@article {1416, title = {Antimicrobial surfaces containing cationic nanoparticles: how immobilized, clustered, and protruding cationic charge presentation affects killing activity and kinetics.}, journal = {Colloids Surf B Biointerfaces}, volume = {125}, year = {2015}, month = {2015 Jan 1}, pages = {255-63}, abstract = {

This work examines how the antimicrobial (killing) activity of net-negative surfaces depends on the presentation of antimicrobial cationic functionality: distributed versus clustered, and flat clusters versus raised clusters. Specifically, the ability to kill Staphylococcus aureus by sparsely distributed 10 nm cationic nanoparticles, immobilized on a negative surface and backfilled with a PEG (polyethylene glycol) brush, was compared with that for a dense layer of the same immobilized nanoparticles. Additionally, sparsely distributed 10 nm poly-L-lysine (PLL) coils, adsorbed to a surface to produce flat cationic \"patches\" and backfilled with a PEG brush were compared to a saturated adsorbed layer of PLL. The latter resembled classical uniformly cationic antimicrobial surfaces. The protrusion of the cationic clusters substantially influenced killing but the surface concentration of the clusters had minor impact, as long as bacteria adhered. When surfaces were functionalized at the minimum nanoparticle and patch densities needed for bacterial adhesion, killing activity was substantial within 30 min and nearly complete within 2 h. Essentially identical killing was observed on more densely functionalized surfaces. Surfaces containing protruding (by about 8 nm) nanoparticles accomplished rapid killing (at 30 min) compared with surfaces containing similarly cationic but flat features (PLL patches). Importantly, the overall surface density of cationic functionality within the clusters was lower than reported thresholds for antimicrobial action. Also surprising, the nanoparticles were far more deadly when surface-immobilized compared with free in solution. These findings support a killing mechanism involving interfacial stress.

}, issn = {1873-4367}, doi = {10.1016/j.colsurfb.2014.10.043}, author = {Fang, Bing and Jiang, Ying and N{\"u}sslein, Klaus and Rotello, Vincent M and Santore, Maria M} } @article {1421, title = {Biodegradation of low concentrations of 1,2-dibromoethane in groundwater is enhanced by phenol.}, journal = {Appl Microbiol Biotechnol}, volume = {98}, year = {2014}, month = {2014 Feb}, pages = {1329-38}, abstract = {

The lead scavenger 1,2-dibromoethane (EDB), a former additive to leaded gasoline, is a common groundwater contaminant, yet not much knowledge is available for its targeted bioremediation, especially under in situ conditions. The study site was an aviation gas spill site, which, although all hydrocarbons and most of the EDB were remediated in the mid-1990s, still exhibits low levels of EDB remaining in the groundwater (about 11 \μg EDB/l). To evaluate the effect of phenol on biostimulation of low concentration of EDB, microcosms were established from an EDB-contaminated aquifer. After 300 days at environmentally relevant conditions (12\ \±\ 2 \°C, static incubation), EDB was not significantly removed from unamended microcosms compared to the abiotic control. However, in treatments amended with phenol, up to 80 \% of the initial EDB concentration had been degraded, while added phenol was removed completely. Microbial community composition in unamended and phenol-amended microcosms remained unchanged, and Polaromonas sp. dominated both types of microcosms, but total bacterial abundance and numbers of the gene for phenol hydroxylase were higher in phenol-amended microcosms. Dehalogenase, an indicator suggesting targeted aerobic biodegradation of EDB, was not detected in either treatment. This finding suggests phenol hydroxylase, rather than a dehalogenation reaction, may be responsible for 1,2-dibromoethane oxidation under in situ conditions. In addition, biostimulation of EDB is possible through the addition of low levels of phenol in aerobic groundwater sites.

}, keywords = {Bacteria, Biota, Ethylene Dibromide, Groundwater, Metabolic Networks and Pathways, Phenol, Water Pollutants}, issn = {1432-0614}, doi = {10.1007/s00253-013-4963-1}, author = {Baek, Kyunghwa and Wang, Meng and McKeever, Robert and Rieber, Kahlil and Park, Chul and N{\"u}sslein, Klaus} } @article {1418, title = {Easy come easy go: surfaces containing immobilized nanoparticles or isolated polycation chains facilitate removal of captured Staphylococcus aureus by retarding bacterial bond maturation.}, journal = {ACS Nano}, volume = {8}, year = {2014}, month = {2014 Feb 25}, pages = {1180-90}, abstract = {

Adhesion of bacteria is a key step in the functioning of antimicrobial surfaces or certain types of on-line sensors. The subsequent removal of these bacteria, within a \∼ 10-30 min time frame, is equally important but complicated by the tendency of bacterial adhesion to strengthen within minutes of initial capture. This study uses Staphylococcus aureus as a model bacterium to demonstrate the general strategy of clustering adhesive surface functionality (at length scales smaller than the bacteria themselves) on otherwise nonadhesive surfaces to capture and retain bacteria (easy come) while limiting the progressive strengthening of adhesion. The loose attachment facilitates bacteria removal by moderate shearing flow (easy go). This strategy is demonstrated using surfaces containing sparsely and randomly arranged immobilized amine-functionalized nanoparticles or poly-l-lysine chains, about 10 nm in size. The rest of the surface is backfilled with a nonadhesive polyethylene glycol (PEG) brush that, by itself, repels S. aureus. The nanoparticles or polymer chains cluster cationic functionality, providing small regions that attract negatively charged S. aureus cells. Compared with surfaces of nearly uniform cationic character where S. aureus adhesion quickly becomes strong (on a time scale less than 5 min), placement of cationic charge in small clusters retards or prevents processes that increase bacteria adhesion on a time scale of \∼ 30 min, providing \"easy go\" surfaces.

}, keywords = {Nanoparticles, Polyamines, Staphylococcus aureus, Surface Properties}, issn = {1936-086X}, doi = {10.1021/nn405845y}, author = {Fang, Bing and Jiang, Ying and Rotello, Vincent M and N{\"u}sslein, Klaus and Santore, Maria M} } @article {1417, title = {Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.}, journal = {Mol Ecol}, volume = {23}, year = {2014}, month = {2014 Jun}, pages = {2988-99}, abstract = {

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.

}, keywords = {Agriculture, Carbon Cycle, Ecosystem, Genes, Bacterial, Genes, Fungal, Genetic Variation, Metagenome, Multigene Family, Nitrogen Cycle, Oligonucleotide Array Sequence Analysis, Soil Microbiology, Trees, Tropical Climate}, issn = {1365-294X}, doi = {10.1111/mec.12786}, author = {Paula, Fabiana S and Rodrigues, Jorge L M and Zhou, Jizhong and Wu, Liyou and Mueller, Rebecca C and Mirza, Babur S and Bohannan, Brendan J M and N{\"u}sslein, Klaus and Deng, Ye and Tiedje, James M and Pellizari, Vivian H} } @article {1419, title = {Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.}, journal = {ISME J}, volume = {8}, year = {2014}, month = {2014 Jul}, pages = {1548-50}, abstract = {

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.

}, keywords = {Brazil, Conservation of Natural Resources, DNA Barcoding, Taxonomic, DNA, Fungal, DNA, Ribosomal, Ecosystem, Fungi, Phylogeny, Plant Roots, Soil Microbiology, Trees, Tropical Climate}, issn = {1751-7370}, doi = {10.1038/ismej.2013.253}, author = {Mueller, Rebecca C and Paula, Fabiana S and Mirza, Babur S and Rodrigues, Jorge L M and N{\"u}sslein, Klaus and Bohannan, Brendan J M} } @article {1420, title = {Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.}, journal = {Appl Environ Microbiol}, volume = {80}, year = {2014}, month = {2014 Jan}, pages = {281-8}, abstract = {

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

}, keywords = {Agriculture, Bacteria, Biota, Carbon, Cluster Analysis, Conservation of Natural Resources, Human Activities, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen, Nitrogen Fixation, Oxidoreductases, Phylogeny, Sequence Analysis, DNA, Soil, Soil Microbiology, South America, Trees}, issn = {1098-5336}, doi = {10.1128/AEM.02362-13}, author = {Mirza, Babur S and Potisap, Chotima and N{\"u}sslein, Klaus and Bohannan, Brendan J M and Rodrigues, Jorge L M} } @article {1423, title = {Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, year = {2013}, month = {2013 Jan 15}, pages = {988-93}, abstract = {

The Amazon rainforest is the Earth\&$\#$39;s largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

}, keywords = {Agriculture, Animals, Bacteria, Biodiversity, Brazil, Cattle, Ecosystem, Humans, Phylogeny, Rain, Soil Microbiology, Trees, Tropical Climate}, issn = {1091-6490}, doi = {10.1073/pnas.1220608110}, author = {Rodrigues, Jorge L M and Pellizari, Vivian H and Mueller, Rebecca and Baek, Kyunghwa and Jesus, Ederson da C and Paula, Fabiana S and Mirza, Babur and Hamaoui, George S and Tsai, Siu Mui and Feigl, Brigitte and Tiedje, James M and Bohannan, Brendan J M and N{\"u}sslein, Klaus} } @article {1422, title = {Identification and characterization of a NaCl-responsive genetic locus involved in survival during desiccation in Sinorhizobium meliloti.}, journal = {Appl Environ Microbiol}, volume = {79}, year = {2013}, month = {2013 Sep}, pages = {5693-700}, abstract = {

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci asnO and ngg by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring ngg::Tn5luxAB was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a d-alanine-d-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to \β-lactam antibiotics. asnO::Tn5luxAB is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing \β-lactam inhibitors and increased resistance to \β-lactam antibiotics may indicate that asnO is involved in the production of a \β-lactam inhibitor.

}, keywords = {Desiccation, DNA Transposable Elements, Gene Expression Regulation, Bacterial, Gene Knockout Techniques, Genes, Bacterial, Genetic Loci, Microbial Viability, Mutagenesis, Insertional, Osmotic Pressure, Sinorhizobium meliloti, Sodium Chloride, Stress, Physiological}, issn = {1098-5336}, doi = {10.1128/AEM.01037-13}, author = {Vriezen, Jan A C and de Bruijn, Frans J and N{\"u}sslein, Klaus} } @article {726, title = {Biodegradation of ethylene dibromide (1,2-dibromoethane [EDB]) in microcosms simulating in situ and biostimulated conditions.}, journal = {J Hazard Mater}, volume = {209-210}, year = {2012}, month = {2012 Mar 30}, pages = {92-8}, abstract = {Although 1,2-dibromoethane (EDB) is a common groundwater contaminant, there is the lack of knowledge surrounding EDB biodegradation, especially under aerobic conditions. We have performed an extensive microcosm study to investigate the biodegradation of EDB under simulated in situ and biostimulated conditions. The materials for soil microcosms were collected from an EDB-contaminated aquifer at the Massachusetts Military Reservation in Cape Cod, MA. This EDB plume has persisted for nearly 40 years in both aerobic and anaerobic EDB zones of the aquifer. Microcosms were constructed under environmentally relevant conditions (field EDB and DO concentrations; incubated at 12{\textdegree}C). The results showed that natural attenuation occurred under anaerobic conditions but not under aerobic conditions, explaining why aerobic EDB contamination is so persistent. EDB degradation rates were greater under biostimulated conditions for both the aerobic and anaerobic microcosms. Particularly for aerobic biostimulation, methane-amended microcosms degraded EDB, on average, at a first order rate eight times faster than unamended microcosms. The best performing replicate achieved an EDB degradation rate of 7.0 yr(-1) (half-life (t(1/2))=0.10 yr). Residual methane concentrations and the emergence of methanotrophic bacteria, measured by culture independent bacterial analysis, provided strong indications that EDB degradation in aerobic methane-amended microcosms occurred via cometabolic degradation. These results indicate the potential for enhanced natural attenuation of EDB and that methane could be considered co-substrate for EDB bioremediation for the EDB-contaminated groundwater in aerobic zone.}, keywords = {Aerobiosis, Anaerobiosis, Biodegradation, Environmental, Ethylene Dibromide, Water Microbiology, Water Pollutants, Chemical}, issn = {1873-3336}, doi = {10.1016/j.jhazmat.2011.12.067}, author = {McKeever, Robert and Sheppard, Diane and N{\"u}sslein, Klaus and Baek, Kyung-Hwa and Rieber, Khalil and Ergas, Sarina J and Forbes, Rose and Hilyard, Mark and Park, Chul} } @article {1424, title = {How Bacteria Adhere to Brushy PEG Surfaces: Clinging to Flaws and Compressing the Brush.}, journal = {Macromolecules}, volume = {45}, year = {2012}, month = {2012 Oct 23}, pages = {8373-8381}, abstract = {

This study examined the compression of solvated polymer brushes on bioengineered surfaces during the initial stages of Staphylococcus Aureus (S. aureus) adhesion from gentle flow. A series of PEG [poly(ethylene glycol)] brushes, 7 to 17 nm in height and completely non-adhesive 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 towards negative bacteria or proteins. S. aureus 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. S. aureus adhesion driven by patches within otherwise protein-resistant PEG brushes was explained by the bacteria\&$\#$39;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 in-vitro protein resistance is a poor predictor of in-vitro implant failure related to cell-surface adhesion.

}, issn = {0024-9297}, doi = {10.1021/ma300981r}, author = {Gon, S and Kumar, Kushi-Nidhi and N{\"u}sslein, Klaus and Santore, Maria M} } @article {722, title = {Molecular approach to evaluate biostimulation of 1,2-dibromoethane in contaminated groundwater.}, journal = {Bioresour Technol}, volume = {123C}, year = {2012}, month = {2012 May 29}, pages = {207-213}, abstract = {This study investigated the effect of co-substrate amendments on EDB biodegradation under aerobic conditions. Microcosms were established using contaminated soil and groundwater samples and maintained under in situ conditions to determine EDB degradation rates, and the diversity and abundance of EDB degrading indigenous bacteria. After 100days of incubation, between 25\% and 56\% of the initial EDB was degraded in the microcosms, with added jet fuel providing highest degradation rates (2.97{\textpm}0.49yr(-1)). In all microcosms, the quantity of dehalogenase genes did not change significantly, while the number of BTEX monooxygenase and phenol hydroxylase genes increased with jet fuel amendments. These results indicate that EDB was not degraded by prior dehalogenation, but rather by cometabolism with adapted indigenous microorganisms. This is also reflected in the history of the plume, which originated from an aviation gasoline pipeline leak. This study suggests that biostimulation of EDB is possible at aerobic groundwater sites.}, issn = {1873-2976}, doi = {10.1016/j.biortech.2012.05.119}, author = {Baek, Kyunghwa and McKeever, Robert and Rieber, Kahlil and Sheppard, Diane and Park, Chul and Ergas, Sarina J and N{\"u}sslein, Klaus} } @article {723, title = {New bactericidal surgical suture coating.}, journal = {Langmuir}, volume = {28}, year = {2012}, month = {2012 Aug 21}, pages = {12134-9}, abstract = {This paper demonstrates the effectiveness of a new antimicrobial suture coating. An amphiphilic polymer, poly[(aminoethyl methacrylate)-co-(butyl methacrylate)] (PAMBM), inspired by antimicrobial peptides, was bactericidal against S. aureus in time-kill experiments. PAMBM was then evaluated in a variety of polymer blends using the Japanese Industrial Standard (JIS) method and showed excellent antimicrobial activity at a low concentration (0.5 wt \%). Using a similar antimicrobial coating formula to commercial Vicryl Plus sutures, disk samples of the coating material containing PAMBM effectively killed bacteria (98\% reduction at 0.75 wt \%). Triclosan, the active ingredient in Vicryl Plus coatings, did not kill the bacteria. Further Kirby-Bauer assays of these disk samples showed an increasing zone of inhibition with increasing concentration of PAMBM. Finally, the PAMBM-containing coating was applied to sutures, and the morphology of the coating surface was characterized by SEM, along with Vicryl and uncoated sutures. The PAMBM-containing sutures killed bacteria more effectively (3 log(10) reduction at 2.4 wt \%) than Vicryl Plus sutures (0.5 log(10) reduction).}, issn = {1520-5827}, doi = {10.1021/la302732w}, author = {Li, Yan and Kumar, Kushi N and Dabkowski, Jeffrey M and Corrigan, Meagan and Scott, Richard W and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {724, title = {Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water.}, journal = {Front Microbiol}, volume = {3}, year = {2012}, month = {2012}, pages = {175}, abstract = {Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37\%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R(2) = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community.}, issn = {1664-302X}, doi = {10.3389/fmicb.2012.00175}, author = {Unal, Burcu and Perry, Verlin Ryan and Sheth, Mili and Gomez-Alvarez, Vicente and Chin, Kuk-Jeong and N{\"u}sslein, Klaus} } @article {725, title = {Using flow to switch the valency of bacterial capture on engineered surfaces containing immobilized nanoparticles.}, journal = {Langmuir}, volume = {28}, year = {2012}, month = {2012 May 22}, pages = {7803-10}, abstract = {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 (Staphylococcus aureus) 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.}, issn = {1520-5827}, doi = {10.1021/la205080y}, author = {Fang, Bing and Gon, Saugata and Park, Myoung-Hwan and Kumar, Kushi-Nidhi and Rotello, Vincent M and N{\"u}sslein, Klaus and Santore, Maria M} } @article {730, title = {Phytoprotective influence of bacteria on growth and cadmium accumulation in the aquatic plant Lemna minor.}, journal = {Water Res}, volume = {44}, year = {2010}, month = {2010 Sep}, pages = {4970-9}, abstract = {Certain plants are known to accumulate heavy metals, and can be used in remediation of polluted soil or water. Plant-associated bacteria, especially those that are metal tolerant, may enhance the total amount of metal accumulated by the plant, but this process is still unclear. In this study, we investigated metal enhancement vs. exclusion by plants, and the phytoprotective role plant-associated bacteria might provide to plants exposed to heavy metal. We isolated cadmium-tolerant bacteria from the roots of the aquatic plant Lemna minor grown in heavy metal-polluted waters, and tested these isolates for tolerance to cadmium. The efficiency of plants to accumulate heavy metal from their surrounding environment was then tested by comparing L. minor plants grown with added metal tolerant bacteria to plants grown axenically to determine, whether bacteria associated with these plants increase metal accumulation in the plant. Unexpectedly, cadmium tolerance was not seen in all bacterial isolates that had been exposed to cadmium. Axenic plants accumulated slightly more cadmium than plants inoculated with bacterial isolates. Certain isolates promoted root growth, but overall, addition of bacterial strains did not enhance plant cadmium uptake, and in some cases, inhibited cadmium accumulation by plants. This suggests that bacteria serve a phytoprotective role in their relationship with Lemna minor, preventing toxic cadmium from entering plants.}, keywords = {Adaptation, Physiological, Araceae, Bacteria, Biodegradation, Environmental, Cadmium, Hydrogen-Ion Concentration, Molecular Sequence Data, Plant Roots, Siderophores, Water}, issn = {1879-2448}, doi = {10.1016/j.watres.2010.07.073}, author = {Stout, Lisa M and Dodova, Elena N and Tyson, Julian F and N{\"u}sslein, Klaus} } @article {732, title = {The role of nano-scale heterogeneous electrostatic interactions in initial bacterial adhesion from flow: a case study with Staphylococcus aureus.}, journal = {Colloids Surf B Biointerfaces}, volume = {76}, year = {2010}, month = {2010 Apr 1}, pages = {489-95}, abstract = {This study investigated the initial adhesion of Staphylococcus aureus from flowing buffer onto modified albumin films with the objective of probing the influence of electrostatic heterogeneity on bacterial adhesion. Electrostatic heterogeneity, on the lengthscale of 10-100 nm, was incorporated into the protein film through the irreversible random deposition of small amounts of polycation coils to produce isolated positive "patches" on the otherwise negative albumin surface before exposure to bacteria, which also possess a net negative surface charge. The system was benchmarked against an appropriate analog using 1 microm silica spheres and the same cationic patches on a silica substrate. Bacterial adhesion from flow was measured with the surface oriented vertically to eliminate gravitational forces between the bacteria and collector. In both systems, a threshold in the surface density of polycation patches needed for bacterial (or silica particle) capture indicated multivalent binding: multiple polycation patches were needed to adhere the bacteria (particles). The shifting of the threshold to greater patch concentrations at lower ionic strengths confirmed that the electrostatic interaction area (zone of influence) was a key factor in modulating the interactions. The role of the contact area in this manner is important because it enables a quantitative explanation of counterintuitive bacterial adhesion onto net negative surfaces. The study further revealed a hydrodynamic crossover from a regime where flow aids bacterial adhesion to one where flow impedes adhesion. An explanation is put forth in terms of the relative hydrodynamic and surface forces.}, keywords = {Adsorption, Bacterial Adhesion, Methacrylates, Nylons, Particle Size, Serum Albumin, Bovine, Silicon Dioxide, Staphylococcus aureus, Static Electricity, Surface Properties}, issn = {1873-4367}, doi = {10.1016/j.colsurfb.2009.12.009}, author = {Kalasin, Surachate and Dabkowski, Jeffrey and N{\"u}sslein, Klaus and Santore, Maria M} } @article {733, title = {Antimicrobial polymers prepared by ring-opening metathesis polymerization: manipulating antimicrobial properties by organic counterion and charge density variation.}, journal = {Chemistry}, volume = {15}, year = {2009}, month = {2009 Nov 2}, pages = {11715-22}, abstract = {The synthesis and characterization of a series of poly(oxanorbornene)-based synthetic mimics of antimicrobial peptides (SMAMPs) is presented. In the first part, the effect of different organic counterions on the antimicrobial properties of the SMAMPs was investigated. Unexpectedly, adding hydrophobicity by complete anion exchange did not increase the SMAMPs{\textquoteright} antimicrobial activity. It was found by dye-leakage studies that this was due to the loss of membrane activity of these polymers caused by the formation of tight ion pairs between the organic counterions and the polymer backbone. In the second part, the effect of molecular charge density on the biological properties of a SMAMP was investigated. The results suggest that, above a certain charge threshold, neither minimum inhibitory concentration (MIC90) nor hemolytic activity (HC50) is greatly affected by adding more cationic groups to the molecule. A SMAMP with an MIC90 of 4 microg mL(-1) against Staphylococcus aureus and a selectivity (=HC50/MIC90) of 650 was discovered, the most selective SMAMP to date.}, keywords = {Anti-Infective Agents, Biomimetic Materials, Cations, Diamines, Hemolysis, Hydrophobic and Hydrophilic Interactions, Microbial Sensitivity Tests, Polymers}, issn = {1521-3765}, doi = {10.1002/chem.200900606}, author = {Lienkamp, Karen and Madkour, Ahmad E and Kumar, Kushi-Nidhi and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {739, title = {Comparison of facially amphiphilic versus segregated monomers in the design of antibacterial copolymers.}, journal = {Chemistry}, volume = {15}, year = {2009}, month = {2009}, pages = {433-9}, abstract = {A direct comparison of two strategies for designing antimicrobial polymers is presented. Previously, we published several reports on the use of facially amphiphilic (FA) monomers which led to polynorbornenes with excellent antimicrobial activities and selectivities. Our polymers obtained by copolymerization of structurally similar segregated monomers, in which cationic and non-polar moieties reside on separate repeat units, led to polymers with less pronounced activities. A wide range of polymer amphiphilicities was surveyed by pairing a cationic oxanorbornene with eleven different non-polar monomers and varying the comonomer feed ratios. Their properties were tested using antimicrobial assays and copolymers possessing intermediate hydrophobicities were the most active. Polymer-induced leakage of dye-filled liposomes and microscopy of polymer-treated bacteria support a membrane-based mode of action. From these results there appears to be profound differences in how a polymer made from FA monomers interacts with the phospholipid bilayer compared with copolymers from segregated monomers. We conclude that a well-defined spatial relationship of the whole polymer is crucial to obtain synthetic mimics of antimicrobial peptides (SMAMPs): charged and non-polar moieties need to be balanced locally, for example, at the monomer level, and not just globally. We advocate the use of FA monomers for better control of biological properties. It is expected that this principle will be usefully applied to other backbones such as the polyacrylates, polystyrenes, and non-natural polyamides.}, keywords = {Anti-Bacterial Agents, Bacteria, Cell Membrane, Drug Design, Hemolysis, Plastics, Polymers, Surface-Active Agents}, issn = {1521-3765}, doi = {10.1002/chem.200801233}, author = {Gabriel, Gregory J and Maegerlein, Janet A and Nelson, Christopher F and Dabkowski, Jeffrey M and Eren, Tarik and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {734, title = {"Doubly selective" antimicrobial polymers: how do they differentiate between bacteria?}, journal = {Chemistry}, volume = {15}, year = {2009}, month = {2009 Nov 2}, pages = {11710-4}, abstract = {We have investigated how doubly selective synthetic mimics of antimicrobial peptides (SMAMPs), which can differentiate not only between bacteria and mammalian cells, but also between Gram-negative and Gram-positive bacteria, make the latter distinction. By dye-leakage experiments on model vesicles and complementary experiments on bacteria, we were able to relate the Gram selectivity to structural differences of these bacteria types. We showed that the double membrane of E. coli rather than the difference in lipid composition between E. coli and S. aureus was responsible for Gram selectivity. The molecular-weight-dependent antimicrobial activity of the SMAMPs was shown to be a sieving effect: while the 3000 g mol(-1) SMAMP was able to penetrate the peptidoglycan layer of the Gram-positive S. aureus bacteria, the 50000 g mol(-1) SMAMP got stuck and consequently did not have antimicrobial activity.}, keywords = {Anti-Infective Agents, Biomimetic Materials, Escherichia coli, Microbial Sensitivity Tests, Peptidoglycan, Polymers, Staphylococcus aureus}, issn = {1521-3765}, doi = {10.1002/chem.200802558}, author = {Lienkamp, Karen and Kumar, Kushi-Nidhi and Som, Abhigyan and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {736, title = {Hydrogenotrophic denitrification and perchlorate reduction in ion exchange brines using membrane biofilm reactors.}, journal = {Biotechnol Bioeng}, volume = {104}, year = {2009}, month = {2009 Oct 15}, pages = {483-91}, abstract = {Halophilic (salt loving), hydrogenotrophic (H(2) oxidizing) denitrifying bacteria were investigated for treatment of nitrate (NO3-) and perchlorate (ClO4-) contaminated groundwater and ion exchange (IX) brines. Hydrogenotrophic denitrifying bacteria were enriched from a denitrifying wastewater seed under both halophilc and non-halophilc conditions. The cultures were inoculated into bench-scale membrane biofilm reactors (MBfRs) with an "outside in" configuration, with contaminated water supplied to the lumen of the membranes and H(2) supplied to the shell. Abiotic mass transfer tests showed that H(2) mass transfer coefficients were lower in brines than in tap water at highest Reynolds number, possibly due to increased transport of salts and decreased H(2) solubility at the membrane/liquid interface. An average NO3- removal efficiency of 93\% was observed for the MBfR operated in continuous flow mode with synthetic contaminated groundwater. Removal efficiencies of 30\% for NO3- and 42\% for ClO4- were observed for the MBfR operated with synthetic IX brine in batch operating mode with a reaction time of 53 h. Phylogenetic analysis focused on the active microbial community and revealed that halotolerant, NO3- -reducing bacteria of the bacterial classes Gamma-Proteobacteria and Sphingobacteria were the metabolically dominant members within the stabilized biofilm. This study shows that, despite decreased H(2) transfer under high salt conditions, hydrogenotrophic biological reduction may be successfully used for the treatment of NO3- and ClO- in a MBfR.}, keywords = {Bacteroidetes, Biofilms, Cluster Analysis, DNA, Bacterial, DNA, Ribosomal, Gammaproteobacteria, Hydrogen, Ion Exchange, Membranes, Molecular Sequence Data, Nitrites, Oxidation-Reduction, Perchloric Acid, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Water Pollutants, Chemical, Water Purification}, issn = {1097-0290}, doi = {10.1002/bit.22414}, author = {Sahu, Ashish K and Conneely, Teresa and N{\"u}sslein, Klaus and Ergas, Sarina J} } @article {738, title = {Hydrophilic modifications of an amphiphilic polynorbornene and the effects on its hemolytic and antibacterial activity.}, journal = {Biomacromolecules}, volume = {10}, year = {2009}, month = {2009 Feb 9}, pages = {353-9}, abstract = {Here we report the modification of an amphiphilic antibacterial polynorbornene, Poly3, via incorporation of hydrophilic, biocompatible groups. The sugar, zwitterionic, and polyethylene glycol based moieties were incorporated in varying ratios by copolymerization and postpolymerization techniques. Well-defined copolymers with molecular weights of 3 kDa and narrow polydispersity indices ranging from 1.08 to 1.15 were obtained. The effects of these modifications on the biological activity of these polymers were analyzed by determining their minimum inhibitory concentrations (MIC) and their hemolytic activities (HC50).}, keywords = {Anti-Bacterial Agents, Bacteria, Biocompatible Materials, Carbohydrates, Hemolysis, Microbial Sensitivity Tests, Plastics, Polyethylene, Static Electricity}, issn = {1526-4602}, doi = {10.1021/bm801129y}, author = {Colak, Semra and Nelson, Christopher F and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {742, title = {Antimicrobial polymers prepared by ROMP with unprecedented selectivity: a molecular construction kit approach.}, journal = {J Am Chem Soc}, volume = {130}, year = {2008}, month = {2008 Jul 30}, pages = {9836-43}, abstract = {Synthetic Mimics of Antimicrobial Peptides (SMAMPs) imitate natural host-defense peptides, a vital component of the body{\textquoteright}s immune system. This work presents a molecular construction kit that allows the easy and versatile synthesis of a broad variety of facially amphiphilic oxanorbornene-derived monomers. Their ring-opening metathesis polymerization (ROMP) and deprotection provide several series of SMAMPs. Using amphiphilicity, monomer feed ratio, and molecular weight as parameters, polymers with 533 times higher selectivitiy (selecitviy = hemolytic concentration/minimum inhibitory concentration) for bacteria over mammalian cells were discovered. Some of these polymers were 50 times more selective for Gram-positive over Gram-negative bacteria while other polymers surprisingly showed the opposite preference. This kind of "double selectivity" (bacteria over mammalian and one bacterial type over another) is unprecedented in other polymer systems and is attributed to the monomer{\textquoteright}s facial amphiphilicity.}, keywords = {Anti-Infective Agents, Antimicrobial Cationic Peptides, Biomimetic Materials, Erythrocytes, Escherichia coli, Hemolysis, Humans, Hydrophobic and Hydrophilic Interactions, Microbial Sensitivity Tests, Molecular Weight, Norbornanes, Polymers, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Staphylococcus aureus, Structure-Activity Relationship}, issn = {1520-5126}, doi = {10.1021/ja801662y}, author = {Lienkamp, Karen and Madkour, Ahmad E and Musante, Ashlan and Nelson, Christopher F and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {741, title = {Investigating the effect of increasing charge density on the hemolytic activity of synthetic antimicrobial polymers.}, journal = {Biomacromolecules}, volume = {9}, year = {2008}, month = {2008 Oct}, pages = {2805-10}, abstract = {The current study is aimed at investigating the effect of fine-tuning the cationic character of synthetic mimics of antimicrobial peptides (SMAMPs) on the hemolytic and antibacterial activities. A series of novel norbornene monomers that carry one, two, or three Boc-protected amine functionalities was prepared. Ring-opening metathesis polymerization (ROMP) of the monomers, followed by deprotection of the amine groups resulted in cationic antimicrobial polynorbornenes that carry one, two, and three charges per monomer repeat unit. Increasing the number of amine groups on the most hydrophobic polymer reduced its hemolytic activity significantly. To understand the membrane activity of these polymers, we conducted dye leakage experiments on lipid vesicles that mimic bacteria and red blood cell membranes, and these results showed a strong correlation with the hemolysis data.}, keywords = {Amines, Anti-Infective Agents, Antimicrobial Cationic Peptides, Chemistry, Pharmaceutical, Drug Design, Erythrocytes, Escherichia coli, Hemolysis, Humans, Lipids, Magnetic Resonance Spectroscopy, Models, Chemical, Peptides, Polymers, Staphylococcus aureus}, issn = {1526-4602}, doi = {10.1021/bm800569x}, author = {Al-Badri, Zoha M and Som, Abhigyan and Lyon, Sarah and Nelson, Christopher F and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {740, title = {Synthetic mimic of antimicrobial peptide with nonmembrane-disrupting antibacterial properties.}, journal = {Biomacromolecules}, volume = {9}, year = {2008}, month = {2008 Nov}, pages = {2980-3}, abstract = {Polyguanidinium oxanorbornene ( PGON) 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), PGON did not disrupt membranes in vesicle-dye leakage assays and microscopy experiments. The unique biological properties of PGON, in same ways similar to cell-penetrating peptides, strongly encourage the examination of other novel guanidino containing macromolecules as powerful and selective antimicrobial agents.}, keywords = {Anti-Bacterial Agents, Antimicrobial Cationic Peptides, Erythrocytes, Gram-Negative Bacteria, Gram-Positive Bacteria, Guanidines, Humans, Microbial Sensitivity Tests, Molecular Mimicry, Polymers}, issn = {1526-4602}, doi = {10.1021/bm800855t}, author = {Gabriel, Gregory J and Madkour, Ahmad E and Dabkowski, Jeffrey M and Nelson, Christopher F and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {743, title = {Arsenic sequestration by nitrate respiring microbial communities in urban lake sediments.}, journal = {Chemosphere}, volume = {70}, year = {2007}, month = {2007 Dec}, pages = {329-36}, abstract = {Changes in microbial community composition and activity were related to geochemical conditions favoring arsenic sequestration in sediments collected from the urban, arsenic-contaminated Upper Mystic Lake. After amendment with nitrate, >94\% total soluble arsenic is sequestered by Fe(III)-(oxy)hydroxides generated in live sediments. Of this sequestered arsenic, >75\% existed as As(III), indicating As redox state alone is not responsible for changes in mobility. Arsenic sequestration was concurrent with the microbial respiration of nitrate as indicated by steady state hydrogen concentration and the presence of organisms similar to nitrate-reducing, iron-oxidizing bacteria belonging to the genus Dechloromonas in 16S rDNA clone libraries.}, keywords = {Arsenic, Betaproteobacteria, Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Fresh Water, Geologic Sediments, Massachusetts, Nitrates, Oxidation-Reduction, RNA, Ribosomal, 16S, Urbanization, Water Microbiology, Water Pollutants, Chemical}, issn = {0045-6535}, doi = {10.1016/j.chemosphere.2007.05.094}, author = {Gibney, Brian P and N{\"u}sslein, Klaus} } @article {746, title = {Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages.}, journal = {FEMS Microbiol Ecol}, volume = {60}, year = {2007}, month = {2007 Apr}, pages = {60-73}, abstract = {Volcanic activity creates new landforms that can change dramatically over time as a consequence of biotic succession. Nonetheless, volcanic deposits present severe constraints for microbial colonization and activity. We have characterized bacterial diversity on four recent deposits at Kilauea volcano, Hawaii (KVD). Much of the diversity was either closely related to uncultured organisms or distinct from any reported 16S rRNA gene sequences. Diversity indices suggested that diversity was highest in a moderately vegetated 210-year-old ash deposit (1790-KVD), and lowest for a 79-year-old lava flow (1921-KVD). Diversity for a 41-year-old tephra deposit (1959-KVD) and a 300-year-old rainforest (1700-KVD) reached intermediate values. The 1959-KVD and 1790-KVD communities were dominated by Acidobacteria, Alpha- and Gammaproteobacteria, Actinobacteria, Cyanobacteria, and many unclassified phylotypes. The 1921-KVD, an unvegetated low pH deposit, was dominated by unclassified phylotypes. In contrast, 1700-KVD was primarily populated by Alphaproteobacteria with very few unclassified phylotypes. Similar diversity indices and levels of trace gas flux were found for 1959-KVD and 1790-KVD; however, statistical analyses indicated significantly different communities. This study not only showed that microorganisms colonize recent volcanic deposits and are able to establish diverse communities, but also that their composition is governed by variations in local deposit parameters.}, keywords = {Bacteria, DNA, Bacterial, Ecosystem, Genes, rRNA, Genetic Variation, Hawaii, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil Microbiology, Time Factors, Volcanic Eruptions}, issn = {0168-6496}, doi = {10.1111/j.1574-6941.2006.00253.x}, author = {Gomez-Alvarez, Vicente and King, Gary M and N{\"u}sslein, Klaus} } @article {744, title = {Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter.}, journal = {Appl Environ Microbiol}, volume = {73}, year = {2007}, month = {2007 Jul}, pages = {4171-9}, abstract = {The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl(-) in a subsurface shale rich in CH(4) derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH(4)-producing zone lacked electron acceptors such as O(2), NO(3)(-), Fe(3+), or SO(4)(2-). Acetate was detected only in high-salinity waters, suggesting that acetoclastic methanogenesis is inhibited at Cl(-) concentrations above approximately 1,000 mM. Most-probable-number series revealed differences in methanogen substrate utilization (acetate, trimethylamine, or H(2)/CO(2)) associated with chlorinity. The greatest methane production in enrichment cultures was observed for incubations with salinity at or close to the native pore water salinity of the inoculum. Restriction fragment length polymorphism analyses of archaeal 16S rRNA genes from seven wells indicated that there were links between archaeal communities and pore water salinity. Archaeal clone libraries constructed from sequences from 16S rRNA genes isolated from two wells revealed phylotypes similar to a halophilic methylotrophic Methanohalophilus species and a hydrogenotrophic Methanoplanus species at high salinity and a single phylotype closely related to Methanocorpusculum bavaricum at low salinity. These results show that several distinct communities of methanogens persist in this subsurface, CH(4)-producing environment and that each community is adapted to particular conditions of salinity and preferential substrate use and each community induces distinct geochemical signatures in shale formation waters.}, keywords = {Archaea, Base Sequence, Cloning, Molecular, DNA Primers, Genes, Archaeal, Genetic Variation, Geologic Sediments, Methane, Michigan, Molecular Sequence Data, Organic Chemicals, Phylogeny, RNA, Archaeal, RNA, Ribosomal, 16S, Sodium Chloride, Soil, Soil Microbiology, Water Microbiology}, issn = {0099-2240}, doi = {10.1128/AEM.02810-06}, author = {Waldron, Patricia J and Petsch, Steven T and Martini, Anna M and N{\"u}sslein, Klaus and N{\"u}slein, Klaus} } @article {747, title = {Broad-spectrum antibacterial activity by a novel abiogenic peptide mimic.}, journal = {Microbiology}, volume = {152}, year = {2006}, month = {2006 Jul}, pages = {1913-8}, abstract = {The human-mediated use and abuse of classical antibiotics has created a strong selective pressure for the rapid evolution of antibiotic resistance. As resistance levels rise, and the efficacy of classical antibiotics wanes, the intensity of the search for alternative antimicrobials has increased. One class of molecules that has attracted much attention is the antimicrobial peptides (AMPs). They exhibit broad-spectrum activity, they are potent and they are widespread as part of the innate defence system of both vertebrates and invertebrates. However, peptides are complex molecules that suffer from proteolytic degradation. The ability to capture the essential properties of antimicrobial peptides in simple easy-to-prepare molecules that are abiotic in origin and non-proteolytic offers many advantages. Mechanistic and structural knowledge of existing AMPs was used to design a novel compound that mimics the biochemical activity of an AMP. This report describes the development and in vitro characterization of a small peptide mimic that exhibited quick-acting and selective antibacterial activity against a broad range of bacteria, including numerous clinically relevant strains, at low MIC values.}, keywords = {Anti-Bacterial Agents, Drug Design, Humans, Microbial Sensitivity Tests, Peptides}, issn = {1350-0872}, doi = {10.1099/mic.0.28812-0}, author = {N{\"u}sslein, Klaus and Arnt, Lachelle and Rennie, Jason and Owens, Cullen and Tew, Gregory N} } @article {748, title = {Distribution of extensive nifH gene diversity across physical soil microenvironments.}, journal = {Microb Ecol}, volume = {51}, year = {2006}, month = {2006 May}, pages = {441-52}, abstract = {The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant-microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 microm to the clay fraction at < 75 microm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.}, keywords = {Bacteria, Base Sequence, DNA Primers, Genes, Bacterial, Multigene Family, Oxidoreductases, Phylogeny, Polymerase Chain Reaction, Soil Microbiology}, issn = {0095-3628}, doi = {10.1007/s00248-006-9044-x}, author = {Izquierdo, Javier A and N{\"u}sslein, Klaus} } @article {751, title = {Shifts in rhizoplane communities of aquatic plants after cadmium exposure.}, journal = {Appl Environ Microbiol}, volume = {71}, year = {2005}, month = {2005 May}, pages = {2484-92}, abstract = {In this study we present the comparative molecular analysis of bacterial communities of the aquatic plant Lemna minor from a contaminated site (RCP) and from a laboratory culture (EPA), as well as each of these with the addition of cadmium. Plants were identified as L. minor by analysis of the rpl16 chloroplast region. Comparative bacterial community studies were based on the analyses of 16S rRNA clone libraries, each containing about 100 clones from the root surfaces of plants. Bacterial communities were compared at three phylogenetic levels of resolution. At the level of bacterial divisions, differences in diversity index scores between treatments, with and without cadmium within the same plant type (EPA or RCP), were small, indicating that cadmium had little effect. When we compared genera within the most dominant group, the beta-proteobacteria, differences between unamended and cadmium-amended libraries were much larger. Bacterial diversity increased upon cadmium addition for both EPA and RCP libraries. Analyses of diversity at the phylotype level showed parallel shifts to more even communities upon cadmium addition; that is, percentage changes in diversity indices due to cadmium addition were the same for either plant type, indicating that contamination history might be independent of disturbance-induced diversity shifts. At finer phylogenetic levels of resolution, the effects of cadmium addition on bacterial communities were very noticeable. This study is a first step in understanding the role of aquatic plant-associated microbial communities in phytoremediation of heavy metals.}, keywords = {Araceae, Bacteria, Base Sequence, Cadmium, Molecular Sequence Data, Phylogeny, Plant Roots, RNA, Ribosomal, 16S}, issn = {0099-2240}, doi = {10.1128/AEM.71.5.2484-2492.2005}, author = {Stout, Lisa M and N{\"u}sslein, Klaus} } @article {750, title = {Simple oligomers as antimicrobial peptide mimics.}, journal = {J Ind Microbiol Biotechnol}, volume = {32}, year = {2005}, month = {2005 Jul}, pages = {296-300}, abstract = {New approaches to antibiotic design are desperately needed. The design of simple oligomers that capture the shape and biological function of natural antimicrobial peptides could prove to be versatile and highly successful. We discuss the use of aromatic backbones to design facially amphiphilic (FA) beta-sheet like structures which are potently antimicrobial. These oligomers capture the physiochemical properties of peptides like the Magainins and Defensins, which fold into specific conformations that are amphiphilic resulting in antimicrobial activity. However, natural peptides are expensive to prepare and difficult to produce on large scale. The design of polymers and oligomers that mimic the complex structures and remarkable biological properties of proteins is an important endeavor and provides attractive alternatives to the difficult synthesis of natural peptides. We therefore have designed a series of FA oligomers that are easy to prepare from inexpensive monomers. They adopt structures very reminiscent of amphiphilic beta-sheets and have significant activity with minimal inhibitory concentrations at 6 h in the low microgram per ml range (muM to nM). They are active against a broad spectrum of bacteria including gram-positive and gram-negative as well as antibiotic resistant strains.}, keywords = {Amides, Anti-Bacterial Agents, Antimicrobial Cationic Peptides, Drug Resistance, Bacterial, Gram-Negative Bacteria, Gram-Positive Bacteria, Inhibitory Concentration 50, Peptides, Protein Conformation}, issn = {1367-5435}, doi = {10.1007/s10295-005-0219-0}, author = {Rennie, Jason and Arnt, Lachelle and Tang, Haizhong and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {752, title = {Tuning the hemolytic and antibacterial activities of amphiphilic polynorbornene derivatives.}, journal = {J Am Chem Soc}, volume = {126}, year = {2004}, month = {2004 Dec 8}, pages = {15870-5}, abstract = {Amphiphilic cationic polynorbornene derivatives, soluble in water, were prepared from modular norbornene monomers, with a wide range of molecular weights (M(n) = 1600-137 500 g/mol) and narrow polydispersities (PDI = 1.1-1.3). The antibacterial activity determined by growth inhibition assays and the hemolytic activity against human red blood cells were measured and compared to determine the selectivity of the polymers for bacterial over mammalian cells. The effects of monomer repeat unit hydrophobicity and polymer molecular weight on antibacterial and hemolytic activities were determined. The hydrophobicity of the repeat unit was observed to have dramatic effects on antibacterial and hemolytic activities. Lipid membrane disruption activities of the polymers was confirmed by measuring polymer-induced dye leakage from large unilamellar vesicles. By tuning the overall hydrophobicity of the polymer through random copolymerizations of modular norbornene derivatives, highly selective, nonhemolytic antibacterial activities were obtained. For appropriate monomer composition, selectivity against bacteria versus human red blood cells was determined to be over 100.}, keywords = {Anti-Bacterial Agents, Bacillus subtilis, Cell Membrane, Cholesterol, Erythrocytes, Escherichia coli, Hemolysis, Humans, Liposomes, Microbial Sensitivity Tests, Molecular Weight, Norbornanes, Polymers, Structure-Activity Relationship}, issn = {0002-7863}, doi = {10.1021/ja045664d}, author = {Ilker, M Firat and N{\"u}sslein, Klaus and Tew, Gregory N and Coughlin, E Bryan} }