover in the treatment peatland. Psychrotolerant pure cultures of arsenic-metabolizing microorganisms from peatlands are needed to close the knowledge gaps pertaining to microbial arsenic turnover in peatlands located in cold climate regions, and the isolates and enrichments obtained in this study are a good starting point to establish model systems. Improved understanding of their metabolism could moreover lead to their use in biotechnological applications intended for bioremediation of arsenic-contaminated waters.

scholarly journals Evaluation of Fe-Mg Binary Oxide for As (III) Adsorption—Synthesis, Characterization and Kinetic Modelling

Nanomaterials ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 805
Author(s):  
Saif Ullah Khan ◽  
Rumman Zaidi ◽  
Feroz Shaik ◽  
Izharul Haq Farooqi ◽  
Ameer Azam ◽  
...  
Keyword(s):  
Arsenic Removal ◽  
Kinetic Modelling ◽  
Arsenic Concentration ◽  
Experimental Studies ◽  
Precipitation Method ◽  
Arsenic Adsorption ◽  
Adsorbent Dosage ◽  
X Ray ◽  
Co Precipitation ◽  
Contaminated Waters

Nanotechnology has received much attention in treating contaminated waters. In the present study, a facile co-precipitation method was employed to synthesize a novel iron and magnesium based binary metal oxide using a stoichiometrically fixed amount of FeNO3.9H2O and MgNO3.6H2O in a proportion of molar concentration 1:1 and was later evaluated in removing As (III) from contaminated waters. Characterization of the prepared nanomaterial was done using X-ray diffraction (XRD), scanning electron microscopy (SEM), Energy Dispersive X-Ray Analysis (EDAX) and ultraviolet–visible spectrophotometry (UV-VIS). Experimental studies on batch scale were carried out, examining the effect of varying initial concentrations of metal, adsorbent dosage, application time and initial pH on removal efficiency. Arsenic removal increased on increasing adsorbent dosage (0.1–1 g/L) but trend reversed on increasing initial arsenic concentration attaining qmax of 263.20 mg/g. Adsorption was quite efficient in pH range 4–8. Freundlich fitted better for adsorption isotherm along with following Pseudo-2nd order kinetics. The reusability and effect of co-existing ions on arsenic adsorption, namely SO42−, CO32− and PO43− were also explored with reusability in 1st and 2nd cycles attained adsorptive removal up to 77% and 64% respectively. The prepared nano-adsorbent showed promising results in terms of high arsenic uptake (qmax of 263.20 mg/g) along with facile and cost-effective synthesis. Thus, the co-precipitation technique used in this work is a simple one step procedure without any use of any precursor as compared to most of the other procedures used for synthesis.

scholarly journals Independent origins of the Golgi phosphoprotein 3 oncoprotein gene

2021 ◽  
Author(s):  
Juan C. Opazo ◽  
Michael W. Vandewege ◽  
Javier Gutierrez ◽  
Kattina Zavala ◽  
Luis Vargas-Chacoff ◽  
...  
Keyword(s):  
Gene Family ◽  
Transcript Abundance ◽  
Single Copy ◽  
Model Systems ◽  
Deep Roots ◽  
Starting Point ◽  
Amino Acid Divergence ◽  
Evolutionarily Conserved ◽  
History Of ◽  
Divergence Estimates

AbstractGolgi phosphoprotein 3 (GOLPH3) is considered the first oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.

scholarly journals Diversity of Active Viral Infections within the Sphagnum Microbiome

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Joshua M. A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Content Type ◽  
Virus Diversity

ABSTRACT Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome. IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.

Control of the Microstructure of Al Metallization by Graphoepitaxy

1995 ◽  
Vol 391 ◽  
Author(s):  
Marc J.C. Van Den Homberg ◽  
P.F.A. Alkemade ◽  
J.L. Hurd ◽  
G.J. Leusink ◽  
S. Radelaar
Keyword(s):  
Substrate Material ◽  
Model Systems ◽  
Grain Structure ◽  
Gradual Change ◽  
X Ray Diffraction ◽  
Rapid Thermal Anneal ◽  
Single Crystalline ◽  
Additional Control ◽  
Starting Point ◽  
Al Metallization

AbstractMicrostructure is an important factor determining the lifetime of Al metallization lines. Deposition conditions, substrate material, alloying elements, and anneal treatments are the key parameters that influence microstructure. In this work we explore the use of graphoepitaxy as a tool for additional control over the grain structure of metallization lines. Onto a submicrometer topography in SiO2 (viz., a large number of parallel grooves), a pure Al film is grown by dc magnetron sputtering, followed by an in situ rapid thermal anneal. The topography of the annealed Al is investigated by cross section SEM. It is observed that if it is heated up to its melting point, Al fills the grooves and leaves the ridges between the grooves uncovered. X-Ray Diffraction, TEM, and Backscatter Kikuchi Diffraction are used to determine the global as well as the local crystallographic orientation of the grains in the quenched aluminum. The analyses are performed for various anneal and cool down treatments. Depending on the treatment, the Al lines in the grooves are either polycrystalline with an almost perfect (111) texture, or single crystalline but with a gradual change of 0.067°/μm in orientation. In the latter case, there is no preferred orientation. The single crystalline Al lines will be used as a starting point for the fabrication of model systems for fundamental electromigration studies.

scholarly journals Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia

2021 ◽  
Vol 12 ◽  
Author(s):  
Rúben M. Costa ◽  
Anny Cárdenas ◽  
Céline Loussert-Fonta ◽  
Gaëlle Toullec ◽  
Anders Meibom ◽  
...  
Keyword(s):  
Surface Topography ◽  
Carrying Capacity ◽  
Model Organism ◽  
Model Systems ◽  
Functional Studies ◽  
Stony Corals ◽  
Starting Point ◽  
Colony Forming Units ◽  
Surface Topographies ◽  
Microbial Host

Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.

Generic System Models

2020 ◽  
pp. 304-323
Author(s):  
Benjamin Hadorn
Keyword(s):  
General System ◽  
System Thinking ◽  
Model Systems ◽  
Human Centered Design ◽  
Holistic Approaches ◽  
Starting Point ◽  
Non Linear Systems ◽  
Conversation Theory ◽  
Generic System ◽  
Research Domain

Systemic and holistic approaches provide a new way of thinking about, understanding and designing systems. In this chapter we aim to highlight the most significant and influential work in this trend, and in particular the achievements of cybernetics, systemics and coordination modeling. Starting with cybernetics, related topics like cybernetic orders, self-organization, autopoiesis and conversation theory are explained. Systemics, and especially general system theory, provide a general language and terminology to express and model systems independent of any research domain. Together with integral and system thinking, this leads to a paradigm shift in understanding and modeling complex and non-linear systems. Concretely, we introduce the meta model of Schwarz which was the starting point of our own generic system model URANOS. Finally, the coordination theories and models which had a great impact on our research on human-centered design are outlined.

Tuning Fractional Order Proportional Integral Controllers for Time Delayed Systems With a Fractional Pole

2011 ◽  
Author(s):  
Hadi Malek ◽  
Ying Luo ◽  
YangQuan Chen
Keyword(s):  
Time Delay ◽  
Fractional Order ◽  
Model Systems ◽  
Delay Model ◽  
Delayed Systems ◽  
First Order ◽  
Tuning Method ◽  
Starting Point ◽  
Reaction Curve ◽  
Pi Controllers

First order plus time delay model is widely used to model systems with S-shaped reaction curve. Its generalized form is the use of a single fractional pole to replace the first order (single-time constant) model, which is believed to better characterize the reaction curve. Using time delayed system model with a fractional pole as the starting point, in this paper, designing fractional order controllers for this class of fractional order systems is investigated. The novelty of this paper is on designing the integer order PID and fractional order PI and [PI] controllers for these class of systems. The simulation and lab experimental results are both included to illustrate the effectiveness of the proposed tuning method. By comparing the results of PID controller, fractional order PI and [PI] controllers, the advantages of the fractional order controller are clearly demonstrated in the case of controlling the single fractional pole plants with constant time delay.

scholarly journals Diversity of active viral infections within the Sphagnum microbiome

2018 ◽  
Author(s):  
Joshua M.A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Housekeeping Gene ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Virus Diversity

AbstractSphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced. Metatranscriptomes were assembled and contigs screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein, gp23, as a marker for phage diversity, we identified 33 contigs representing undocumented phage s that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) major capsid protein were used as markers for ssRNA viruses and NCLDV, respectively. In total 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent near-complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinto-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades, and suggest viruses may play a considerable role in the ecology of the Sphagnum microbiome.SignificanceSphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor its own growth over other plant species. This slows rates of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss’s growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome, and identifying new potential model systems to study virus-host interactions in the peatland ecosystem.

scholarly journals Sulfur-fueled chemolithoautotrophs replenish organic carbon inventory in groundwater

2021 ◽  
Author(s):  
Martin Taubert ◽  
Beatrix M. Heinze ◽  
Will A. Overholt ◽  
Georgette Azemtsop ◽  
Rola Houhou ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Organic Carbon ◽  
Temporal Dynamics ◽  
Inorganic Compounds ◽  
Physiological Activity ◽  
Stable Isotope Probing ◽  
Model Systems ◽  
Reduced Sulfur Compounds ◽  
Genetic Potential

AbstractMetagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity.Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.

Man and the Ice Age

1923 ◽  
Vol 60 (1) ◽  
pp. 1-6 ◽  
Author(s):  
W. J. Sollas
Keyword(s):  
Cold Climate ◽  
Ice Age ◽  
The Third ◽  
Starting Point ◽  
Exhaustive Study

The exact and exhaustive study of the Quaternary terraces of the Somme, which we owe to Commont, may well serve as a starting point in any consideration of this subject. In its results it is not without its surprises, for we should scarcely expect to find, as we do, that the gravels which form the earliest deposits on each of the three lower terraces all contain the remains of a “warm” fauna; the third or highest of these terraces affordingElephas meridionalis, the first and secondE. antiquusand its companion Hippopotamus. Associated with these faunas are flint implements of early types. Pre-Chelléan in the third terrace, typical Chelléan in the second, and Chelléan “evolué” in the first. No signs of a cold climate are to be discovered in any of these gravels until we reach that of the first terrace, where a newer gravel is to be seen invading the older and bringing with it Acheuléan implements and the mammoth.

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