Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

Reported values in the literature on the number of cells in the body differ by orders of magnitude and are very seldom supported by any measurements or calculations. Here, we integrate the most up-to-date information on the number of human and bacterial cells in the body. We estimate the total number of bacteria in the 70 kg "reference man" to be 3.8·1013. For human cells, we identify the dominant role of the hematopoietic lineage to the total count (≈90%) and revise past estimates to 3.0·1013 human cells. Our analysis also updates the widely-cited 10:1 ratio, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and their total mass is about 0.2 kg.

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Revised Estimates for the Number of Human and Bacteria Cells in the Body.

Microbial degradation of hydrocarbons in the environment.

Phytoplankton can become limited by the availability of nutrients when light and temperature are adequate and loss rates are not excessive. The current paradigms for nutrient limitations in freshwater, estuarine, and marine environments are quite different. A review of the experimental and observational data used to infer P or N limitation of phytoplankton growth indicates that P limitation in freshwater environments can be demonstrated rigorously at several hierarchical levels of system complexity, from algal cultures to whole lakes. A similarly rigorous demonstration of N limitation has not been achieved for marine waters. Therefore, we conclude that the extent and severity of N limitation in the marine environment remain an open question. Culture studies have established that internal cellular concentrations of nutrients determine phytoplankton growth rates, and these studies have shown that it is often difficult to relate growth rates to external concentrations, especially in natural situations. This should lead to a greater reliance on the composition of particulate matter and biomass-based physiological rates to infer nutrient limitation. Such measurements have demonstrated their utility in a wide variety of freshwater and marine environments, and, most importantly, they can be applied to systems that are difficult to manipulate experimentally or budget accurately. Dissolved nutrient concentrations are most useful in determining nutrient loading rates of aquatic ecosystems. The relative proportions of nutrients supplied to phytoplankton can be a strong selective force shaping phytoplankton communities and affecting the biomass yield per unit of limiting nutrient. A current dogma of aquatic science is that marine and estuarine phytoplankton tend to be nitrogen limited, while freshwater phytoplankton tend to be phosphorus limited. Carpenter and Capone (1983) documented the preeminence of N studies in the literature on brackish and marine ecosystems. In 1970 there were equal numbers of references per year to N and P. The decade of the seventies saw a nearly fourfold increase in references to N, while the number of P references per year remained essentially unchanged. No trend was evident for the freshwater literature despite the fact that by the late seventies the evidence for P limitation had become so great that phosphorus control was recommended as the legislated basis for controlling eutrophication in North American and European inland waters (e.g.

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Nutrient limitation of phytoplankton in freshwater and marine environments: A review of recent evidence on the effects of enrichment1

The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1. Unlike characterized ammonia-oxidizing bacteria, SCM1 is adapted to life under extreme nutrient limitation, sustaining high specific oxidation rates at ammonium concentrations found in open oceans. Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold (<or=10 nM) closely resemble kinetics of in situ nitrification in marine systems and directly link ammonia-oxidizing Archaea to oligotrophic nitrification. The remarkably high specific affinity for reduced nitrogen (68,700 l per g cells per h) of SCM1 suggests that Nitrosopumilus-like ammonia-oxidizing Archaea could successfully compete with heterotrophic bacterioplankton and phytoplankton. Together these findings support the hypothesis that nitrification is more prevalent in the marine nitrogen cycle than accounted for in current biogeochemical models.

/pdf/ammonia-oxidation-kinetics-determine-niche-separation-of-nhbbcia8ex.pdf

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

Dilution culture, a method for growing the typical small bacteria from natural aquatic assemblages, has been developed. Each of 11 experimental trials of the technique was successful. Populations are measured, diluted to a small and known number of cells, inoculated into unamended sterilized seawater, and examined three times for the presence of 104 or more cells per ml over a 9-week interval. Mean viability for assemblage members is obtained from the frequency of growth, and many of the cultures produced are pure. Statistical formulations for determining viability and the frequency of pure culture production are derived. Formulations for associated errors are derived as well. Computer simulations of experiments agreed with computed values within the expected error, which verified the formulations. These led to strategies for optimizing viability determinations and pure culture production. Viabilities were usually between 2 and 60% and decreased with >5 mg of amino acids per liter as carbon. In view of difficulties in growing marine oligobacteria, these high values are noteworthy. Significant differences in population characteristics during growth, observed by high-resolution flow cytometry, suggested substantial population diversity. Growth of total populations as well as of cytometry-resolved subpopulations sometimes were truncated at levels of near 104 cells per ml, showing that viable cells could escape detection. Viability is therefore defined as the ability to grow to that population; true viabilities could be even higher. Doubling times, based on whole populations as well as individual subpopulations, were in the 1-day to 1-week range. Data were examined for changes in viability with dilution suggesting cell-cell interactions, but none could be confirmed. The frequency of pure culture production can be adjusted by inoculum size if the viability is known. These apparently pure cultures produced retained the size and apparent DNA-content characteristic of the bulk of the organisms in the parent seawater. Three cultures are now available, two of which have been carried for 3 years. The method is thus seen as a useful step for improving our understanding of typical aquatic organisms.

Viability and Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results

Marine bacteria in Resurrection Bay near Seward, Alaska, and in the central North Sea off the Dutch coast were cultured in filtered autoclaved seawater following dilution to extinction. The populations present before dilution varied from 0.11 × 109 to 1.07 × 109 cells per liter. The mean cell volume varied between 0.042 and 0.074 μm3, and the mean apparent DNA content of the cells ranged from 2.5 to 4.7 fg of DNA per cell. All three parameters were determined by high-resolution flow cytometry. All 37 strains that were obtained from very high dilutions of Resurrection Bay and North Sea samples represented facultatively oligotrophic bacteria. However, 15 of these isolates were eventually obtained from dilution cultures that could initially be cultured only on very low-nutrient media and that could initially not form visible colonies on any of the agar media tested, indicating that these cultures contained obligately oligotrophic bacteria. It was concluded that the cells in these 15 dilution cultures had adapted to growth under laboratory conditions after several months of nutrient deprivation prior to isolation. From the North Sea experiment, it was concluded that the contribution of facultative oligotrophs and eutrophs to the total population was less than 1% and that while more than half of the population behaved as obligately oligotrophic bacteria upon first cultivation in the dilution culture media, around 50% could not be cultured at all. During one of the Resurrection Bay experiments, 53% of the dilution cultures obtained from samples diluted more than 2.5 × 105 times consisted of such obligate oligotrophs. These cultures invariably harbored a small rod-shaped bacterium with a mean cell volume of 0.05 to 0.06 μm3 and an apparent DNA content of 1 to 1.5 fg per cell. This cell type had the dimensions of ultramicrobacteria. Isolates of these ultramicrobacterial cultures that were eventually obtained on relatively high-nutrient agar plates were, with respect to cell volume and apparent DNA content, identical to the cells in the initially obligately oligotrophic bacterial dilution culture. Determination of kinetic parameters from one of these small rod-shaped strains revealed a high specific affinity for the uptake of mixed amino acids (a°A, 1,860 liters/g of cells per h), but not for glucose or alanine as the sole source of carbon and energy (a°A, ± 200 liters/g of cells per h). The ultramicrobial strains obtained are potentially a very important part of picoplankton biomass in the areas investigated.

Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions

Formulations are presented that describe the concentration dependency of nutrient-limited transport and growth in molecular terms. They relate the rate of transport at steady state through a two-sequence process, transport and metabolism, to ambient concentrations according to the amounts and kinetic characteristics of the two rate-limiting proteins in these sequences. Sequences are separated by a metabolic pool. A novel feature of these formulations is the translation coefficient, which relates the transport rate attained at given ambient nutrient concentrations and membrane transporter characteristics to the nutrient concentrations sustained in the metabolic pools. The formulations, termed janusian kinetics, show that hyperbolic kinetics are retained during independent changes in transporter and enzyme contents or characteristics. Specific affinity (a°A) depends strongly on the amount and kinetic characteristics of the transporters; it is also mildly affected by the amount and characteristics of the rate-limiting enzyme. This kinetic constant best describes the ability to accumulate substrate from limiting concentrations. Maximal velocity (Vmax) describes uptake from concentrated solutions and can depend strongly on either limiting enzyme content or the associated content of transporters. The whole-cell Michaelis constant (KT), which depends on the ratio of rate-limiting enzyme to transporter, can be relatively independent of change in a°A and is best used to describe the concentration at which saturation begins to occur. Theory specifies that good oligotrophs have a large a°A for nutrient collection and a small Vmax for economy of enzyme, giving a small KT. The product of the two constants is universally rather constant so that oligotrophy is scaled on a plot of a°A versus KT, with better oligotrophs toward one end. This idea is borne out by experimental data, and therefore typical small difficult-to-culture aquatic bacteria may be classified as oligobacteria.

Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant.

The abilities of organisms to sequester substrate are described by the two kinetic constants specific affinity, a°, and maximal velocity Vmax. Specific affinity is derived from the frequency of substrate-molecule collisions with permease sites on the cell surface at subsaturating concentrations of substrates. Vmax is derived from the number of permeases and the effective residence time, τ, of the transported molecule on the permease. The results may be analyzed with affinity plots (v/S versus v, where v is the rate of substrate uptake), which extrapolate to the specific affinity and are usually concave up. A third derived parameter, the affinity constant KA, is similar to KM but is compared to the specific affinity rather than Vmax  and is defined as the concentration of substrate necessary to reduce the specific affinity by half. It can be determined in the absence of a maximal velocity measurement and is equal to the Michaelis constant for a system with hyperbolic kinetics. Both are taken as a measure of τ, with departure of KM from KA being affected by permease/enzyme ratios. Compilation of kinetic data indicates a 108-fold range in specific affinities and a smaller (103-fold) range in Vmax values. Data suggest that both specific affinities and maximal velocities can be underestimated by protocols which interrupt nutrient flow prior to kinetic analysis. A previously reported inverse relationship between specific affinity and saturation constants was confirmed. Comparisons of affinities with ambient concentrations of substrates indicated that only the largest a°S values are compatible with growth in natural systems.

https://mmbr.asm.org/content/mmbr/62/3/636.full.pdf

Nutrient Uptake by Microorganisms according to Kinetic Parameters from Theory as Related to Cytoarchitecture

The forward light scatter intensity of bacteria analyzed by flow cytometry varied with their dry mass, in accordance with theory. A standard curve was formulated with Rayleigh-Gans theory to accommodate cell shape and alignment. It was calibrated with an extinction-culture isolate of the small marine organism Cycloclasticus oligotrophus, for which dry weight was determined by CHN analysis and 14C-acetate incorporation. Increased light scatter intensity due to formaldehyde accumulation in preserved cells was included in the standard curve. When differences in the refractive indices of culture media and interspecies differences in the effects of preservation were taken into account, there was agreement between cell mass obtained by flow cytometry for various bacterial species and cell mass computed from Coulter Counter volume and buoyant density. This agreement validated the standard curve and supported the assumption that cells were aligned in the flow stream. Several subpopulations were resolved in a mixture of three species analyzed according to forward light scatter and DNA-bound DAPI (4′,6-diamidino-2-phenylindole) fluorescence intensity. The total biomass of the mixture was 340 μg/liter. The lowest value for mean dry mass, 0.027 ± 0.008 pg/cell, was for the subpopulation of C. oligotrophus containing cells with a single chromosome. Calculations from measurements of dry mass, Coulter Counter volume, and buoyant density revealed that the dry weight of the isolate was 14 to 18% of its wet weight, compared to 30% for Escherichia coli. The method is suitable for cells with 0.005 to about 1.2 pg of dry weight at concentrations of as low as 103 cells/ml and offers a unique capability for determining biomass distributions in mixed bacterial populations.

Determination of the Biomasses of Small Bacteria at Low Concentrations in a Mixture of Species with Forward Light Scatter Measurements by Flow Cytometry

D. K. Button

Papers

Viability and Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results

Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions

Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant.

Nutrient Uptake by Microorganisms according to Kinetic Parameters from Theory as Related to Cytoarchitecture

Determination of the Biomasses of Small Bacteria at Low Concentrations in a Mixture of Species with Forward Light Scatter Measurements by Flow Cytometry