Vertical microscale patchiness in nano- and microplankton distributions in a stratified estuary

Microscale (decimetre) vertical heterogeneity in the distributionof nano- and microplankton was studied on August 23, 1999 attwo different sites (separated by ~40 m) in Aarhus Bay, Denmark.At the time of sampling, the water column was stratified withrespect to both temperature and salinity and a subsurface fluorescencemaximum (corresponding to ~10 µg chlorophyll a l^-1) occurredimmediately below the primary pycnocline (9 m). Samples forspecies identification were taken at the surface, near the bottomof the water column and at 20 15-cm intervals in and aroundthe depth of maximum fluorescence. The plankton communitiesrecorded in the three different regions of the water columndiffered dramatically from one another. In addition, significantdifferences were found in the distribution patterns of speciesand functional groups in the region of sampling around the fluorescencepeak. The same patterns in vertical species distributions wereobserved at the two stations. In the region surrounding thesubsurface fluorescence peak, diatoms were, generally, regularlydistributed, although the total diatom biomass decreased slightlywith depth. Dinoflagellate species were mainly non-regularlydistributed and could be divided into two groups: (i) autotrophicor potentially mixotrophic species (Dinophysis norvegica, Dinophysisacuminata, Dinophysis cf. dens, Prorocentrum micans, Gymnodiniumchlorophorum and Ceratium macroceros) that mainly decreasedin numbers with depth or were aggregated in their distribution;and (ii) heterotrophic or potentially mixotrophic species (Ceratiumlineatum, Ceratium longipes, Ceratium furca, Ceratium tripos,Ceratium fusus, Protoperidinium curtipes, Protoperidinium steinii,Diplopsalis spp. and Katodinium glaucum). In the latter group,the species mainly increased in numbers with depth or were randomlydistributed. Most ciliates were uniformly distributed verticallyin the water column. However, small cells of the photosynthesizingciliate Mesodinium rubrum were most abundant at the depth ofmaximal fluorescence while large M. rubrum cells were equallyabundant at all the depths sampled, suggesting the two sizegroups of this organism may differ ecologically. Overall, thestudy demonstrates that traditional plankton sampling methodsmay lead to misinterpretations of speciesco-existence and interactions.     

Feeding preference as a main determinant of microscale patchiness among terrestrial nematodes

Soil biota are responsible for essential ecosystem services such as carbon storage, nutrient cycling and water retention. However, assessment of the condition of soil biota is hampered by an overwhelming level of diversity. With representatives in all trophic levels of the food web, nematode communities can be used as bioindicators. Accurate assessment of nematode assemblages requires insight into the distribution of specimens with distinct food preferences. With the availability of taxon‐specific quantitative PCR assays, distribution patterns of multiple nematode groups can be investigated simultaneously. Here, microscale patchiness of 45 nematode taxa was studied on 12 sampling sites (each with four adjacent microplots) located on arable fields or semi‐natural grasslands (‘system’), and on marine, river clay or sandy soils (‘soil type’). From each microplot, five composite samples were collected. Contrary to our expectations, an increase in the number of cores per composite sample did not result in more accurate measurements, and apparently the levels of microscale patchiness of the taxa are low compared to what has been reported for oligophagous plant‐parasites. System and soil type did not affect microscale distribution. To investigate the level of patchiness in more detail, detection probability (DP) and variability of abundances were calculated. Common and widespread bacterivorous and fungivorous taxa had DP ≥ 90%, confirming low level of microscale patchiness. With DPs of 40%–70%, predators and most omnivores showed degrees of local clustering. An overview of mean variabilities of abundances is presented that offers insight into how feeding preferences impact the microscale distribution both between and within trophic groups.     

Dispersal of motile bacteria from a plane layer.

The dispersal of an initially well-defined concentration of the motile bacterium Escherichia coli was measured under nonchemotactic conditions. The distribution of bacteria along a glass observation cell was measured by recording the intensity of light scattered by the organisms. For comparison, the diffusion of fluorescein was also measured by determining the distribution of fluorescence throughout the observation cell. The dispersal of bacteria from a plane layer, under nonchemotactic conditions, can be adequately described by the Gaussian solution of the diffusion equation.     

Measurement of in situ growth rates of phytoplankton under conditions of simulated turbulence

In situ measurement of the growth rates of planktonic populationscan be improved by using dialysis chambers (‘cage cultures’)to avoid shifts in the chemical environment during incubation.Vertical mixing and small-scale turbulence affect the growthof planktonic populations, there fore natural mixing conditionsshould be simulated as closely as possible during the incubation.A new device is described here which combines the advantagesof a dialysis chamber with a programmable vertical mixing regime.Realistic phytoplankton growth rates can thus be measured insitu under con ditions of vertical mixing and small-scale turbulence.The chamber made of transparent, UV-transmitting acrylic glasswas fitted at both ends with permeable polycarbonate membranes.It was moved vertically through the water column by a pocket-sizedlift and rotated simultaneously on its central axis. The methodwas applied to two typos of experiments on growth and lossesof phytoplankton in the River Severn, UK. The first one comparedchanges in biovolume of phytoplankton in a water parcel flowingdownstream (6% h^–1 decline) with those in a simultaneouslyincubated dialysis chamber moved between water surface and riverbottom (7% h^–1 increase). The difference equates to algallosses prevented in the chamber but suffered along the river(mainly sedimentation and grazing of benthic filter feeders).Loss rate of diatoms was three times higher than those of chlorophytes.In another experiment growth of phytoplankton from the mainstream and lateral dead zone was compared under different mixingconditions. Algae from the main stream grew faster than fromthe dead zone. Only cryptophytes preferred calm conditions,all the other algal groups grew faster in chambers moved throughthe water column than in stationary ones. Further possible applicationsin both standing and flowing waters are discussed.     

Sedimentation loss of phytoplankton cells from the mixed layer: effects of turbulence levels

In this paper, we describe a study of the role of turbulencein the loss by sedimentation of phytoplankton cells from themixed layer. The approach presented allows the quantificationof the sedimentation rate of phytoplankton in the whole rangeof turbulence levels of this layer. Two types of phytoplanktercan be distinguished according to the effect that turbulencecan exert on their sedimentation rate. The rate of those cellswhose settling velocity is lower than –1 m day^–1will not be modified by turbulence. The sedimentation rate ofcells with higher settling velocities can, however, be modifiedby the level of turbulence. A set of dimensionless numbers isgiven to delimit several processes that are important in thedynamics of phytoplankton sedimentation in a turbulent regime.The use of these dimensionless numbers suggests that an increasein the turbulence level in the mixed layer does not always implya decrease in the sedimentation rate of phytoplankton cells.     

Fungal--bacterial interactions: a mixed bag of mingling microbes

Fungi and bacteria co-inhabit a wide variety of environments, from soils and food products to plants and mammals. Interactions between bacteria and fungi can have dramatic effects on the survival, colonization and pathogenesis of these organisms. There are instances where bacteria provide fungi with compounds that enhance the production of fungal virulence determinants. Other bacteria produce factors that are likely to inhibit pathogenesis by repressing fungal filamentation. Furthermore, mixed bacterial-fungal biofilms can have properties that are distinct from their single-species counterparts. Clinical studies, in combination with in vitro model systems, are necessary to understand how bacterial-fungal interactions impact human health.     

Estimation of additive genetic variance in commercial layer poultry and simulated populations under selection

Changes in genetic parameters over generations for a selected commercial population and simulated populations of poultry with different sizes were studied. The traits analyzed from the commercial population were rate of lay, age at first egg, egg weight, deformation, and body weight. In the simulated population, a trait measured on both sexes and a sex-limited trait, measured only on one sex, each with a heritability of 0.1 and 0.5, were analyzed. In the commercial and simulated populations, males and females were selected on the basis of family selection indexes and data was available only after many generations of selection. Parameters for each generation were estimated by fitting an animal model using derivative free maximum likelihood (DFREML) with different data structures. In structure 1, data included the given (base) generation for which the parameters were to be estimated, and all subsequent generations. In structure 2, only data on birds in the given generation and their progeny were included. In both structures, parents of base-generation birds were assumed unrelated and pedigrees traced back to these parents. With commercial data using structure 1, estimates of _a ² and h² decreased by 14 to 37% across five generations. With structure 2, no trends were observed, though estimates were lower than for structure 1. For simulated data, with a heritability of 0.1, both structures yielded apparently unbiased estimates of the observed additive genetic variances in the (selected) base generation, no matter how many generations of data were utilized, for both sex-limited and normal traits. However, with a heritability of 0.5 the estimated additive genetic variance for both types of trait decreased with a decrease in the number of generations used in the estimation. Estimates based on the first two generations underestimated, while estimates based on five generations of data overestimated, the observed genetic variances in the defined base. The combinations of conditions that lead to varying degrees of bias remain undefined.     

Prevalence and characterization of motile Salmonella in commercial layer poultry farms in Bangladesh

Salmonella is a globally widespread food-borne pathogen having major impact on public health. All motile serovars of Salmonella enterica of poultry origin are zoonotic, and contaminated meat and raw eggs are an important source to human infections. Information on the prevalence of Salmonella at farm/holding level, and the zoonotic serovars circulating in layer poultry in the South and South-East Asian countries including Bangladesh, where small-scale commercial farms are predominant, is limited. To investigate the prevalence of Salmonella at layer farm level, and to identify the prevalent serovars we conducted a cross-sectional survey by randomly selecting 500 commercial layer poultry farms in Bangladesh. Faecal samples from the selected farms were collected following standard procedure, and examined for the presence of Salmonella using conventional bacteriological procedures. Thirty isolates were randomly selected, from the ninety obtained from the survey, for serotyping and characterized further by plasmid profiling and pulsed-field gel electrophoresis (PFGE). Results of the survey showed that the prevalence of motile Salmonella at layer farm level was 18% (95% confidence interval 15-21%), and Salmonella Kentucky was identified to be the only serovar circulating in the study population. Plasmid analysis of the S. Kentucky and non-serotyped isolates revealed two distinct profiles with a variation of two different sizes (2.7 and 4.8 kb). PFGE of the 30 S. Kentucky and 30 non-serotyped isolates showed that all of them were clonally related because only one genotype and three subtypes were determined based on the variation in two or three bands. This is also the first report on the presence of any specific serovar of Salmonella enterica in poultry in Bangladesh.     

Vertical distribution and composition of phytoplankton under the influence of an upper mixed layer

The vertical distribution of phytoplankton is of fundamental importance for the dynamics and structure of aquatic communities. Here, using an advection-reaction-diffusion model, we investigate the distribution and competition of phytoplankton species in a water column, in which inverse resource gradients of light and a nutrient can limit growth of the biomass. This problem poses a challenge for ecologists, as the location of a production layer is not fixed, but rather depends on many internal parameters and environmental factors. In particular, we study the influence of an upper mixed layer (UML) in this system and show that it leads to a variety of dynamic effects: (i) Our model predicts alternative density profiles with a maximum of biomass either within or below the UML, thereby the system may be bistable or the relaxation from an unstable state may require a long-lasting transition. (ii) Reduced mixing in the deep layer can induce oscillations of the biomass; we show that a UML can sustain these oscillations even if the diffusivity is less than the critical mixing for a sinking phytoplankton population. (iii) A UML can strongly modify the outcome of competition between different phytoplankton species, yielding bistability both in the spatial distribution and in the species composition. (iv) A light limited species can obtain a competitive advantage if the diffusivity in the deep layers is reduced below a critical value. This yields a subtle competitive exclusion effect, where the oscillatory states in the deep layers are displaced by steady solutions in the UML. Finally, we present a novel graphical approach for deducing the competition outcome and for the analysis of the role of a UML in aquatic systems.     

Small-scale spatial beta diversity of bacteria in the mixed upper layer of a lake

Bacterial community composition among individual, experimentally generated ‘lake snow’ particles may be highly variable. Since such aggregates are seasonally abundant in the mixed upper layer of lakes, we hypothesized that particle-attached (PA) bacteria disproportionally contribute to the small-scale spatial beta diversity of pelagic communities. Community composition was analysed in sets of small (10 mL) samples collected from a pre-alpine lake in May, July and October 2018. Bacteria were classified as free-living (FL) or PA depending on their presence in large, 5-μm pre-filtered reference samples. FL exhibited clear seasonal differences in community composition and assembly. They were spatially uniform in May and July, and only a few FL taxa exhibited significant spatial variability. Spatial heterogeneity of FL in October was caused by high alpha and beta diversity of rare taxa, many with a presumably ‘tychoplanktic’ (alternating attached and free-living) lifestyle. The spatial beta diversity of PA was always high, and only about 10% of their seasonal richness was present in any single sample. Thus, most compositional variability of pelagic bacteria at spatial scales of cm to m either directly or indirectly originated from PA. On a functional level, this genotypic heterogeneity might affect the spatial distribution of rare metabolic traits.     

A study of time-dependent primary productivity in a natural upper-ocean mixed layer using a biophysical model

A one-dimensional biophysical model of time-dependent photosynthesisin the upper-ocean mixed layer was applied near 36.5°N,74.5°W. The photosynthesis submodel was formulated and parameterizedbased on daylong, light-manipulation experiments performed ontwo phytoplankton communities collected prior to dawn on October13, 1992: one from 5 m depth in the upper mixed layer and theother from 28 m depth below the pycnocline. Time course biologicalmeasurements included chlorophyll a concentration, primary productivityand DCMU fluorescence ratio. The biophysical model was thenused to predict the physical and biological response of thewater column on October 14, 1992. A pre-dawn conductivity-temperature-depth-fluorescence-transmission-rosette(CTDFT-rosette) cast provided data to initialize the water columnstratification and the distribution of phytoplankton biomass.The biophysical model was forced using meteorological and oceanographicmeasurements collected continuously throughout the subsequentdaylight period. CTDFT-rosette casts and measurements of chlorophylla concentration, primary productivity and DCMU fluorescenceratio throughout that daylight period provided the data forcomparison with the model predictions. In general, the biophysicalmodel predicted the physical and biological evolution of thesampled water column. Although the inclusion of vertical mixinginitially improved the accuracy of prediction, agreement decreasedwith time, especially in the lower part of the water column.The one-dimensional model suffered from the effects of excludedhorizontal gradients.     

Mucus transport in a miniaturized simulated cough machine: effect of constriction and serous layer simulant

The transport of mucus gel simulant (MGS) in a constricted simulated cough machine, using blood plasma as a serous layer simulant (SLS), was investigated. MGS was prepared from locust bean gum solutions crosslinked with varying amounts of added borate to produce gels of varying spinnability (filance). The model trachea was a plexiglass channel of rectangular cross-section with the plane bottom surface. The upper surface included a sinusoidal protrusion which provided a flow convergence with minimum gaps of 6, 4 and 2 mm. Experiments for mucus transport were conducted for these minimum gaps, as well as for the non-convergent case (12 mm gap). Miniaturization of sample quantity was achieved by keeping the MGS layer depth constant (0.5 or 1 mm) but reducing the zone of loading from 13.4 cm to 1 cm, thus reducing the sample requirement to as little as 0.2 ml. MGS transport was determined as the minimum displacement of a line of marker dye placed in the MGS layer at the point of minimum constriction gap. It was shown that in all cases (dry as well as with SLS), MGS transport increased as the minimum constriction gap between the plane and the convergent top surface decreased. This increase was further enhanced if an SLS of lesser viscosity was used. It was also found that the transport of MGS increased as the depth of MGS layer increased or as the filance decreased in both non-constricted and constricted cases. The relationship between MGS transport and filance was maintained even in the presence of an SLS layer.     

Application of Taylor''s hypothesis to an unsteady convective field for the spectral analysis of turbulence in the aorta

Two types of unsteadiness must be considered when spectral analysis is applied to unsteady turbulence such as that found in the aorta. Firstly, the statistical properties of the turbulence itself change in time and so the definition of spectral density must be reconsidered. Secondly, the turbulent velocity fluctuations, whether they are steady or unsteady, are carried by an unsteady convective velocity which alters their properties as seen by a stationary observer.

In the present study, unsteadiness of turbulence in the latter sense is discussed by applying Taylor's hypothesis of ‘frozen turbulence’ to turbulence with an unsteady convective velocity. If both a ‘frozen’ pattern of turbulence and a constant convective velocity are assumed, measured frequency spectra can be easily transformed into wavenumber (spatial) spectra, usually as a trivial part of normalisation. In the case of unsteady turbulence, however, the convection velocity is no longer constant and the conventional method can not be used. A new method of estimating the spatial properties of unsteady turbulence is proposed in which the temporal fluctuations of the turbulent velocity are transformed into spatial fluctuations using a nonlinear transformation based upon the unsteady convective velocity. The transformed data are then Fourier analysed to yield a wavenumber spectrum directly.

The proposed method is applied to data obtained in the canine ascending aorta. Spectra calculated by the proposed method differ significantly from those obtained by the conventional method, particularly in the high wavenumber (or frequency) range. This difference is discussed as an ‘aliasing’ phenomenon that has also been known in steady turbulence.     

Canopy transpiration of mountain mixed forest as a function of environmental conditions in boundary layer

The canopy transpiration of mountain mixed forest was investigated during summer 2006 at research plot Smrekovec in Tatra National Park in Slovakia after heavy windstorm in November 2004 on the area of 12,000 hectares. The research plot is situated in untouched forest at altitude 1249 m on the southern-east oriented slope. The forest is mixed with 80% of spruce trees and 20% of larch trees with rich under storey vegetation, 120 years old, 7th altitudinal vegetation stage. Whole tree sap flow based on up to dated stem tissue heat balance method was continuously measured in nine 120-years old larch and spruce trees. Stem basal area was used for tree-canopy up-scaling. Meteorological parameters were measured on the top of eddy stuff tower above investigated forest. Two virtual monocultures were assumed for characterizing of both species. The sap flow and tree transpiration were calculated for the whole measured period for both spruce and larch virtual forests.     

The role of topography in promoting fractal patchiness in a carbonate shelf landscape

Satellite remote sensing has shown numerous aspects of coral reef seascapes to be fractal. That is, they display characteristics of scale-invariance and complexity. To date, an understanding of why reefscapes adopt this curious scaling has been lacking. This property was investigated using high-resolution terrain models built using bathymetric LiDAR soundings of the shallow Puerto Rico insular shelf. A computer-simulation model constructed using simple random processes was adequate to describe many of the intricacies of actual coral reef terrain. This model, based on fractional Brownian motion (fBm), produced surfaces that were visually and statistically indistinguishable from natural seabeds, at spatial scales of 0.001–25 km². The conformity between model and nature allowed us to ascertain the importance of topography as a driver for the fractal patchiness that has been shown to occur in plan-view maps of reefscapes (e.g. Purkis et al. J Sediment Res 75:861–876, 2005, J Geol 115:493–508, 2007). For the considered Puerto Rican shelf, the necessary Brownian-like seabed topography likely arose through karst erosion overprinted by several episodes of reef development. Communicated by Geology Editor Dr. Bernhard Riegl     

Uric acid inhibits liver phosphorylase a activity under simulated in vivo conditions

We have reported that glycogen synthesis and degradation can occur in vivo without a significant change in the amount of phosphorylase a present. These data suggest the presence of a regulatable mechanism for inhibiting phosphorylase a activity in vivo. Several effectors have been described. AMP stimulates, whereas ADP, ATP, and glucose inhibit activity. Of these effectors, only the glucose concentration changes under normal conditions; thus it could regulate phosphorylase a activity in vivo. We previously have reported that, when all of these effectors were present at physiological concentrations, the net effect was no change in phosphorylase a activity. Addition of caffeine, an independent inhibitor of activity, to the above effectors not only resulted in inhibition but also restored a glucose concentration-dependent inhibition. Because uric acid is an endogenous xanthine derivative, we decided to determine whether it had an effect on phosphorylase a activity. Independently, uric acid did not affect activity; however, when added at a presumed physiological concentration in combination with AMP, ADP, ATP, and glucose, it inhibited activity. A modest but not statistically significant glucose concentration-dependent inhibition was also present. Thus uric acid may play an important role in regulating phosphorylase a activity in vivo.