Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests

Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests

How Bacteria Adhere to Brushy PEG Surfaces: Clinging to Flaws and Compressing the Brush

This study examined the compression of solvated polymer brushes on bioengineered surfaces during the initial stages of <i>Staphylococcus aureus</i> (<i>S. aureus</i>) adhesion from gentle flow. A series of PEG [poly­(ethylene glycol)] brushes, 7–17 nm in height and completely nonadhesive to proteins and bacteria, were modified by the incorporation of sparse isolated ∼10 nm cationic polymer “patches” at their bases. These nanoscale regions, which lacked PEG tethers, were electrostatically attractive toward negative bacteria or proteins. <i>S. aureus</i> drawn to the interface by multiple adhesive patches compressed the PEG brush in the remaining contact region. The observed onset of bacterial or fibrinogen capture with increases in patch content was compared with calculations. Balancing the attraction energy (proportional to the number of patches engaging a bacterium during capture) against steric forces (calculated using the Alexander–DeGennes treatment) provided perspective on the brush compression. The results were consistent with a bacteria–surface gap on the order of the Debye length in these studies. In this limit of strong brush compression, structural features (height, persistence length) of the brush were unimportant so that osmotic pressure dominated the steric repulsion. Thus, the dominant factor for bacterial repulsion was the mass of PEG in the brush. This result explains empirical reports in the literature that identify the total PEG content of a brush as a criteria for prevention of bioadhesion, independent of tether length and spacing, within a reasonable range for those parameters. Bacterial capture was also compared to that of protein capture. It was found, surprisingly, that the patchy brushes were more protein- than bacteria-resistant. <i>S. aureus</i> adhesion was explained by the bacteria’s greater tendency to compress large areas of brush to interact with many patches. By contrast, proteins are thought to penetrate the brush at a few sites of PEO-free patches. The finding provides a mechanism for the literature reports that <i>in vitro</i> protein resistance is a poor predictor of <i>in vitro</i> implant failure related to cell–surface adhesion

Synthetic Mimic of Antimicrobial Peptide with Nonmembrane-Disrupting Antibacterial Properties

Polyguanidinium oxanorbornene (<b>PGON</b>) was synthesized from norbornene monomers via ring-opening metathesis polymerization. This polymer was observed to be strongly antibacterial against Gram-negative and Gram-positive bacteria as well as nonhemolytic against human red blood cells. Time-kill studies indicated that this polymer is lethal and not just bacteriostatic. In sharp contrast to previously reported SMAMPs (synthetic mimics of antimicrobial peptides), <b>PGON</b> did not disrupt membranes in vesicle-dye leakage assays and microscopy experiments. The unique biological properties of <b>PGON</b>, in same ways similar to cell-penetrating peptides, strongly encourage the examination of other novel guanidino containing macromolecules as powerful and selective antimicrobial agents

Using Flow to Switch the Valency of Bacterial Capture on Engineered Surfaces Containing Immobilized Nanoparticles

Toward an understanding of nanoparticle–bacterial interactions and the development of sensors and other substrates for controlled bacterial adhesion, this article describes the influence of flow on the initial stages of bacterial capture (<i>Staphylococcus aureus</i>) on surfaces containing cationic nanoparticles. A PEG (poly­(ethylene glycol)) brush on the surface around the nanoparticles sterically repels the bacteria. Variations in ionic strength tune the Debye length from 1 to 4 nm, increasing the strength and range of the nanoparticle attractions toward the bacteria. At relatively high ionic strengths (physiological conditions), bacterial capture requires several nanoparticle–bacterial contacts, termed “multivalent capture”. At low ionic strength and gentle wall shear rates (on the order of 10 s^–1), individual bacteria can be captured and held by single surface-immobilized nanoparticles. Increasing the flow rate to 50 s^–1 causes a shift from monovalent to divalent capture. A comparison of experimental capture efficiencies with statistically determined capture probabilities reveals the initial area of bacteria–surface interaction, here about 50 nm in diameter for a Debye length κ^–1 of 4 nm. Additionally, for κ^–1 = 4 nm, the net per nanoparticle binding energies are strong but highly shear-sensitive, as is the case for biological ligand–receptor interactions. Although these results have been obtained for a specific system, they represent a regime of behavior that could be achieved with different bacteria and different materials, presenting an opportunity for further tuning of selective interactions. These finding suggest the use of surface elements to manipulate individual bacteria and nonfouling designs with precise but finite bacterial interactions