Abiotic Systems Research Articles

Turbidity patterns of spontaneous peptidization in an aqueous abiotic system and possible secondary peptide structures

The non-linear dynamics of spontaneous peptidization running in 10 monocomponent and binary abiotic liquid systems of L- and D-Ala and L- and D-Phe is investigated with use of turbidimetry with continuous registration, high-performance liquid chromatography with light scattering detection (HPLC-ELSD), mass spectrometry (MS), and spectroscopy of far UV circular dichroism (CD). The turbidity patterns represent a sum of the light scattering effects caused by insoluble peptides of unknown yields, structures, and molecular weights. The auxiliary analytical techniques confirm the non-linear nature of peptidization (HPLC-ELSD) and spontaneous formation of the homo- and heteropeptides (MS). CD spectroscopy seems to confirm the presence of the secondary α-helix structures. The similarity of turbidity patterns is revealed with the monocomponent (L or D) and binary (L-L or D-D) systems of equichiral α-amino acids, and dissimilarity of patterns is observed with the binary systems of inequichiral α-amino acids (L-D). The tentative conclusion is drawn that the peptides assembled of equichiral α-amino acid units are able to assume the secondary (right- or left-handed α-helix) structures, which in a certain way could foster the similarity of turbidity patterns, and the peptides built of inequichiral α-amino acid units cannot ensure an efficient enough stringing of monomer molecules into equichiral heptades to form complete segments of an α-helix. This randomness of the α-amino acids arrangement in the inequichiral peptide molecules most probably manifests itself as a lack of similarity among the respective turbidity patterns.

Cyborg landscapes: Choreographing resilient interactions between infrastructure, ecology, and society

Contemporary challenges of climate change, population growth, resource scarcity, and environmental decline prompt designers to envision new relationships between nature and culture. Infrastructure design and adaptation are key to addressing theses issues. This article argues for the formulation of a landscape approach that integrates biotic and abiotic systems to envision more dynamic interactions among infrastructure, ecology, and urbanism. Conceptualized as cyborg landscapes, this approach embraces notions of change, adaptation, and feedback to create hybrid infrastructures of human and non-human systems, of living and non-living entities, across a range of spatial and temporal scales. Three examples illustrate that the profession is already (knowingly or unknowingly) working within this framework. Designed as co-dependent socioecological networks, these projects transform and choreograph landscape processes across multiple spatial and temporal scales. They promote an aesthetic that is predicated on relationships between dynamic things and systems. By stressing co-evolutionary processes between human agency and ecological systems, cyborg landscapes aspire to create multifunctional landscapes that do not simply operate in the present, but learn from experiences in order to adapt and grow smarter.

A highly selective Schiff base fluorescent chemosensor for Lu3+

A Schiff base derivative shows high selectivity to Lu3+ in both abiotic systems and living cells.

Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity.

Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials..

A Model of a Synthetic Biological Communication Interface between Mammalian Cells and Mechatronic Systems.

The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system. We use these synthetic networks to encode motion commands within the cell's endogenous, oscillatory calcium signaling pathways. We then describe a potential system whereby this oscillatory signal could be outputted and monitored as a change in cellular fluorescence. Next, we use the changes resulting from the synthetic biological modifications as new parameters in a simulation of a well-established mathematical model for intracellular calcium signaling. The resulting signal is processed in the frequency domain, with specific frequencies activating cognate robot motion subroutines.

Fluctuation Analysis of Redox Potential to Distinguish Microbial Fe(II) Oxidation.

We developed a novel method for distinguishing abiotic and biological iron oxidation in liquid media using oxidation-reduction (redox) potential time series data. The instrument and processing algorithm were tested by immersing the tip of a Pt electrode with an Ag-AgCl reference electrode into an active iron-oxidizing biofilm in a groundwater discharge zone, as well as in two abiotic systems: a killed sample and a chemical control from the same site. We used detrended fluctuation analysis to characterize average root mean square fluctuation behavior, which was distinct in the live system. The calculated α value scaling exponents determined by detrended fluctuation analysis were significantly different at p < 0.001. This indicates that time series of electrode response data may be used to distinguish live and abiotic chemical reaction pathways. Due to the simplicity, portability, and small size, it may be suitable for characterization of extraterrestrial environments where water has been observed, such as Mars and Europa. Key Words: Oxidation-reduction potential-Detrended fluctuation analysis-Iron-oxidizing bacteria. Astrobiology 16, 846-852.

Zinc isotope fractionation during adsorption to calcite at high and low ionic strength

The biogeochemical cycle of Zn in the oceans has been of interest for decades, and the newly discovered isotopic variations among major reservoirs of Zn in the marine system have raised new questions and provided some new insights regarding the processes that control the concentration and isotopic distribution of this bioessential element. Fundamental understanding of Zn isotope fractionation mechanisms will be required to optimize the value of data now being generated by efforts such as GEOTRACES. In particular, fractionation driven by reactions taking place at fluid-solid interfaces will be crucial to quantify, since these reactions exert significant control on fluid concentrations and bioavailability of Zn and other trace metals. In this study, we aimed to determine whether interaction between dissolved Zn and Zn bound to calcite surfaces drives significant isotope fractionation. Zinc adsorption experiments were conducted in simple, abiotic systems at low ionic strength (deionized water) and high ionic strength (synthetic seawater) as several series of small batch reactions, at pH8.3, with experimental duration from 0.5 to 120h. We observed that the Zn adsorbed on calcite was isotopically heavier than in the co-existing solutions, with Δ66/64Znadsorbed-solution averaging 0.41±0.18‰ (2SD) and 0.73±0.08‰ (2SD) in low and high ionic strength systems, respectively. One possible mechanistic interpretation of this result is that isotope fractionation between dissolved and adsorbed Zn is an equilibrium effect driven by the coordination number difference between aqueous Zn(H2O)62+ (six-fold) and adsorbed (four-fold) complexes. Alternatively, direct adsorption of isotopically heavy ZnCO30(aq) without further fractionation is possible, since this species has been shown previously with theoretical calculations to be enriched in heavy isotopes relative to other Zn species expected in solution. Our results show that the magnitude of equilibrium fractionation between dissolved and calcite-sorbed Zn is clearly sensitive to aqueous Zn speciation, and a simple mass balance exercise using theoretical predictions in the literature for isotopic fractionation among aqueous species demonstrates that a pool of isotopically light Zn is complexed with chloride ions in high ionic strength solutions, leading to a heavier pool of Zn adsorbed to the calcite surface. Further work will be needed to determine whether the pool of isotopically heavy Zn adsorbing to calcite surfaces can be incorporated during calcite crystal growth to impart an isotopically heavy signature to the resulting calcite.

Adoption of Machine Learning Techniques in Ecology and Earth Science

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to infer understanding and make predictions. Machine-learning-based methods have an advantage over traditional statistical methods in studying these systems because the former do not impose unrealistic assumptions (such as linearity), are capable of inferring missing data, and can reduce long-term expert annotation burden. Thus, a wider adoption of machine learning methods in ecology and earth science has the potential to greatly accelerate the pace and quality of science. Despite these advantages, machine learning techniques have not had wide spread adoption in ecology and earth science. This is largely due to 1) a lack of communication and collaboration between the machine learning research community and natural scientists, 2) a lack of easily accessible tools and services, and 3) the requirement for a robust training and test data set. These impediments can be overcome through financial support for collaborative work and the development of tools and services facilitating ML use. Natural scientists who have not yet used machine learning methods can be introduced to these techniques through Random Forest, a method that is easy to implement and performs well. This manuscript will 1) briefly describe several popular ML methods and their application to ecology and earth science, 2) discuss why ML methods are underutilized in natural science, and 3) propose solutions for barriers preventing wider ML adoption.

Interactions Between Fe(III)-Oxides and Fe(III)-Phyllosilicates During Microbial Reduction 1: Synthetic Sediments

ABSTRACTFe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies on microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area (HSA) goethite. Cryogenic (12K) 57Fe Mössbauer spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) [Fe(II)-phyllosilicate] in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl2⋅2H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26–87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe(II) addition and system redox potential may account for the microbial and abiotic reaction systems. Our experiments provide new insight into pathways for Fe(III) reduction in mixed Fe(III)-oxide/Fe(III)-phyllosilicate assemblages, and provide key mechanistic insight for interpreting microbial reduction experiments and field data from complex natural soils and sediments.

Functional diversity of reproductive traits increases across succession in the Atlantic forest

Abstract Niche and neutral processes shape community assembly with a possible shift of niche and neutral importance in communities undergoing temporal changes during succession. Functional diversity helps to discriminate assembly processes since trait distribution is dependent on those processes. We evaluated the changes in reproductive traits related to pollination and seed dispersal in a successional gradient in an Atlantic Forest area, Southern Brazil. We surveyed forests undergoing regeneration varying in age from 2 to 80 years after pasture abandonment. We expected an increase in functional diversity of reproductive traits and a greater role of limiting similarity across succession. Abiotic and mixed pollination systems, dioecious sexual system, biotic dispersed, many-seeded and small-seeded species decreased as the forest got older. Conversely, bee-pollinated, bell-shaped, small and androgynous flowers increased across forest succession as well biotic dispersed and large-seeded species. Functional richness and functional dispersion were higher in older forests. Changes in functional diversity were positively related to species richness, indicating that species enrichment in older forests added new sets of reproductive traits. These changes in trait distribution and functional diversity across succession in the Atlantic Forest suggest an increased role of biotic interactions and limiting similarity process structuring plant assemblages of second-growth tropical forests.

Reductive transformation of carbamazepine by abiotic and biotic processes

The antiepileptic drug carbamazepine (CBZ) is ubiquitously present in the anthropogenic water cycle and is therefore of concern regarding the potable water supply. Despite of its persistent behavior in the aquatic environment, a redox dependent removal at bank filtration sites with anaerobic aquifer passage was reported repeatedly but not elucidated in detail yet. The reductive transformation of CBZ was studied, using abiotic systems (catalytic hydrogenation, electrochemistry) as well as biologically active systems (column systems, batch degradation tests). In catalytic hydrogenation CBZ is gradually hydrogenated and nine transformation products (TPs) were detected by liquid chromatography high-resolution mass spectrometry. 10,11-Dihydro-CBZ ((2H)-CBZ) was the major stable product in these abiotic, surface catalyzed reduction processes and turned out to be not a precursor of the more hydrogenated TPs. In the biotic reduction processes the formation of (2H)-CBZ alone could not explain the observed CBZ decline. There, also traces of (6H)-CBZ and (8H)-CBZ were formed by microbes under anaerobic conditions and four phase-II metabolites of reduced CBZ could be detected and tentatively identified. Thus, the spectrum of reduction products of CBZ is more diverse than previously thought. In environmental samples CBZ removal along an anaerobic soil passage was confirmed and (2H)-CBZ was determined at one of the sites.

The diversity and composition of moth assemblages of protected and degraded raised bogs in Ireland

Abstract Peatlands are globally important habitats, which act as net carbon stores. As a result of drainage, peat extraction and agricultural intensification, raised bogs in the midlands of Ireland are a diminishing and increasingly fragmented peatland habitat. A network of protected sites has been established, which is intended to represent the best abiotic and plant community systems. Lepidoteran communities are an important component of raised bog biodiversity and may be useful as biodiversity indicators, yet they are a neglected area of research. We address this by surveying night‐flying macro‐moths on six protected and six degraded raised bogs to establish whether there is a distinct moth fauna associated with the wettest areas of protected sites by comparing them to assemblages found on degraded sites where this wet habitat has been lost. In general, differences between moth assemblages on protected and degraded raised bogs are rather subtle, with assemblages on both site types generally similar. But, a number of species were found to be associated with protected sites, three of which are bog‐associated species of conservation concern and may be particularly vulnerable due to the continuing loss of the wettest areas of raised bogs. Degraded sites were found to harbour a significant number of bog‐associated species of conservation concern and may have a role to play in peatland invertebrate conservation, hitherto undervalued. To determine this, further research is required to describe the invertebrate fauna of these sites and of marginal areas of protected sites.

Effects of Microbial Fe(III) Reduction on the Sorption of Cs and Sr on Biotite and Chlorite

ABSTRACTMicrobially mediated reduction of Fe(III) in chlorite and biotite by Shewanella oneidensis MR-1 leads to a significant reduction in sorption of both Cs and Sr compared to the abiotic systems. As seen in previous studies, biotite is a more efficient sorbent than chlorite. Reduction of the mineral-associated Fe(III) causes increased dissolution of both minerals and reduces the sites available for Cs and Sr sorption. As this dissolution progresses it causes desorption of Cs and Sr from chlorite, but not biotite. Subsequent exposure to air increases sorption due to precipitation of secondary Fe(III) oxyhydroxide minerals derived from the Fe(II) released by bio-reduction. In contrast to successful bioremediation of redox active elements, this study suggests that microbial Fe(III) reduction could enhance the migration of Cs and Sr through phyllosilicate-dominated strata.

On Spontaneously Pulsating Proline-Phenylalanine Peptide Microfibers.

Earlier, we have collected an experimental evidence showing that low molecular weight chiral carboxylic acids (amino acids included) can spontaneously undergo an oscillatory chiral conversion and an oscillatory condensation in abiotic aqueous and non-aqueous liquid systems, stored for certain amount of time under mild external conditions. These earlier findings are summarized in the introductory part of this study. In the second part, a preliminary report is given on spontaneous pulsation of peptide microfibers in the aged proline-phenylalanine (Pro-Phe) solution in 70% aqueous acetonitrile. The experimental evidence originates from a number of advanced analytical techniques. In view of our earlier and present findings, a presumption is made that the mechanism of spontaneous pulsation (formation and decay) of Pro-Phe microfibers is directly related to the oscillatory chiral conversion and oscillatory peptidization. The entity of the discussed results pointing out to spontaneous and uncontrolled instability of peptide structures might be a bad prognostic for employing such structures in nanobiotechnology.

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil.

BackgroundHigh concentrations of petroleum hydrocarbon (PHC) pollution can be hazardous to human health and leave soils incapable of supporting agricultural crops. A cheap solution, which can help restore biodiversity and bring land back to productivity, is cultivation of high biomass yielding willow trees. However, the genetic mechanisms which allow these fast-growing trees to tolerate PHCs are as yet unclear.MethodsSalix purpurea ‘Fish Creek’ trees were pot-grown in soil from a former petroleum refinery, either lacking or enriched with C10-C50 PHCs. De novo assembled transcriptomes were compared between tree organs and impartially annotated without a priori constraint to any organism.ResultsOver 45 % of differentially expressed genes originated from foreign organisms, the majority from the two-spotted spidermite, Tetranychus urticae. Over 99 % of T.urticae transcripts were differentially expressed with greater abundance in non-contaminated trees. Plant transcripts involved in the polypropanoid pathway, including phenylalanine ammonia-lyase (PAL), had greater expression in contaminated trees whereas most resistance genes showed higher expression in non-contaminated trees.ConclusionsThe impartial approach to annotation of the de novo transcriptomes, allowing for the possibility for multiple species identification, was essential for interpretation of the crop’s response treatment. The meta-transcriptomic pattern of expression suggests a cross-tolerance mechanism whereby abiotic stress resistance systems provide improved biotic resistance. These findings highlight a valuable but complex biotic and abiotic stress response to real-world, multidimensional contamination which could, in part, help explain why crops such as willow can produce uniquely high biomass yields on challenging marginal land.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0636-9) contains supplementary material, which is available to authorized users.

An Abiotic Glass-Bead Collector Exhibiting Active Transport.

Animals relocate objects as needed by active motion. Active transport is ubiquitous in living organisms but has been difficult to realize in abiotic systems. Here we show that a self-propelled droplet can gather scattered beads toward one place on a floor and sweep it clean. This is a biomimetic active transport with loadings and unloadings, because the transport was performed by a carrier and the motion of the carrier was maintained by the energy of the chemical reaction. The oil droplet produced fluctuation of the local number density of the beads on the floor, followed by its autocatalytic growth. This mechanism may inspire the technologies based on active transport wherein chemical and physical substances migrate as in living organisms.

Indigenous Concepts of ‘Living Systems’: Aristotelian ‘Soul’ meets Constructal Theory

I examine similarities among the ways of thinking concerning the natural world of Indigenous peoples of North America and Australia and two aspects of Western Science from different historical periods. The first comparison is with constructal theory, a set of ideas and models recently developed to explain how ‘design’ arises in both biotic and abiotic systems. Both traditions emphasize the importance of flow and motion and how these generate connections, not only within biotic systems, but also between biotic and abiotic phenomena. The second comparison goes back to the beginnings of the Western scientific tradition, and involves the Aristotelian concept of the ‘soul,’ an entity which is not considered to be supernatural, but more of an emergent property of living systems that also involves flow, especially of heat and air within living systems. Both comparisons reveal that indigenous knowledge is thoroughly scientific, but not in the sense characterized by the Baconian/Cartesian tradition, which is more focused on mechanism and application to human affairs than to understanding how natural systems actually function. Indigenous knowledge focuses more on relationships than on mechanisms, and thus is best compared to Western scholarly traditions that also emphasize relationships and emergent properties.

Process oriented thinking as a key for integration of ecohydrology, biotechnology and engineering for sustainable water resources management and ecosystems

Abstract. The recent high rate of environmental degradation due to unsustainable use of water and other natural resources and mismanagement, is, in many cases, the result of a dominant sectoral approach, limited communication between different users and agencies, and lack of knowledge transfer between different disciplines, and especially lack of dialogue between environmental scientists and engineers. There is no doubt that the genuine improvement of human well-being has to be based on understanding the complexity of interactions between abiotic, biotic and socio-economic systems. The major drivers of biogeosphere evolution and function have been the cycles of water and nutrients in a complex array of differing climates and catchment geomorphologies. In the face of global climate change and unequally distributed human populations, the recent sectoral mechanistic approach in natural resources management has to be replaced by an evolutionary systems approach based on well-integrated problem-solving and policy-oriented environmental science. Thus the principles of ecohydrology should be the basis for further integration of ecology, hydrology, engineering, biotechnology and other environmental sciences. Examples from UNESCO IHP VII show how the integration of these will not only increase the efficiency of measures to harmonize ecosystem potentials with societal needs, but also significantly reduce the costs of sustainable environmental management.

The continuous re-equilibration of carbon isotope compositions of hydrous Mg carbonates in the presence of cyanobacteria

The hydrous magnesium carbonate minerals dypingite (Mg5(CO3)4(OH)2·5H2O) and nesquehonite (MgCO3·3H2O) were precipitated in the presence and absence of Gloeocapsa sp. and Synechococcus sp. cyanobacteria in batch reactors. The Δ13Cmineral–DIC is similar in both biotic and abiotic systems. Stable carbon isotope analyses of the precipitated minerals and co-existing fluids indicated that the δ13C values of the precipitated carbonates co-vary over time with the δ13CDIC of the fluid phase, even after the precipitation of the carbonate is complete. This observation indicates the continuous isotopic exchange between the carbonates and the fluid, a process that efficiently resets the original δ13C values of the solids. Therefore although cyanobacterial-induced Mg carbonates are 10±5‰ enriched in 13C compared to inorganic carbonates, the δ13C values of natural hydrous Mg carbonates may reflect post precipitation processes and may not be reliable for paleo-environmental reconstructions.

Electrochemically and bioelectrochemically induced ammonium recovery.

Streams such as urine and manure can contain high levels of ammonium, which could be recovered for reuse in agriculture or chemistry. The extraction of ammonium from an ammonium-rich stream is demonstrated using an electrochemical and a bioelectrochemical system. Both systems are controlled by a potentiostat to either fix the current (for the electrochemical cell) or fix the potential of the working electrode (for the bioelectrochemical cell). In the bioelectrochemical cell, electroactive bacteria catalyze the anodic reaction, whereas in the electrochemical cell the potentiostat applies a higher voltage to produce a current. The current and consequent restoration of the charge balance across the cell allow the transport of cations, such as ammonium, across a cation exchange membrane from the anolyte to the catholyte. The high pH of the catholyte leads to formation of ammonia, which can be stripped from the medium and captured in an acid solution, thus enabling the recovery of a valuable nutrient. The flux of ammonium across the membrane is characterized at different anolyte ammonium concentrations and currents for both the abiotic and biotic reactor systems. Both systems are compared based on current and removal efficiencies for ammonium, as well as the energy input required to drive ammonium transfer across the cation exchange membrane. Finally, a comparative analysis considering key aspects such as reliability, electrode cost, and rate is made. This video article and protocol provide the necessary information to conduct electrochemical and bioelectrochemical ammonia recovery experiments. The reactor setup for the two cases is explained, as well as the reactor operation. We elaborate on data analysis for both reactor types and on the advantages and disadvantages of bioelectrochemical and electrochemical systems.