Bulk Biomass Research Articles

Microcosm design and evaluation to study stream microbial biofilms

Biofilms represent the dominant form of microbial life in stream ecosystems. Research of complex environmental biofilms requires appropriate cultivation techniques to address questions central to biofilm structure‐function‐coupling and ecosystem implications. Whereas the cultivation of medical and industrial biofilms has received considerable attention, cultivation devices for environmental biofilms have not. Here we describe and systematically assess the reproducibility of laboratory‐based microcosms that allow the study of the structure and function of stream biofilms under different flow regimes. Microcosms were assembled from 1.3‐m‐long Plexiglas flumes fed with water that recirculated between a header tank and a sink. Each flume was paved with 104 individual unglazed ceramic coupons that served as growth substratum. We operated 3 microcosms designed to simulate laminar, transitional, and turbulent flow. Each microcosm consisted of two duplicate sets of flumes where two flumes shared the same water. We monitored biofilm coverage, bacterial abundance, and chlorophyll a as bulk biomass parameters over a growth period of 28 days and tested for community composition shifts using denaturing gradient gel electrophoresis (DGGE). Based on these variables, we assessed the reproducibility at different levels of microcosm assembly: (1) within individual flumes (i.e., longitudinal gradients), (2) within a shared water body, and (3) within flow regime treatments. Our results revealed good reproducibility at the various levels of the experimental setup and suggest microcosm flumes as highly valuable tools for biofilm studies with multitreatment and multireference designs.

UV Effects on Marine Planktonic Food Webs: A Synthesis of Results from Mesocosm Studies

UV irradiance has a broad range of effects on marine planktonic organisms. Direct and indirect effects on individual organisms have complex impacts on food-web structure and dynamics, with implications for carbon and nutrient cycling. Mesocosm experiments are well suited for the study of such complex interrelationships. Mesocosms offer the possibility to conduct well-controlled experiments with intact planktonic communities in physical, chemical and light conditions mimicking those of the natural environment. In allowing the manipulation of UV intensities and light spectral composition, the experimental mesocosm approach has proven to be especially useful in assessing the impacts at the community level. This review of mesocosm studies shows that, although a UV increase even well above natural intensities often has subtle effects on bulk biomass (carbon and chlorophyll), it can significantly impact the food-web structure because of different sensitivity to UV among planktonic organisms. Given the complexity of UV impacts, as evidenced by results of mesocosm studies, interactions between UV and changing environmental conditions (e.g. eutrophication and climate change) are likely to have significant effects on the function of marine ecosystems.

Fractionation of carbon isotopes in biosynthesis of fatty acids by a piezophilic bacterium Moritella japonica strain DSK1

We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica strain DSK1. The bacterium was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using sterile-filtered natural seawater supplied with glucose as the sole carbon source. Strain DSK1 synthesized typical bacterial fatty acids (C 14–19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6 ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed Δδ FA-glucose (−1.0‰ to −11.9‰) at 0.1 MPa was comparable to or slightly higher than fractionations reported in surface bacteria. However, bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation (Δδ FA-glucose) at high pressures was much higher than that for surface bacteria: −15.7‰, −15.3‰, and −18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions that are affected by hydrostatic pressure and to biosynthetic pathways that are different for short-chain and long-chain fatty acids. A simple quantitative calculation suggests that in situ piezophilic bacterial contribution of polyunsaturated fatty acids to marine sediments is nearly two orders of magnitude higher than that of marine phytoplankton and that the carbon isotope imprint of piezophilic bacteria can override that of surface phytoplankton. Our results have important implications for marine biogeochemistry. Depleted fatty acids reported in marine sediments and the water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i.e., methane). The interpretation of carbon isotope signatures of marine lipids must be based on principles derived from piezophilic bacteria.

Diurnal variation of the δ13C of pine needle respired CO2 evolved in darkness

The delta 13C of pine needle CO2 evolved in darkness (delta 13Cr) for slash pine trees (Pinus elliottii) was determined by placing recently collected pine needles in darkness and collecting respired CO2 over a short time period (<15 min). Delta 13Cr measurements were made over several 24 h periods to test the hypothesis that significant variation in delta 13Cr would be observed during a diurnal cycle. The delta 13Cr measurements from the 24 h time series trials showed a consistent midday 13C-enrichment (5-10 per thousand) relative to bulk biomass. The delta 13Cr values became more 13C-depleted at night and following shading, and approached bulk-biomass delta 13C values by dawn. The effect of night-time respired 13C-enriched CO2 on the delta 13C value of the remaining assimilate is shown to be minimal (13C depleted by 0.22 per thousand) under field conditions for P. elliottii needles.

Cadmium(II) Biosorption by Aeromonas caviae: Kinetic Modeling

Biosorption of cadmium from aqueous solutions on Aeromonas caviae particles was investigated in a well‐stirred batch reactor. Equilibrium and kinetic experiments were performed at various initial bulk concentrations, biomass loads, temperatures, and ionic background. Equilibrium data were well described by typical Langmuir and Freundlich adsorption isotherms. Furthermore, a detailed analysis was conducted to test several chemical reaction kinetic models in order to identify a suitable kinetic equation, assuming that biosorption is chemical sorption controlled. Predictions based on the so‐called pseudo second order rate expression were found in satisfactory accordance with experimental data.

Stress-induced physiological responses to starvation periods as well as glucose and lactose pulses in Bacillus licheniformis CCMI 1034 continuous aerobic fermentation processes as measured by multi-parameter flow cytometry

Multi-parameter flow cytometry (MPFC) coupled with specific fluorescent stains were used to monitor the physiological response of individual cells to starvation periods as well as lactose and glucose pulses during the steady state of a continuous culture of Bacillus licheniformis. Measurements of off-gas (CO 2 produced and O 2 consumed) and optical density measurements were also made and used to follow bulk biomass proliferation and metabolic activity of the microbial population. It was clear that the physiological response to each perturbation was different in type and extent dependent on the conditions experienced and that these responses could be followed by the techniques employed. The use of MPFC, a rapid, real time analysis of individual microbial cells, is enhancing our knowledge of how different physiological sub-populations develop with time (population dynamics) throughout a bio-process further demonstrating the inherent complex heterogeneity of microbial cultures even during the so called ‘steady-state’ of a continuous culture fermentation. These results are discussed in terms of devising better control systems based on measurements made at the individual cell level for optimisation of bioprocess performance.

Carbon isotope composition and water-use efficiency in plants with crassulacean acid metabolism.

The relationship between water-use efficiency, measured as the transpiration ratio (g H2O transpired g-1 above- plus below-ground dry mass accumulated), and 13C / 12C ratio (expressed as δ13C value) of bulk biomass carbon was compared in 15 plant species growing under tropical conditions at two field sites in the Republic of Panama. The species included five constitutive crassulacean acid metabolism (CAM) species [Aloe vera (L.) Webb & Berth., Ananas comosus (L.) Merr., Euphorbia tirucalli L., Kalanchoë daigremontiana Hamet et Perr., Kalanchoë pinnata (Lam.) Pers.], two species of tropical C3 trees (Tectona grandis Linn. f. and Swietenia macrophylla King), one C4 species (Zea mays L.), and seven arborescent species of the neotropical genus Clusia, of which two exhibited pronounced CAM. The transpiration ratios of the C3 and CAM species, which ranged between 496 g H2O g-1 dry mass in the C3-CAM species Clusia pratensis Seeman to 54 g H2O g-1 dry mass in the constitutive CAM species Aloe vera, correlated strongly with δ13C values and nocturnal CO2 gain suggesting that δ13C value can be used to estimate both water-use efficiency and the proportion of CO2 gained by CAM species during the light and the dark integrated over the lifetime of the tissues.

Carbon-isotopic shifts associated with heterotrophy and biosynthetic pathways in direct- and indirect-developing sea urchins

Natural abundances of 13 C were measured in bulk biomass and in individual lipids isolated from 2 species of sea urchins, Heliocidaris erythrogramma and H. tuberculata, and from cal- careous and green benthic algae on which they were feeding. Planktonic larvae of H. erythrogramma are lecithotrophic whereas those of H. tuberculata are planktotrophic. The organisms were collected from a subtidal environment in Botany Bay, Sydney, Australia. The biomass of both consumers was enriched in 13 C relative to their diets by up to 1.8 ‰. The carbon skeletons of sterols from the urchins derive at least in part from de novo biosynthesis by the urchins. Depending on chain length and de- gree of unsaturation, carboxylic acids from the urchins derive from de novo biosynthesis (14:0, unsat- urated acids), from the diet (18:0), or from both these sources (16:0). H. tuberculata synthesizes a greater distribution and proportion of unsaturated carboxylic acids. Odd-C and branched-chain car- boxylic acids derive in part from bacterial sources and are enriched in 13 C relative to algal lipids and depleted relative to those in urchins. Only H. erythrogramma, which uses wax esters as storage lipids in its relatively large and buoyant eggs, produces significant quantities of n-alkanols; n-alkanols in H. tuberculata derive from the diet. In terms of molecular distributions and isotopic compositions, the lipids in fecal matter from both heterotrophs resemble those of the diet rather than those of the urchins.

Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane.

Massive microbial mats covering up to 4-meter-high carbonate buildups prosper at methane seeps in anoxic waters of the northwestern Black Sea shelf. Strong 13C depletions indicate an incorporation of methane carbon into carbonates, bulk biomass, and specific lipids. The mats mainly consist of densely aggregated archaea (phylogenetic ANME-1 cluster) and sulfate-reducing bacteria (Desulfosarcina/Desulfococcus group). If incubated in vitro, these mats perform anaerobic oxidation of methane coupled to sulfate reduction. Obviously, anaerobic microbial consortia can generate both carbonate precipitation and substantial biomass accumulation, which has implications for our understanding of carbon cycling during earlier periods of Earth's history.

Naphthalene degradation and incorporation of naphthalene-derived carbon into biomass by the thermophile Bacillus thermoleovorans.

The thermophilic aerobic bacterium Bacillus thermoleovorans Hamburg 2 grows at 60 degrees C on naphthalene as the sole source of carbon and energy. In batch cultures, an effective substrate degradation was observed. The carbon balance, including naphthalene, metabolites, biomass, and CO(2), was determined by the application of [1-(13)C]naphthalene. The incorporation of naphthalene-derived carbon into the bulk biomass as well as into specified biomass fractions such as fatty acids and amino acids was confirmed by coupled gas chromatography-mass spectrometry (GC-MS) and isotope analyses. Metabolites were characterized by GC-MS; the established structures allow tracing the degradation pathway under thermophilic conditions. Apart from typical metabolites of naphthalene degradation known from mesophiles, intermediates such as 2, 3-dihydroxynaphthalene, 2-carboxycinnamic acid, and phthalic and benzoic acid were identified for the pathway of this bacterium. These compounds indicate that naphthalene degradation by the thermophilic B. thermoleovorans differs from the known pathways found for mesophilic bacteria.

Carbon isotope discrimination in leaf and stem sugars, water-use efficiency and mesophyll conductance during different developmental stages in rice subjected to drought

Carbon isotope discrimination (Δ), growth analysis, water-use efficiency (WUE) and gas exchange characteristics were studied in rice plants (Oryza sativa L.) subjected to drought during different developmental stages. Drought caused major effects on growth, WUE, Δ and photosynthetic CO2 assimilation. Substantial differences in the Δ of the bulk biomass among different organs and in carbohydrates extracted from leaves and stems were observed. Possible influences of chemical composition, fractionation during translocation and seasonal changes in the ratio of intercellular and atmospheric partial pressures of CO2 on such differences in Δ are discussed. Stem carbohydrate Δ was correlated with relative growth rate, and, during early grain filling, was negatively correlated with WUE measured between flowering and early grain filling. Δ in leaf sugars was used to estimate mesophyll conductance (gm), the conductance to CO2 diffusion inside leaves, from the intercellular air spaces to the chloroplast. During ontogeny, gm showed a marked progressive decrease, evident in both droughted plants and fully irrigated controls. There was a positive correlation between the rate of CO2 assimilation and gm. The analysis of Δ in leaf and stem carbohydrates is proposed as a useful indicator of growth, WUE and photosynthetic parameters relevant for yield of rice under drought-prone conditions.

The Relationship Between Bite Rate and Local Forage Abundance in Wild Thomson's Gazelles

The foraging of female Thomson's gazelles (Gazella thomsoni) on shortgrass plains was monitored over one annual cycle in southwestern Kenya. Sward dry green biomasses and protein densities were estimated regularly throughout the study site. Changes in protein densities with season and locale were strongly correlated with underlying changes in grass physiognomy: sward height and dry green bulk biomass density were particularly important and were found to vary inversely. The relationship between bite rates and underlying sward parameters varied with season: gazelle bite rates in the dry season were positively correlated with underlying dry green biomass and protein densities, as predicted by either the Process 1 or Process 2 foraging model of Spalinger and Hobbs. Nonlinear regressions of within—bout bite rates on these model equations significantly explained 21.8 and 23.7% of the dry season variance, respectively. In contrast, bite rates in the early wet season showed significant negative correlations with underlying protein densities: the fit of the within—bout bite rate data to Spalinger and Hobbs' Process 3 model explained 18.4% of the overall variation. The late wet season showed a flat (insignificant) relationship between bite rates and protein levels and was thus intermediate between early wet— and later dry—season patterns. Logistic regression of the type of correlation between bite rate and protein density (positive, flat, negative) on two principal components of grass physiognomy suggested that a component heavily weighting sward height was the major correlate of foraging process, whereas a second major component heavily weighting bulk density and other grass quality measures was less critical. At least during this single annual cycle, shorter swards were associated with Processes 1 or 2, whereas taller swards showed Process 3 foraging. One interpretation of these results is that sward height modulates bite mass, which in turn plays the major role in controlling foraging process. Whether the switching point remains the same in subsequent years or not, the results make it clear that the direction of the bite rate vs. foraging density relationship can change markedly with season, as predicted by the Spalinger and Hobbs models.

15N/14N and 13C/12C m Weddel Sea invertebrates- implications for feeding diversity

Biomass 813C, b 1 5 ~ , and C/N were measured for each of 29 taxa of pelagic invertebrates sampled from the Weddell Sea in March 1986. The 613c values of these animals ranged from -33.2 to -23.9%0, and a significant negative logarithmic relationship was observed between these values and biomass C/N. This implies that the relative proportion of carbon-rich 13C-depleted lipid in these animals significantly influenced the 6I3C of their bulk biomass. No such relationship with C/N is evident with respect to biomass b15N where values ranged from 1.2 to +7.3 %o. This spread of values reflects a wide diversity of food sources and trophic positions among the species analyzed. Isotopic abundances within krill Euphausia superba varied with individual length, apparently reflecting dietary changes during growth. Isotope values within E. superba from the Weddell Sea overlap those of krill from other Southern Ocean locations in the Scotia Sea/Drake Passage, the Ross Sea, and Prydz Bay, Antarctica.

Physical oceanography of coastal waters

Nine macroalgal blooms were studied in five coastal lagoons of the SE Gulf of California. The nutrient loads from point and diffuse sources were estimated in the proximity of the macroalgal blooms. Chlorophyll a and macroalgal biomass were measured during the dry, rainy and cold seasons. Shrimp farms were the main point source of nitrogen and phosphorus loads for the lagoons. High biomasses were found during the dry season for phytoplankton at site 6 (791.7 ± 34.6 mg m−2) and during the rainy season for macroalgae at site 4 (296.0 ± 82.4 g m−2). Depending on the season, the phytoplankton biomass ranged between 40.0 and 791.7 mg m−2 and the macroalgal biomass between 1 and 296.0 g m−2. The bulk biomass (phytoplankton + macroalgal) displayed the same tendency as the nutrient loads entering the coastal lagoons. Phytoplankton and macroalgal biomass presented a significant correlation with the atomic N:P ratio.