Estimation of the quantity of bacteria encapsulated in Lentikats Biocatalyst via phospholipid fatty acids content: a preliminary study

The content of phospholipid fatty acids (PLFA) was determined in samples of polyvinyl alcohol lenses (Lentikats Biocatalyst, LB) with encapsulated Paracoccus denitrificans withdrawn during long-term denitrification experiments. The total PLFA content correlated highly with specific denitrification activities of LB as well as biomass estimation based on image analyses of microscopic photos. The results confirmed the applicability of PLFA determination for estimation of the amount of living encapsulated microbial biomass during biotechnological applications.     

Metabolic systems analysis to advance algal biotechnology

Algal fuel sources promise unsurpassed yields in a carbon neutral manner that minimizes resource competition between agriculture and fuel crops. Many challenges must be addressed before algal biofuels can be accepted as a component of the fossil fuel replacement strategy. One significant challenge is that the cost of algal fuel production must become competitive with existing fuel alternatives. Algal biofuel production presents the opportunity to fine-tune microbial metabolic machinery for an optimal blend of biomass constituents and desired fuel molecules. Genome-scale model-driven algal metabolic design promises to facilitate both goals by directing the utilization of metabolites in the complex, interconnected metabolic networks to optimize production of the compounds of interest. Network analysis can direct microbial development efforts towards successful strategies and enable quantitative fine-tuning of the network for optimal product yields while maintaining the robustness of the production microbe. Metabolic modeling yields insights into microbial function, guides experiments by generating testable hypotheses, and enables the refinement of knowledge on the specific organism. While the application of such analytical approaches to algal systems is limited to date, metabolic network analysis can improve understanding of algal metabolic systems and play an important role in expediting the adoption of new biofuel technologies.     

Importance quantitative de différentes classes de taille phytoplanctoniques en milieu lacustre eutrophe

The distribution of three phytoplanktonic size fractions was studied in an eutrophic lake. Size fractionation experiments were performed using cell enumeration by inverted microscopy and chlorophyll a estimation. The results were also compared with the ATP content in the analysed algal fractions.The (1–12 µm) fraction represented only on average 5 % of the total biomass, when estimated by the cell enumeration method, but made up 26 % of the total chlorophyll a and 33 % of the total ATP. This discrepancy confirms that cell enumeration with an inverted microscope seriously underestimates the nanoplankton biomass.The (12–45 µm) fraction made up to 50% of the total biomass regardless the method of analysis used. The chlorophyll a and biovolume estimation in this fraction were positively correlated.The contribution of algal species with large cell size (45–160 µm) to the total algal biomass was higher (39%) when based on their biovolume estimation than when on the chlorophyll a (27%). The low ATP contribution of this fraction (17%) may be attributable to high percentage of dead cells.

     

The characterisation of eukaryotic microbial communities on sandstone buildings in Belfast,UK, using TRFLP and 454 pyrosequencing

Eukaryotic microorganisms, notably microbial algae and fungi, can have a major impact on the biodeterioration of building stone, particularly when they form green biofilms. However, comparatively little is known about the composition and structure of eukaryotic communities living on the surface of stone. The twin aims of this study were to a) characterise algal and fungal communities living on heritage structures in Belfast, UK and b) to investigate the relationship between eukaryotic community composition and a variety of substrate characteristics. We used molecular techniques (TRFLP and 454 pyrosequencing) to characterise the communities. We found unexpectedly high levels of taxonomic richness in algal communities, but low overall levels of diversity in both the algal and the fungal assemblages resulting from inequitable distributions of taxa. Our findings suggest the existence of a small pool of cosmopolitan algal species and relatively homogeneous algal communities on sandstone structures. In contrast, fungal communities were much richer and more spatially heterogeneous. It is likely that the aggressive chemical cleaning of one of the structures in the 1980s has had an ongoing impact on microbial community structure. Furthermore, whilst substrate characteristics seem to impact on the abundance/biomass of eukaryotic microbial communities, they do not influence diversity.     

Grazer biomass correlates more strongly with production than with biomass of algal turfs on a coral reef

The biomass of large herbivorous grazing fish on the shallow reef crest of Myrmidon Reef, Great Barrier Reef, is 7.0 times that on the reef slope (15 m depth), and 2.3 times that on the reef flat. Biomass of algal turfs on the crest was only 1.4 and 1.0 times that on the slope and flat, respectively. In contrast, rate of production of algal turfs on the crest was 5.3 and 2.8 times that on the slope and flat, respectively. A multiple correlation between large grazer biomass, algal turf biomass, and algal turf production across the three zones showed that only rate of algal production correlated significantly with large grazer biomass (algal production p=0.007, algal biomass p=0.418). This result suggests that large grazers may aggregate in zones of highest algal turf production. The mechanisms by which fish respond to habitat-specific differences in food production remain unclear.     

OPTICAL PROPERTIES OF DENSE ALGAL CULTURES OUTDOORS AND THEIR APPLICATION TO REMOTE ESTIMATION OF BIOMASS AND PIGMENT CONCENTRATION IN SPIRULINA PLATENSIS (CYANOBACTERIA)1

Reflectance and vertical attenuation coefficient spectra from 400 to 1100 nm were investigated in detail on dense algal cultures of Spirulina in order to create algorithms for remote estimation of pigment and biomass concentration. Reflectance and the vertical attenuation coefficients were compared with biomass and pigment concentration in outdoor algal cultures. For assessing biomass concentration, the sum of reflectance above the base line from 670 to 950 nm was used. This allows the estimation of biomass with an error of less than 0.06 g·L^?1 For chlorophyll a and phycocyanin estimation, vertical attenuation coefficients at the wavelengths 440 nm (or 676 nm) and 624 nm, respectively, were employed. The developed algorithms were tested by using independent data sets in the range of chlorophyll a from 0.2 to 20mg·L^?1 and biomass from 0.15 to 1.1 g·L^?1. An error of pigment estimation of less than 0.80 mg·L^?1 was achieved. The potential use of the algorithms in algal biotechnology is further discussed.     

Methods for the quantification ofFrankia cell biomass

Six methods for the estimation of microbial biomass were compared for determination ofFrankia cell concentrations. Six strains ofFrankia were cultivated in stationary culture, harvested by centrifugation, washed with saline buffer and diluted to five standardized concentrations. These cell suspensions were then used to assess reliability of each of the biomass determination methods. The destructive total protein determination methods were the most sensitive and reliable. Two non-destructive methods, packed cell volume and turbidity measurement, were also accurate, and because of their simplicity hold advantage for routine growth measurements and inoculum dilutions. Dry weight determinations were inconsistent for the small cell masses used in this study. An ELISA procedure demonstrated reliability but little sensitivity.     

On-line biomass monitoring by capacitance measurement.

An in-situ, steam-sterilizable capacitance probe was used to follow the biomass concentration on-line, in bioreactors from 20 to 2000 l total volume. Microbial cultures of Saccharomyces cerevisiae, Pichia pastoris and Streptomyces virginiae were grown in batch and fed-batch culture in both defined and complex media in order to demonstrate the wide dynamic operating range of the instrument. A linear correlation was found between the on-line capacitance measurement and the off-line measurements (optical density, OD620; packed mycelial volume, PMV; biomass concentration X, and colony forming units, CFU ml-1) for biomass concentrations (dry cell weight) up to 30 g l-1 (St. virginiae), 106 g l-1 (S. cerevisiae) and 89 g l-1 (P. pastoris). The on-line capacitance measurement was slightly influenced by variations in agitation speed and strong extraneous radio frequencies. A specific capacitance constant (Cs) was defined for all microbial cells which was dependent on cell viability and cell size. The Cs was easy to calculate using the on-line capacitance measurement and an off-line estimation of biomass concentration. The Biomass Monitor proved suitable for precise on-line monitoring of both homogeneous (uni-cellular) and heterogeneous (mycelial) cultures in bioreactors.     

Benthic algal biomass in an unshaded first-order lowland stream: distribution and regulation

The vertical distribution of algal biomass in the bed sediment and the seasonal development of benthic algae on stones and fine-grained sediments were studied in a small unshaded stream. In addition, field experiments were conducted on the role of irradiance and phosphorus in regulating algal biomass. We found that algal biomass was high at a sediment depth of ten centimetres. Comparison of studies on algal biomass where different depths of the sediment are used should therefore be made with caution. Substrata-dependent differences in algal biomass development were substantial. While algal biomass development on stones was controlled by macroinvertebrate grazing, that on the fine-grained sediment followed the dynamics of incident irradiance, but was attenuated by sediment rebedding. Because of the high grazing pressure on algal biomass on stony substrata, no significant response to phosphorus enrichment was attained. In contrast, algal biomass development on fine-grained sediments was phosphorus-limited. Heavy shading of the fine-grained sediments did not significantly affect algal biomass development, thus suggesting that phosphorus limitation prevents algae from fully utilizing the light resource in this stream. This revised version was published online in July 2006 with corrections to the Cover Date.     

Estimating phytoplankton carbon from microscopic counts: an application for riverine systems

Algal biomass, in addition to cell numbers, is a measure of the successful conversion of inorganic to organic carbon. Consequently, carbon is the main currency used in aquatic models and in flux and budget studies. On the other hand, microscopic observation and counts remain the only means for determining species composition and biomass, which is relevant to many aspects of aquatic ecology. In this study, we focus on the way to convert biovolume to carbon biomass for algal assemblages of two rivers, using a computerized system that records dimensions of phytoplankton (Gosselain & Hamilton, 2000). We first compare different equations found in the literature for converting algal cell volume to cellular carbon content. We then evaluate the accuracy of a biomass estimate based on less time-consuming measurements, using pre-determined biovolume values instead of measuring cells in all samples. Biovolume/carbon equations are evaluated using total phytoplankton carbon biomass determined from measured chlorophyll a. Equations established for freshwater taxa seem to provide better estimates of algal biomass in the two case studies presented here, the Rideau and Meuse rivers (Canada and Belgium, respectively) than do more numerous equations defined for marine taxa. Furthermore, equations that make a distinction between diatoms and other algae appear more appropriate than those considering all algal groups as a whole. Finally, mean values of algal biovolumes, determined using sufficient measurements of cell dimensions from representative sampling series, may prove sufficient for carbon estimates of taxa in relatively homogenous size ranges. The careful choice of appropriate volumetric shapes and taxa categories remains of prime importance to get precise results.     

Uncertainty analysis of forest carbon sink forecast with varying measurement errors: a data assimilation approach

Aims Accurate forecast of ecosystem states is critical for improving natural resource management and climate change mitigation. Assimilating observed data into models is an effective way to reduce uncertainties in ecological forecasting. However, influences of measurement errors on parameter estimation and forecasted state changes have not been carefully examined. This study analyzed the parameter identifiability of a process-based ecosystem carbon cycle model, the sensitivity of parameter estimates and model forecasts to the magnitudes of measurement errors and the information contributions of the assimilated data to model forecasts with a data assimilation approach.Methods We applied a Markov Chain Monte Carlo method to assimilate eight biometric data sets into the Terrestrial ECOsystem model. The data were the observations of foliage biomass, wood biomass, fine root biomass, microbial biomass, litter fall, litter, soil carbon and soil respiration, collected at the Duke Forest free-air CO₂ enrichment facilities from 1996 to 2005. Three levels of measurement errors were assigned to these data sets by halving and doubling their original standard deviations.Important findings Results showed that only less than half of the 30 parameters could be constrained, though the observations were extensive and the model was relatively simple. Higher measurement errors led to higher uncertainties in parameters estimates and forecasted carbon (C) pool sizes. The long-term predictions of the slow turnover pools were affected less by the measurement errors than those of fast turnover pools. Assimilated data contributed less information for the pools with long residence times in long-term forecasts. These results indicate the residence times of C pools played a key role in regulating propagation of errors from measurements to model forecasts in a data assimilation system. Improving the estimation of parameters of slow turnover C pools is the key to better forecast long-term ecosystem C dynamics.     

Determination of low concentration of Paracoccus denitrificans encapsulated in polyvinyl alcohol LentiKat’s pellets

The aim of this work was to compare three methods to determinate low concentrations of Paracoccus denitrificans encapsulated in polyvinyl alcohol pellets, which is important for evaluation and optimization of pellet production as well as for monitoring of biomass growth. Pellets with different and well-defined biomass concentrations were used for experiments. The following fast and simple methods were tested: (1) dissolution of polyvinyl alcohol in hot water followed by dry weight estimation, (2) dissolution of polyvinyl alcohol in hot water followed by optical density measurement, (3) and extraction and quantification of proteins. Dry weight estimation proved to be problematic as it was difficult to separate biomass from polymeric carrier. Optical density measurement showed good linearity of dependence of optical density on biomass content, but determined limits of detection and limits of quantification were not within the range necessary for intended application. The only tested method meeting the requirements for sensitivity was determination of protein concentration after protein extraction.     

Microbial community composition and function in permanently cold seawater and sediments from an arctic fjord of svalbard

Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.     

Dominance of autochthonous autotrophic carbon in food webs of heterotrophic rivers

This paper addresses the river heterotrophy paradox, “How can animal biomass within riverine food webs be fueled primarily by autochthonous autotrophic production if the ecosystem as a whole is heterotrophic?”. Reviewed, stable isotope data from tropical, temperate, and arctic rivers provide evidence consistent with the revised riverine productivity model (RPM): “The primary, annual energy source supporting overall metazoan production and species diversity in mid‐ to higher‐trophic levels of most rivers (≥4th order) is autochthonous primary production entering food webs via algal‐grazer and decomposer pathways”. The revised RPM does not conflict with the heterotrophy paradox because: (a) the decomposer (microbial loop) food pathway processes most of the transported, allochthonous and autochthonous carbon and, with algal respiration in some cases, is primarily responsible for a river's heterotrophic state (P/R<1); but (b) biomass production of mid‐ to higher‐trophic levels is principally supported by an algal‐grazer (phytoplankton and benthic microalgae) pathway that is only weakly linked to the decomposer pathway. The reason the algal‐grazer pathway supports the majority of metazoan biomass is that allochthonous carbon is mostly recalcitrant, whereas carbon from autochthonous primary production, though much less plentiful, is commonly more labile (easier to assimilate), contains more energy per unit mass, and is typically preferred by metazoa.     

Mechanism and challenges in commercialisation of algal biofuels

Biofuels made from algal biomass are being considered as the most suitable alternative energy in current global and economical scenario. Microalgae are known to produce and accumulate lipids within their cell mass which is similar to those found in many vegetable oils. The efficient lipid producer algae cell mass has been reported to contain more than 30% of their cell weight as lipids. According to US DOE microalgae have the potential to produce 100 times more oil per acre land than any terrestrial plants. This article reviews up to date literature on the composition of algae, mechanism of oil droplets, triacylglycerol (TAG) production in algal biomass, research and development made in the cultivation of algal biomass, harvesting strategies, and recovery of lipids from algal mass. The economical challenges in the production of biofuels from algal biomass have been discussed in view of the future prospects in the commercialisation of algal fuels.     

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea

The stratified water column of the Black Sea produces a vertical succession of redox zones, stimulating microbial activity at the interfaces. Our study of intact polar membrane lipids (IPLs) in suspended particulate matter and sediments highlights their potential as biomarkers for assessing the taxonomic composition of live microbial biomass. Intact polar membrane lipids in oxic waters above the chemocline represent contributions of bacterial and eukaryotic photosynthetic algae, while anoxygenic phototrophic bacteria and sulfate-reducing bacteria comprise a substantial amount of microbial biomass in deeper suboxic and anoxic layers. Intact polar membrane lipids such as betaine lipids and glycosidic ceramides suggest unspecified anaerobic bacteria in the anoxic zone. Distributions of polar head groups and core lipids show planktonic archaea below the oxic zone; methanotrophic archaea are only a minor fraction of archaeal biomass in the anoxic zone, contrasting previous observations based on the apolar derivatives of archaeal lipids. Sediments contain algal and bacterial IPLs from the water column, but transport to the sediment is selective; bacterial and archaeal IPLs are also produced within the sediments. Intact polar membrane lipid distributions in the Black Sea are stratified in accordance with geochemical profiles and provide information on vertical successions of major microbial groups contributing to suspended biomass. This study vastly extends our knowledge of the distribution of complex microbial lipids in the ocean.     

Phycoremediation coupled production of algal biomass,harvesting and anaerobic digestion: Possibilities and challenges

Biogas produced from anaerobic digestion is a versatile and environment friendly fuel which traditionally utilizes cattle dung as the substrate. In the recent years, owing to its high content of biodegradable compounds, algal biomass has emerged as a potential feedstock for biogas production. Moreover, the ability of algae to treat wastewater and fix CO₂ from waste gas streams makes it an environmental friendly and economically feasible feedstock. The present review focuses on the possibility of utilizing wastewater as the nutrient and waste gases as the CO₂ source for algal biomass production and subsequent biogas generation. Studies describing the various harvesting methods of algal biomass as well as its anaerobic digestion have been compiled and discussed. Studies targeting the most recent advancements on biogas enrichment by algae have been discussed. Apart from highlighting the various advantages of utilizing algal biomass for biogas production, limitations of the process such as cell wall resistivity towards digestion and inhibitions caused due to ammonia toxicity and the possible strategies for overcoming the same have been reviewed. The studies compiled in the present review indicate that if the challenges posed in translating the lab scale studies on phycoremediation and biogas production to pilot scale are overcome, algal biogas could become the sustainable and economically feasible source of renewable energy.     

Continuous cultures limited by a gaseous substrate: Development of a simple, unstructured mathematical model and experimental verification with Methanobacterium thermoautotrophicum

This article presents a simple, unstructured mathematical model describing microbial growth in continuous culture limited by a gaseous substrate. The model predicts constant gas conversion rates and a decreasing biomass concentration with increasing dilution rate. It has been found that the parameters influencing growth are primarily the gas transfer rate and the dilution rate. Furthermore, it is shown that, for correct simulation of growth, the influence of gaseous substrate consumption on the effective gas flow through the system has to be taken into account.Continuous cultures of Methanobacterium thermoautotrophicum were performed at three different gassing rates. In addition to the measurement of the rates of biomass production, product formation, and substrate consumption, microbial heat dissipation was assessed using a reaction calorimeter. For the on-line measurement of the concentration of the growth-limiting substrate, H(2), a specially developed probe has been used. Experimental data from continuous cultures were in good agreement with the model simulations. An increase in gassing rate enhanced gaseous substrate consumption and methane production rates. However, the biomass yield as well as the specific conversion rates remained constant, irrespective of the gassing rate. It was found that growth performance in continuous culture limited by a gaseous substrate is substantially different from "classic" continuous culture in which the limiting substrate is provided by the liquid feed. In this report, the differences between both continuous culture systems are discussed.     

Does Microorganism Stoichiometry Predict Microbial Food Web Interactions After a Phosphorus Pulse?

Knowledge of variations in microbial food web interactions resulting from atmospheric nutrient loads is crucial to improve our understanding of aquatic food web structure in pristine ecosystems. Three experiments mimicking atmospheric inputs at different nitrogen/phosphorus (N/P) ratios were performed in situ covering the seasonal biological succession of the pelagic zone in a high-mountain Spanish lake. In all experiments, abundance, biomass, algal cell biovolume, P-incorporation rates, P-cell quota, and N/P ratio of algae strongly responded to P-enrichment, whereas heterotrophic bacteria remained relatively unchanged. Ciliates were severely restricted when a strong algal exploitation of the available P (bloom growth or storage strategies) led to transient (mid-ice-free experiment) or chronic (late ice-free experiment) P-deficiencies in bacteria. In contrast, maximum development of ciliates was reached when bacteria remained P-rich (N/P < 20) and algae approached Redfield proportions (N/P approximately 16). Evidence of a higher P-incorporation rate supports the proposition that algae and bacteria shifted from a mainly commensalistic-mutualistic to a competitive relationship for the available P when bacterial P-deficiency increased, as reflected by their unbalanced N/P ratio (N/P > 20-24). Hence, the bacterial N/P ratio proved be a key factor to understand the algae-bacteria relationship and microbial food web development. This study not only demonstrates the interdependence of life history strategies, stoichiometric nutrient content, and growth but also supports the use of bacterial N/P thresholds for diagnosing ciliate development, a little-studied aspect worthy of further attention.