δ13C variability of benthic algae: effects of water colour via modulation by stream current

1. Increased water motion is expected to reduce boundary layer diffusion resistance of autotrophs, thereby enabling greater isotopic discrimination against ¹³C such that lower δ¹³C values (ratio of ¹³C : ¹²C) should ensue. A field test of this hypothesis was undertaken by sampling benthic algae in streams of differing current speed.
2. Contrary to the expected negative relationship between δ¹³C and water motion, filamentous benthic algae were found to exhibit higher δ¹³C values in rapid water.
3. Under conditions of low current in the streams studied, concentrations of dissolved organic carbon as measured by water colour are elevated through the microbial decomposition of largely terrestrial organic matter. Photoassimilation of this respired carbon by benthic filamentous algae generates ¹³C‐depletion and lower δ¹³C values, and appears to be substantial enough in the streams used in the present study to override the competing influence of water motion on boundary layer thickness.     

A hypersaline microbial mat from the Pacific Atoll Kiritimati: insights into composition and carbon fixation using biomarker analyses and a 13C-labeling approach

Modern microbial mats are widely recognized as useful analogs for the study of biogeochemical processes relevant to paleoenvironmental reconstruction in the Precambrian. We combined microscopic observations and investigations of biomarker composition to investigate community structure and function in the upper layers of a thick phototrophic microbial mat system from a hypersaline lake on Kiritimati (Christmas Island) in the Northern Line Islands, Republic of Kiribati. In particular, an exploratory incubation experiment with ¹³C-labeled bicarbonate was conducted to pinpoint biomarkers from organisms actively fixing carbon. A high relative abundance of the cyanobacterial taxa Aphanocapsa and Aphanothece was revealed by microscopic observation, and cyanobacterial fatty acids and hydrocarbons showed ¹³C-uptake in the labeling experiment. Microscopic observations also revealed purple sulfur bacteria (PSB) in the deeper layers. A cyclic C_19:0 fatty acid and farnesol were attributed to this group that was also actively fixing carbon. Background isotopic values indicate Calvin–Benson cycle-based autotrophy for cyc C_19:0 and farnesol-producing PSBs. Biomarkers from sulfate-reducing bacteria (SRB) in the top layer of the mat and their ¹³C-uptake patterns indicated a close coupling between SRBs and cyanobacteria. Archaeol, possibly from methanogens, was detected in all layers and was especially abundant near the surface where it contained substantial amounts of ¹³C-label. Intact glycosidic tetraether lipids detected in the deepest layer indicated other archaea. Large amounts of ornithine and betaine bearing intact polar lipids could be an indicator of a phosphate-limited ecosystem, where organisms that are able to substitute these for phospholipids may have a competitive advantage.     

Extensive carbon isotopic heterogeneity among methane seep microbiota

To assess and study the heterogeneity of δ¹³C values for seep microorganisms of the Eel River Basin, we studied two principally different sample sets: sediments from push cores and artificial surfaces colonized over a 14 month in situ incubation. In a single sediment core, the δ¹³C compositions of methane seep-associated microorganisms were measured and the relative activity of several metabolisms was determined using radiotracers. We observed a large range of archaeal δ¹³C values (> 50‰) in this microbial community. The δ¹³C of ANME-1 rods ranged from −24‰ to −87‰. The δ¹³C of ANME-2 sarcina ranged from −18‰ to −75‰. Initial measurements of shell aggregates were as heavy as −19.5‰ with none observed to be lighter than −57‰. Subsequent measurements on shell aggregates trended lighter reaching values as ¹³C-depleted as −73‰. The observed isotopic trends found for mixed aggregates were similar to those found for shell aggregates in that the initial measurements were often enriched and the subsequent analyses were more ¹³C-depleted (with values as light as −56‰). The isotopic heterogeneity and trends observed within taxonomic groups suggest that ANME-1 and ANME-2 sarcina are capable of both methanogenesis and methanotrophy. In situ microbial growth was investigated by incubating a series of slides and silicon (Si) wafers for 14 months in seep sediment. The experiment showed ubiquitous growth of bacterial filaments (mean δ¹³C = −38 ± 3‰), suggesting that this bacterial morphotype was capable of rapid colonization and growth.     

Microbial colonization of an in vitro model of a tissue engineered human skin equivalent – a novel approach

This was a preliminary investigation to define the conditions of colonization of a human skin equivalent (SE) model with cutaneous microorganisms. SEs of 24 mm diameter were constructed with a dermal matrix of fibrin containing fibroblasts and a stratified epidermis. Microbial colonization of the SEs was carried out in a dry environment, comparable to ' in vivo ' skin, using a blotting technique to remove inoculation fluid. The microbial communities were sampled by scrub washing and viable cells enumerated on selective growth medium. Staphylococcus epidermidis , Propionibacterium acnes and Malassezia furfur (human skin commensals) and Staphylococcus aureus (transient pathogen) were colonized at inoculum densities of 10²–10⁶ CFU SE⁻¹ on the surface of replicate SEs. Growth of all species was supported for upto 72–120 h, with recovery densities of between 10⁴–10⁹ CFU SE⁻¹. A novel, real-time growth monitoring method was also developed, using S. aureus containing a lux cassette. Light output increased from 20 to 95 h, and colonization increased from 10² to 10⁸ CFU SE⁻¹, as confirmed by conventional recovery. Thus, the SE model has potential to investigate interactions between resident and transient microbial communities with themselves and their habitat, and for testing treatments to control pathogen colonization of human skin.     

Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques

The anaerobic oxidation of methane (AOM) is an important methane sink in marine ecosystems mediated by still uncultured Archaea . We established an experimental system to grow AOM communities in different sediment samples. Approaches to show growth of the slow-growing anaerobic methanotrophs have been either via nucleic acids (quantitative PCR) or required long-term incubations. Previous long-term experiments with ¹³C-labelled methane led to an unspecific distribution of the ¹³C-label. Although quantitative PCR is a sensitive technique to detect small changes in community composition, it does not determine growth yield. Therefore, we tested an alternative method to detect a biomass increase of AOM microorganisms with ¹⁵N-labelled ammonium as N-source. After only 3 weeks, significant ¹⁵N-labelling became apparent in amino acids as major structural units of microbial proteins. This was especially evident in methane-containing incubations, showing the methane-dependent uptake of the ¹⁵N-labelled ammonium by microorganisms. Cell counts demonstrated a two- and fourfold increase at ambient or elevated methane concentrations. With denaturing gradient gel electrophoresis, over 6 months incubation no changes in community composition of sulphate-reducing bacteria and archaea were detected. These data indicate doubling times for AOM microorganisms between 2 and 3.4 months. In conclusion, the ¹⁵N-labelling approach proved to be a sensitive and fast way to show growth of extremely slow-growing microorganisms.     

Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques

A toluene-degrading microbial consortium was enriched directly in a BTEX-contaminated aquifer under sulfate-reducing conditions using in situ microcosms consisting of toluene-loaded activated carbon pellets. Degradation of toluene and concomitant sulfide production by the consortium was subsequently demonstrated in laboratory microcosms. The consortium was physiologically and phylogenetically characterized by isotope tracer experiments using nonlabeled toluene, [¹³C]-α-toluene or [¹³C₇]-toluene as growth substrates. Cells incubated with [¹³C]-α-toluene or [¹³C₇]-toluene incorporated 8–15 at.%¹³C and 51–57 at.%¹³C into total lipid fatty acids, respectively, indicating a lower specific incorporation of ¹³C from [¹³C₇]-toluene. In order to identify the toluene-assimilating bacteria, the incorporation of carbon from both [¹³C]-α-toluene and [¹³C₇]-toluene into rRNA was analyzed by stable isotope probing. Time and buoyant density-resolved 16S rRNA gene-based terminal restriction fragment length polymorphism profiles, combined with cloning and sequencing, revealed that an uncultured bacterium (99% sequence similarity) related to the genus Desulfocapsa was the main toluene-degrading organism in the consortium. The ratio of the respective terminal restriction fragments changed over time, indicating trophic interactions within this consortium.     

Suitability of a rapid gas chromatographic method for total mesophilic bacteria and coliform enumeration in hamburgers

An instrumental method for the rapid determination of total mesophilic bacteria and total coliforms in hamburgers is described. The two procedures are based on the gas chromatographic determination of metabolic CO₂ in equilibrium in the head space of sealed vials containing suitable media and inoculated with aliquots of the sample under examination. Both procedures proved to be suitable for quality control of meat products, being highly sensitive, reproducible, simple and rapid. Good correlation coefficients were obtained with plate counting for microbial concentrations ranging between 10¹ and 10⁸.     

Isotopic analysis of the sources of organic carbon for zooplankton in shallow subarctic and arctic waters

Shallow high-latitude lakes and ponds are usually characterized by an oligotrophic water column overlying a biomass-rich, highly productive benthos. Their pelagic food webs often contain abundant zooplankton but the importance of benthic organic carbon versus seston as their food sources has been little explored. Our objectives were to measure the δ¹³C and δ¹⁵N isotopic signatures of pelagic and benthic particulate organic matter (POM) in shallow water bodies in northern Canada and to determine the relative transfer of this material to zooplankton and other aquatic invertebrates. Fluorescence analysis of colored dissolved organic matter (CDOM) indicated a relatively strong terrestrial carbon influence in five subarctic waterbodies whereas the CDOM in five arctic water columns contained mostly organic carbon of autochthonous origin. The isotopic signatures of planktonic POM and cohesive benthic microbial mats were distinctly different at all study sites, while non-cohesive microbial mats often overlapped in their δ¹³C signals with the planktonic POM. Zooplankton isotopic signatures indicated a potential trophic link with different fractions of planktonic POM and the non-cohesive mats whereas the cohesive mats did not appear to be used as a major carbon source. The zooplankton signals differed among species, indicating selective use of resources and niche partitioning. Most zooplankton had δ¹³C values that were intermediate between the values of putative food sources and that likely reflected selective feeding on components of the pelagic or benthic POM. The results emphasize the likely importance of benthic-pelagic coupling in tundra ecosystems, including for species that are traditionally considered pelagic and previously thought to be dependent only on phytoplankton as their food source.     

Diel rhythmicity in amino acid uptake by Prochlorococcus

The marine cyanobacterium Prochlorococcus , the most abundant phototrophic organism on Earth, numerically dominates the phytoplankton in nitrogen (N)-depleted oceanic gyres. Alongside inorganic N sources such as nitrite and ammonium, natural populations of this genus also acquire organic N, specifically amino acids. Here, we investigated using isotopic tracer and flow cytometric cell sorting techniques whether amino acid uptake by Prochlorococcus is subject to a diel rhythmicity, and if so, whether this was linked to a specific cell cycle stage. We observed, in contrast to diurnally similar methionine uptake rates by Synechococcus cells, obvious diurnal rhythms in methionine uptake by Prochlorococcus cells in the tropical Atlantic. These rhythms were confirmed using reproducible cyclostat experiments with a light-synchronized axenic Prochlorococcus (PCC9511 strain) culture and ³⁵S-methionine and ³H-leucine tracers. Cells acquired the tracers at lower rates around dawn and higher rates around dusk despite >10⁴ times higher concentration of ammonium in the medium, presumably because amino acids can be directly incorporated into protein. Leucine uptake rates by cells in the S+G₂ cell cycle stage were consistently 2.2 times higher than those of cells at the G₁ stage. Furthermore, S+G₂ cells upregulated amino acid uptake 3.5 times from dawn to dusk to boost protein synthesis prior to cell division. Because Prochlorococcus populations can account from 13% at midday to 42% at dusk of total microbial uptake of methionine and probably of other amino acids in N-depleted oceanic waters, this genus exerts diurnally variable, strong competitive pressure on other bacterioplankton populations.     

Denitrification in sediment determined from nitrogen isotope pairing

Abstract A new method for accurate and easy measurement of denitrification in sediments is presented. The water overlying intact sediment cores was enriched with ¹⁵NO₃⁻ which mixed with the ¹⁴NO₃⁻ of the natural sources of NO₃⁻. The formation by denitrification of single-labeled (¹⁴N¹⁵N) and double-labeled (¹⁵N¹⁵N) dinitrogen pairs was measured by mass spectrometry after a few hours incubation. Total denitrification including the formation of unlabeled (¹⁴N¹⁴N) dinitrogen could be calculated assuming random isotope pairing by denitrification of the uniformly mixed NO₃⁻ species. In contrast to previous approaches, by this method it is possible to measure denitrification of both NO₃⁻ diffusing from the overlying water and NO₃⁻ from nitrification within the sediment.     

A single-substrate model to interpret intra-annual stable isotope signals in tree-ring cellulose

The carbon and oxygen stable isotope composition of wood cellulose ( δ ¹³C_cellulose and δ ¹⁸O_cellulose, respectively) reveal well-defined seasonal variations that contain valuable records of past climate, leaf gas exchange and carbon allocation dynamics within the trees. Here, we present a single-substrate model for wood growth to interpret seasonal isotopic signals collected in an even-aged maritime pine plantation growing in South-west France, where climate, soil and flux variables were also monitored. Observed seasonal patterns in δ ¹³C_cellulose and δ ¹⁸O_cellulose were different between years and individuals, and mostly captured by the model, suggesting that the single-substrate hypothesis is a good approximation for tree ring studies on Pinus pinaster , at least for the environmental conditions covered by this study. A sensitivity analysis revealed that the model was mostly affected by five isotopic discrimination factors and two leaf gas-exchange parameters. Modelled early wood signals were also very sensitive to the date when cell wall thickening begins ( t _wt). Our model could therefore be used to reconstruct t _wt time series and improve our understanding of how climate influences this key parameter of xylogenesis.     

CALCIUM FLUXES IN CULTURED AND BULK ISOLATED NEURONAL AND GLIAL CELLS

Abstract— The influx and efflux of ⁴⁵Ca has been studied in cultured human glioma and mouse neuroblastoma cells and in isolated fractions enriched in synaptosomes, neuronal and astrocytic perikarya from rabbit brain.
The uptake of ⁴⁵Ca was somewhat more efficient in glioma compared to neuroblastoma cells, whereas there was little difference in the rate of ⁴⁵Ca uptake by isolated glial cells and neuronal perikarya. Isolated synaptosomes showed the highest rate of ⁴⁵Ca accumulation. An increase of K concentration to 50 m m in the medium, with a corresponding lowering of Na, stimulated both glioma and glial as well as synaptosomal ⁴⁵Ca uptake more markedly than the uptake by neuroblastoma cells and neuronal perikarya. Lowering the Na concentration and replacing it by choline had no effect on the cultured cells and astrocytes. Na-free media caused massive stimulation of ⁴⁵Ca influx in all fractions and cells tested.
The efflux of ⁴⁵Ca was studied after preloading of cells. Three phases could be resolved from the desaturation curves. All cells had nearly similar half-lives for ⁴⁵Ca efflux under standard conditions. Pulses of media containing 50 m m -K stimulated ⁴⁵Ca efflux from glioma cells and astrocytes more efficiently than from neuroblastoma cells, neuronal perikarya and synaptosomes. The stimulated release was exclusively seen in Ca-containing media in experiments with the cultured cells and in Ca-free media in experiments with cell perikarya. The effect of transmitter pulses on the release of ⁴⁵Ca was examined in a limited series. Acetylcholine and isoproterenol were found to stimulate ⁴⁵Ca release more actively from glia than from neurons.     

Natural 13C and 15N abundance of field-collected fungi and their ecological implications

The natural abundance of ¹³C and ¹⁵N was measured in basidiocarps of at least 115 species in 88 genera of ectomycorrhizal, wood-decomposing and litter-decomposing fungi from Japan and Malaysia. The natural abundance of ¹³C and ¹⁵N was also measured in leaves, litter, soil and wood from three different sites. ¹⁵N and ¹³C were enriched in ectomycorrhizal and wood-decomposing fungi, respectively, relative to their substrates. Ectomycorrhizal and wood-decomposing fungi could be distinguished on the basis of their δ¹³C and δ¹⁵N signatures. Although there was high variability in the isotopic composition of fungi, the following isotope- enrichment factors (ε, mean±SD) of the fungi relative to substrates were observed:
ε_{ectomycorrhizal fungi/litter} = 6.1±0.4‰¹⁵N
ε_{ectomycorrhizal fungi/wood} = 1.4±0.8‰¹³C
ε_{wood-decomposing fungi/wood} = −0.6±0.7‰¹⁵N
ε_{wood-decomposing fungi/wood} = 3.5±0.9‰¹³C
The basis of isotope fractionation in C metabolism from wood to wood-decomposing fungus is discussed.     

Relationships between DOC concentration and epilithon stable isotopes in boreal lakes

1. Littoral biota in boreal lakes are known to assimilate epilithon. Being able to predict the stable isotopic composition of these alga will help to identify those systems in which δ¹³C and δ¹⁵N analysis can be used in foodweb investigations of allochthony and biomagnification.
2. In a survey of 15 boreal lakes, the concentration of dissolved organic carbon (DOC) explained 76% of the variation in epilithon δ¹³C, and 86% of the variation in epilithon δ¹⁵N.
3. Because both δ¹³C and δ¹⁵N values were depressed and similar to terrestrial values in humic (high DOC) lakes, it will be more difficult to successfully employ stable isotopic techniques for estimating allochthony in such systems. Lower δ¹⁵N values in humic lakes also indicate that trophic positions estimated by stable isotopes are not directly comparable to those of similar biota inhabiting clearwater lakes, unless autochthonous baseline corrections are made.     

Multipotent mesenchymal stem cells from adult human eye conjunctiva stromal cells

Abstract Identification of mesenchymal stem cells (MSCs) derived from alternative sources has provided an exciting prospect for intensive investigation. This work focused on characterizing a new source of MSCs from stromal cells from human eye conjunctiva. In this study, after conjunctiva biopsies and culture of stromal segment of this tissue, fibroblast-like (SH2⁺, SH3⁺, CD29⁺, CD44⁺, CD166⁺, CD13⁺) human stromal cells, which can be differentiated toward the osteogenic, adipogenic, chondrogenic, and neurogenic lineages, were obtained. These cells expressed Oct-4, Nanog, Rex-1 genes, and some lineage-specific markers like cardiac actin and Keratin. Taken together, the results indicate that conjunctiva stromal-derived cells are a new source of multipotent MSCs and despite originating from an adult source, they express undifferentiated stem cell markers.     

Using the δ13C and δ15N of whitefish scales for retrospective ecological studies: changes in isotope signatures during the restoration of Lake Geneva, 1980–2001

The scales of whitefish Coregonus lavaretus were used in place of dorsal muscle, which necessitates killing the fish, to study food webs from the δ¹³C and δ¹⁵N isotopic ratios in the organic fraction. As scales are composed of both organic and calcified fractions, a protocol for scale decalcification was first devised. The δ¹³C and δ¹⁵N values of the decalcified scales were then shown to be closely correlated to those of the dorsal muscle, demonstrating that scales could be used in place of muscle to study food webs. Changes in the δ¹³C of whitefish were determined from a scale collection that extended over the period during which the trophic state of Lake Geneva was recovering.     

Assessing amino acid uptake by phototrophic nanoflagellates in nonaxenic cultures using flow cytometric sorting

Biologically available concentrations of individual dissolved amino acids in the open ocean are generally <1 nM. Despite this, the microbial turnover of amino acids is usually measured in hours indicating high demand. It is thought that the majority of uptake is due to bacterioplankton, although protists, particularly phototrophic protists, are also expected to take up amino acids. In order to assess the ability of protists to compete with prokaryotes for amino acids at subnanomolar concentrations, we examined the direct uptake of ³H-leucine by phototrophic nanoflagellates (prasinophytes, pelagophytes and trebouxiophytes) and by associated bacteria using flow cytometric cell sorting. In contrast to ³H-leucine-assimilating bacterial copopulations, none of the six studied nanoflagellates showed measurable direct uptake of ³H-leucine, suggesting that the studied phototrophic protists were unable to utilize dissolved ³H-leucine at natural oceanic concentrations. More practically, the flow-sorting technique allowed rapid and unequivocal differentiation of organic nitrogen uptake between prokaryotic cells and eukaryotic cells in mixed microbial populations, reducing the need to establish and maintain axenic algal cultures.     

The Limulus Lysate Endotoxin Assay as a Test of Microbial Quality of Ground Beef

The Limulus lysate test (LLT) for endotoxin assay has been found to be an excellent, simple and rapid test of microbial quality of refrigerated ground beef. In fresh ground beef held at 5°C for 7–12 d, LLT titres increased from 10²–10⁵ and correlated very highly with extract-release volume (ERV) data and total viable Gram negative counts at both 5° and 30°C. The LLT was negative for fresh beef containing low numbers of bacteria and on aged beef in the absence of increasing numbers of Gram negative bacteria. Of 14 Gram negative meat isolates, all gave a positive LLT while none of eight miscellaneous Gram positive bacteria did. The use of this test provides objective information on the microbial quality of fresh refrigerated ground meats in 1 h. Based upon this study, it is suggested that a 0·1 ml inoculum from a 10³ dilution of good quality ground beef should produce a negative lysate test and thus serve as an additional rapid screening test of meat microbial quality.     

Use of 13C labeling to assess carbon partitioning in transgenic and nontransgenic (parental) rice and their rhizosphere soil microbial communities

Photosynthetic assimilation of CO₂ is a primary source of carbon in soil and root exudates and can influence the community dynamics of rhizosphere organisms. Thus, if carbon partitioning is affected in transgenic crops, rhizosphere microbial communities may also be affected. In this study, the temporal effects of gene transformation on carbon partitioning in rice and rhizosphere microbial communities were investigated under greenhouse conditions using the ¹³C pulse-chase labeling method and phospholipid fatty acid (PLFA) analysis. The ¹³C contents in leaves of transgenic (Bt) and nontransgenic (Ck) rice were significantly different at the seedling, booting and heading stages. There were no detectable differences in ¹³C distribution in rice roots and rhizosphere microorganisms at any point during rice development. Although a significantly lower amount of Gram-positive bacterial PLFAs and a higher amount of Gram-negative bacterial PLFAs were observed in Bt rice rhizosphere as compared with Ck at all plant development stages, there were no significant differences in the amount of individual ¹³C-PLFA between Bt and Ck rhizospheres at any growing stage. These findings indicate that the insertion of cry1Ab and marker genes into rice had no persistent or adverse effect on the photosynthate distribution in rice or the microbial community composition in its rhizosphere.