PeerJ Preprints: Environmental Scienceshttps://peerj.com/preprints/index.atom?journal=peerj&subject=1400Environmental Sciences articles published in PeerJ PreprintsDynamic multi-species occupancy models of birds of high-altitude grasslands in eastern South Africahttps://peerj.com/preprints/269322018-05-142018-05-14David H MaphisaHanneline Smit_RobinsonRes Altwegg
Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.
Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencinghttps://peerj.com/preprints/33692017-10-252017-10-25Lauren O'ConnellSong GaoDonald McCorquodaleJay FleisherJose V Lopez
Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution and nutrients to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to their impacts on surrounding marine environments. We hypothesize annual microbial fluctuations based on seasons (wet vs dry), assessed by high throughput 16S rRNA amplicon library sequencing. Surface water samples were collected weekly for one year, creating a high sampling frequency and fine sampling scale. Over 1.4 million 16S rRNA V4 reads generated a total of 16,384 Operational Taxonomic Units (OTUs) from the PEI habitat. We observed Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria as the most dominant phyla. Analysis of potentially pathogenic genera show the presence of Staphylococcus and Bacillus, albeit at lower relative abundances during peak shipping and tourist months (November –April), thus underscoring their relatively low presence. Statistical analyses indicated significant alpha diversity differences when comparing microbial communities with respect to time. This observation probably stems from the low community richness and abundance in August, which had lower than average rainfall levels for Florida’s wet season. The lower rainfall levels may have contributed to less runoff, and subsequently fewer bacterial groups being introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month and season. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages, which may have driven the significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were also observed in these months, possibly creating favorable bacterial growth conditions. To our knowledge, this study represents the first to sample a large port at this fine sampling scale. These data can help establish underlying inlet microbial community baselines, and supplement the vital monitoring of local marine and recreational environments, which appears more poignant in the context of local reef disease outbreaks and worldwide coral reef collapses in the wake of a harsh 2015-16 El Nino event.
Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution and nutrients to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to their impacts on surrounding marine environments. We hypothesize annual microbial fluctuations based on seasons (wet vs dry), assessed by high throughput 16S rRNA amplicon library sequencing.Surface water samples were collected weekly for one year, creating a high sampling frequency and fine sampling scale. Over 1.4 million 16S rRNA V4 reads generated a total of 16,384 Operational Taxonomic Units (OTUs) from the PEI habitat. We observed Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria as the most dominant phyla. Analysis of potentially pathogenic genera show the presence of Staphylococcus and Bacillus, albeit at lower relative abundances during peak shipping and tourist months (November –April), thus underscoring their relatively low presence. Statistical analyses indicated significant alpha diversity differences when comparing microbial communities with respect to time. This observation probably stems from the low community richness and abundance in August, which had lower than average rainfall levels for Florida’s wet season. The lower rainfall levels may have contributed to less runoff, and subsequently fewer bacterial groups being introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month and season. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages, which may have driven the significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were also observed in these months, possibly creating favorable bacterial growth conditions. To our knowledge, this study represents the first to sample a large port at this fine sampling scale. These data can help establish underlying inlet microbial community baselines, and supplement the vital monitoring of local marine and recreational environments, which appears more poignant in the context of local reef disease outbreaks and worldwide coral reef collapses in the wake of a harsh 2015-16 El Nino event.Distinguishing polemic from commentary in science: Some guidelines illustrated with the case of Sage and Burgio, 2017https://peerj.com/preprints/33552017-10-192017-10-19David Robert GrimesDorothy V Bishop
Exposure to non-ionizing radiation used in wireless communication remains a contentious topic in the public mind - while the overwhelming scientific evidence to date suggests that microwave and radio frequencies used in modern communications are safe, public apprehension remains considerable. A recent paper in Child Development has caused concern by alleging a causative connection between non-ionizing radiation and a host of conditions, including autism and cancer. In this work, we outline why these claims are devoid of merit, and why they should not have been given a scientific veneer of legitimacy. We also outline some hallmarks of potentially dubious science, with the hope that authors, reviews and editors might be better able to avoid suspect scientific claims.
Exposure to non-ionizing radiation used in wireless communication remains a contentious topic in the public mind - while the overwhelming scientific evidence to date suggests that microwave and radio frequencies used in modern communications are safe, public apprehension remains considerable. A recent paper in Child Development has caused concern by alleging a causative connection between non-ionizing radiation and a host of conditions, including autism and cancer. In this work, we outline why these claims are devoid of merit, and why they should not have been given a scientific veneer of legitimacy. We also outline some hallmarks of potentially dubious science, with the hope that authors, reviews and editors might be better able to avoid suspect scientific claims.Using iNaturalist observations to detect disease in Red Mangroves (Rhizophora mangle)https://peerj.com/preprints/33262017-10-052017-10-05Ryann E Rossi
Detection of disease over broad spatial scales is important to managing the spread of many diseases. One way to do this is to work with citizen scientists to collect data over broad spatial and temporal scales. Citizen science observations are becoming more widely available through web and app interfaces such as iNaturalist.org. iNaturalist.org provides passive sampling of organisms through photographs with a geolocation. These observations are often used to examine biodiversity and species monitoring, but, disease detection is also possible. Here, I demonstrate the utility of using iNaturlist.org observations of red mangrove to detect foliar disease symptoms such as lesions. I downloaded observations of red mangrove from iNaturalist.org, filtered them and examined images for foliar disease symptoms. Out of 153 filtered images, I found that 42% showed no signs of foliar disease while 58% did show foliar disease symptoms. I also found that observations of red mangrove were recorded from 15 countries in total, with 11 countries having at least one observation with foliar disease symptoms present. While small, this study demonstrates the utility of using resources such as iNaturalist.org to obtain preliminary disease observations which can be used to further focus in person disease surveys and sampling.
Detection of disease over broad spatial scales is important to managing the spread of many diseases. One way to do this is to work with citizen scientists to collect data over broad spatial and temporal scales. Citizen science observations are becoming more widely available through web and app interfaces such as iNaturalist.org. iNaturalist.org provides passive sampling of organisms through photographs with a geolocation. These observations are often used to examine biodiversity and species monitoring, but, disease detection is also possible. Here, I demonstrate the utility of using iNaturlist.org observations of red mangrove to detect foliar disease symptoms such as lesions. I downloaded observations of red mangrove from iNaturalist.org, filtered them and examined images for foliar disease symptoms. Out of 153 filtered images, I found that 42% showed no signs of foliar disease while 58% did show foliar disease symptoms. I also found that observations of red mangrove were recorded from 15 countries in total, with 11 countries having at least one observation with foliar disease symptoms present. While small, this study demonstrates the utility of using resources such as iNaturalist.org to obtain preliminary disease observations which can be used to further focus in person disease surveys and sampling.Ammonium interference reduced copper uptake by formaldehyde-crosslinked Sargassum sp. seaweedhttps://peerj.com/preprints/12282017-09-242017-09-24Wenfa Ng
Sargassum sp., a marine brown macroalgae, is an efficient sorbent for various heavy metals at high concentrations. However, the efficiency at which seaweed removes heavy metals from dilute solutions and the effect of ammonium on metal removal is not well understood; an issue of importance given the ubiquity of nitrogenous compounds in the environment arising from various surface runoffs. Herein, the effect of ammonium on copper removal (at trace to low concentration) by formaldehyde crosslinked Sargassum sp. (treated SW) was studied. Due to high copper background, equilibrium sorption experiments was inconclusive concerning treated SW’s ability in removing copper (<1000 ppb), but rapid copper sorption observed in kinetic experiments suggested potential feasibility of the process. Within initial copper concentration of 4 to 20 ppm and pH 2 to 5, experiments revealed that, above a threshold concentration of [NH4+-N] of 50 ppm, ammonium impede copper update on treated SW in a concentration dependent manner. Specifically, sorption kinetics slowed, and uptake capacity decreased with increase in [NH4+-N] from 0 to 2500 ppm. Collectively, beyond demonstrating that treated SW could remove copper from dilute solutions, revelations that ammonium reduced copper sorption highlighted the importance of accounting for the effect in data interpretation and modelling.
Sargassum sp., a marine brown macroalgae, is an efficient sorbent for various heavy metals at high concentrations. However, the efficiency at which seaweed removes heavy metals from dilute solutions and the effect of ammonium on metal removal is not well understood; an issue of importance given the ubiquity of nitrogenous compounds in the environment arising from various surface runoffs. Herein, the effect of ammonium on copper removal (at trace to low concentration) by formaldehyde crosslinked Sargassum sp. (treated SW) was studied. Due to high copper background, equilibrium sorption experiments was inconclusive concerning treated SW’s ability in removing copper (<1000 ppb), but rapid copper sorption observed in kinetic experiments suggested potential feasibility of the process. Within initial copper concentration of 4 to 20 ppm and pH 2 to 5, experiments revealed that, above a threshold concentration of [NH4+-N] of 50 ppm, ammonium impede copper update on treated SW in a concentration dependent manner. Specifically, sorption kinetics slowed, and uptake capacity decreased with increase in [NH4+-N] from 0 to 2500 ppm. Collectively, beyond demonstrating that treated SW could remove copper from dilute solutions, revelations that ammonium reduced copper sorption highlighted the importance of accounting for the effect in data interpretation and modelling.The proteomic response of the reef coral Pocillopora acuta to experimentally elevated temperatureshttps://peerj.com/preprints/32522017-09-132017-09-13Anderson B MayfieldYi-Jyun ChenChi-Yu LuChii-Shiarng Chen
Although most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a 9-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially expressed proteins (DEPs) were removed from the protein gels and sequenced with mass spectrometry. Sixty unique DEPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more likely to up-regulate protein expression in response to high temperature exposure than the coral hosts in which they resided at the 2-week sampling time. Furthermore, different cellular pathways were affected by elevated temperature exposure in each compartment; Symbiodinium tended to up-regulate the expression of proteins involved in the cellular stress response, whereas the differentially expressed host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates have differing cellular strategies for acclimating to elevated temperatures.
Although most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a 9-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially expressed proteins (DEPs) were removed from the protein gels and sequenced with mass spectrometry. Sixty unique DEPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more likely to up-regulate protein expression in response to high temperature exposure than the coral hosts in which they resided at the 2-week sampling time. Furthermore, different cellular pathways were affected by elevated temperature exposure in each compartment; Symbiodinium tended to up-regulate the expression of proteins involved in the cellular stress response, whereas the differentially expressed host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates have differing cellular strategies for acclimating to elevated temperatures.Agricultural constraints on microbial resource use and niche breadth in drainage ditcheshttps://peerj.com/preprints/32212017-09-022017-09-02Ellard R HuntingHenrik BarmentloMaarten SchramaPeter van BodegomYujia ZhaiMartina Vijver
Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood.
Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM.
Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality.
Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.
Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood.Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM.Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality.Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.Biological facilitation of the giant tree fern Angiopteris evecta in the germination of the invasive velvet tree Miconia calvescenshttps://peerj.com/preprints/26432017-08-292017-08-29Jaemin Lee
Background. Biological facilitation is a type of relationship between two taxa that benefits at least one of the participants and harms neither. Although invasive species are widely known to compete with native taxa, recent studies suggest that invasive and native species can have positive relationships. This study aims to examine the biological facilitation of the germination of invasive Miconia calvescens by giant tree fern Angiopteris evecta, native to French Polynesia.
Methods. Field surveys were conducted to measure A. evecta and M. calvescens by applying the 10×10 m2 quadrat survey method. The density of seedlings, saplings, and matures of M. calvescens growing on the rhizomes of A. evecta and on bare soil was compared, and the correlation between the size of the rhizomes and the number of M. calvescens growing on them was verified. Two separate sets of nutrient measurements of substrates were performed to compare the nutrient of A. evecta rhizome and other environments (abiotic and potential biotic environments). Leaf decomposition rate of five dominant tree species was compared to verify whether A. evecta has quickly decomposing leaves, and therefore induce the germination of M. calvescens indirectly.
Results. Field surveys show that there is a greater number of seedlings and saplings of M. calvescens growing on the rhizomes of A. evecta as compared to bare soil. Furthermore, there is a positive correlation between the size of rhizomes and the number of M. calvescens growing on them. Substrates of A. evecta had higher phosphorus and potassium contents compared to other soils and substrates, but did not differ from bark of other tree species that could potentially offer favorable microenvironments. A. evecta has quickly decomposing leaves.
Discussion. A. evecta facilitates the germination of M. calvescens, supported by the much higher number of seedlings and saplings growing on the rhizomes and the positive correlation between the size of the rhizome and the number of M. calvescens growing on it. Microslopes on the rhizomes of A. evecta prevent leaf litter from accumulating on the rhizomes, and enable more sunlight to reach and facilitate the germination of M. calvescens seeds. Also, quickly decomposing leaves of A. evecta prevent the accumulation of leaf litter on the ground and enable more light to reach seed bank. Although the chemical components is not different from other tree species, physical structure of the rhizome and consequent higher light availability, and higher amount of potassium than bare soil would be the possible reason for the facilitation. Biological facilitation of the germination of invasive M. calvescens by native A. evecta can give better understanding on the invasion success and the relationship between the native and invasive species. Invasion of A. evecta can induce and promote further invasion of M. calvescens. Therefore, thorough management of ongoing invasion of A. evecta is particularly required.
Background. Biological facilitation is a type of relationship between two taxa that benefits at least one of the participants and harms neither. Although invasive species are widely known to compete with native taxa, recent studies suggest that invasive and native species can have positive relationships. This study aims to examine the biological facilitation of the germination of invasive Miconia calvescens by giant tree fern Angiopteris evecta, native to French Polynesia.Methods. Field surveys were conducted to measure A. evecta and M. calvescens by applying the 10×10 m2 quadrat survey method. The density of seedlings, saplings, and matures of M. calvescens growing on the rhizomes of A. evecta and on bare soil was compared, and the correlation between the size of the rhizomes and the number of M. calvescens growing on them was verified. Two separate sets of nutrient measurements of substrates were performed to compare the nutrient of A. evecta rhizome and other environments (abiotic and potential biotic environments). Leaf decomposition rate of five dominant tree species was compared to verify whether A. evecta has quickly decomposing leaves, and therefore induce the germination of M. calvescens indirectly.Results. Field surveys show that there is a greater number of seedlings and saplings of M. calvescens growing on the rhizomes of A. evecta as compared to bare soil. Furthermore, there is a positive correlation between the size of rhizomes and the number of M. calvescens growing on them. Substrates of A. evecta had higher phosphorus and potassium contents compared to other soils and substrates, but did not differ from bark of other tree species that could potentially offer favorable microenvironments. A. evecta has quickly decomposing leaves.Discussion. A. evecta facilitates the germination of M. calvescens, supported by the much higher number of seedlings and saplings growing on the rhizomes and the positive correlation between the size of the rhizome and the number of M. calvescens growing on it. Microslopes on the rhizomes of A. evecta prevent leaf litter from accumulating on the rhizomes, and enable more sunlight to reach and facilitate the germination of M. calvescens seeds. Also, quickly decomposing leaves of A. evecta prevent the accumulation of leaf litter on the ground and enable more light to reach seed bank. Although the chemical components is not different from other tree species, physical structure of the rhizome and consequent higher light availability, and higher amount of potassium than bare soil would be the possible reason for the facilitation. Biological facilitation of the germination of invasive M. calvescens by native A. evecta can give better understanding on the invasion success and the relationship between the native and invasive species. Invasion of A. evecta can induce and promote further invasion of M. calvescens.Therefore, thorough management of ongoing invasion of A. evecta is particularly required.Zeta potential of bacterial cells: Effect of wash buffershttps://peerj.com/preprints/1102017-08-222017-08-22Wenfa NgYen-Peng Ting
Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacterial cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured zeta potential, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis, where various wash buffers (such as 9 g/L NaCl, 0.001M KCl, and 0.1M NaNO3) are routinely used for removing (by charge screening) ions and charged molecules that bind nonspecifically to the cell surface. Using Escherichia coli DH5α grown in LB Lennox (with 2 g/L glucose), experiment data showed that the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L NaCl, and phosphate buffer saline (PBS) wash buffers. As LB Lennox is a low salt medium without a phosphate buffer, it was likely that the extent of nonspecific adsorption of ions on the cell surface was not severe, and the different wash buffers would correspondingly not exert much effect on measured zeta potential. Zeta potential-pH profiles for E. coli grown in a semi-defined medium (with a high capacity phosphate buffer system), on the other hand, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L NaCl, 0.1M NaNO3, 0.1M sodium acetate, and 0.1M sodium citrate wash buffers with the deviation positively correlated with wash buffer’s ionic strength. Furthermore, the point of zero charge (pHzpc) for E. coli grown in the semi-defined medium varies between 1.5 and 3, in an ionic strength dependent manner, for the various wash buffers tested. Collectively, this preliminary study highlights the importance of wash buffer ionic strength in affecting removal efficiency of non-specifically absorbed ions on bacterial cell surface, where a threshold exists (0.15M) for charge screening to be effective. At the upper bound, 0.6M ionic strength might remove cations intrinsic to the cell envelope, leading to possible cell surface damage and erroneous measurements.
Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacterial cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured zeta potential, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis, where various wash buffers (such as 9 g/L NaCl, 0.001M KCl, and 0.1M NaNO3) are routinely used for removing (by charge screening) ions and charged molecules that bind nonspecifically to the cell surface. Using Escherichia coli DH5α grown in LB Lennox (with 2 g/L glucose), experiment data showed that the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L NaCl, and phosphate buffer saline (PBS) wash buffers. As LB Lennox is a low salt medium without a phosphate buffer, it was likely that the extent of nonspecific adsorption of ions on the cell surface was not severe, and the different wash buffers would correspondingly not exert much effect on measured zeta potential. Zeta potential-pH profiles for E. coli grown in a semi-defined medium (with a high capacity phosphate buffer system), on the other hand, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L NaCl, 0.1M NaNO3, 0.1M sodium acetate, and 0.1M sodium citrate wash buffers with the deviation positively correlated with wash buffer’s ionic strength. Furthermore, the point of zero charge (pHzpc) for E. coli grown in the semi-defined medium varies between 1.5 and 3, in an ionic strength dependent manner, for the various wash buffers tested. Collectively, this preliminary study highlights the importance of wash buffer ionic strength in affecting removal efficiency of non-specifically absorbed ions on bacterial cell surface, where a threshold exists (0.15M) for charge screening to be effective. At the upper bound, 0.6M ionic strength might remove cations intrinsic to the cell envelope, leading to possible cell surface damage and erroneous measurements.Formulation of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flaskshttps://peerj.com/preprints/14062017-08-222017-08-22Wenfa NgYen-Peng Ting
Microbes for environmental research should be cultured in growth media with characteristics (e.g., pH, ionic strength, and ionic composition) as close to their original habitat as possible. Additionally, the medium should also enable high cell density to be obtained, which is needed for providing sufficient cells in subsequent experiments. This in-progress report describes the formulation of a medium with an environmentally relevant composition (i.e., lack of complex organics), and that allows aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium comprises four components: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L), vitamins (yeast extract: 12.0 g/L), salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L), and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium were: high capacity phosphate buffer system (89 mM phosphate); 1:1 molar ratio between D-Glucose and NH4Cl; and yeast extract providing trace elements and a secondary carbon and nitrogen source. Growth experiments revealed that an OD600nm of 9 was obtained after 24 hours of cultivation at 37 oC. Glucose and NH4Cl served as primary carbon and nitrogen sources for this growth phase. After 48 hours, the OD600nm reached 11, where carbohydrates, lipids and proteins in yeast extract provided the nutrients for biomass formation. Broth’s pH varied between 5.5 and 7.8 during cultivation, which is conducive for E. coli growth. In comparison, the OD600nm of E. coli reached 1.4, 3.2, and 9.2 in three commonly used complex media; Nutrient Broth, LB Lennox, and Tryptic Soy Broth, respectively, over 48 hours under identical culture conditions. In addition, the formulated medium was able to maintain a large viable cell population for a longer period of time (three days) compared to Tryptic Soy Broth. Thus, preliminary data suggested that the formulated medium holds potential for use as a high cell density aerobic growth medium for Gram-negative bacteria.
Microbes for environmental research should be cultured in growth media with characteristics (e.g., pH, ionic strength, and ionic composition) as close to their original habitat as possible. Additionally, the medium should also enable high cell density to be obtained, which is needed for providing sufficient cells in subsequent experiments. This in-progress report describes the formulation of a medium with an environmentally relevant composition (i.e., lack of complex organics), and that allows aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium comprises four components: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L), vitamins (yeast extract: 12.0 g/L), salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L), and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium were: high capacity phosphate buffer system (89 mM phosphate); 1:1 molar ratio between D-Glucose and NH4Cl; and yeast extract providing trace elements and a secondary carbon and nitrogen source. Growth experiments revealed that an OD600nm of 9 was obtained after 24 hours of cultivation at 37 oC. Glucose and NH4Cl served as primary carbon and nitrogen sources for this growth phase. After 48 hours, the OD600nm reached 11, where carbohydrates, lipids and proteins in yeast extract provided the nutrients for biomass formation. Broth’s pH varied between 5.5 and 7.8 during cultivation, which is conducive for E. coli growth. In comparison, the OD600nm of E. coli reached 1.4, 3.2, and 9.2 in three commonly used complex media; Nutrient Broth, LB Lennox, and Tryptic Soy Broth, respectively, over 48 hours under identical culture conditions. In addition, the formulated medium was able to maintain a large viable cell population for a longer period of time (three days) compared to Tryptic Soy Broth. Thus, preliminary data suggested that the formulated medium holds potential for use as a high cell density aerobic growth medium for Gram-negative bacteria.