Prokaryotic growth and presence of metabolic products and contamination tracers in rocks samples from ODP Leg 187 sites

The microbial population in samples of basalt drilled from the north of the Australian Antarctic Discordance (AAD) during Ocean Drilling Program Leg 187 were studied using deoxyribonucleic acid (DNA)-based methods and culturing techniques. The results showed the presence of a microbial population characteristic for the basalt environment. DNA sequence analysis revealed that microbes grouping within the Actinobacteria, green nonsulfur bacteria, the Cytophaga/Flavobacterium/Bacteroides (CFB) group, the Bacillus/Clostridium group, and the beta and gamma subclasses of the Proteobacteria were present in the basalt samples collected. The most dominant phylogenetic group, both in terms of the number of sequences retrieved and the intensities of the DNA bands obtained with the denaturing gradient gel electrophoresis analysis, was the gamma Proteobacteria. Enrichment cultures showed phylogenetic affiliation with the Actinobacteria, the CFB group, the Bacillus/Clostridium group, and the alpha, beta, gamma, and epsilon subclasses of the Proteobacteria. Comparison of native and enriched samples showed that few of the microbes found in native basalt samples grew in the enrichment cultures. Only seven clusters, two clusters within each of the CFB and Bacillus/Clostridium groups and five clusters within the gamma Proteobacteria, contained sequences from both native and enriched basalt samples with significant similarity. Results from cultivation experiments showed the presence of the physiological groups of iron reducers and methane producers. The presence of the iron/manganese-reducing bacterium Shewanella was confirmed with DNA analysis. The results indicate that iron reducers and lithotrophic methanogenic Archaea are indigenous to the ocean crust basalt and that the methanogenic Archaea may be important primary producers in this basaltic environment.

Effect of ocean acidification on growth and otolith condition of juvenile scup, Stenotomus chrysops

Increasing amounts of atmospheric carbon dioxide (CO2) from human industrial activities are causing changes in global ocean carbonate chemistry, resulting in a reduction in pH, a process termed "ocean acidification." It is important to determine which species are sensitive to elevated levels of CO2 because of potential impacts to ecosystems, marine resources, biodiversity, food webs, populations, and effects on economies. Previous studies with marine fish have documented that exposure to elevated levels of CO2 caused increased growth and larger otoliths in some species. This study was conducted to determine whether the elevated partial pressure of CO2 (pCO2) would have an effect on growth, otolith (ear bone) condition, survival, or the skeleton of juvenile scup, Stenotomus chrysops, a species that supports both important commercial and recreational fisheries. Elevated levels of pCO2 (1200-2600 µatm) had no statistically significant effect on growth, survival, or otolith condition after 8 weeks of rearing. Field data show that in Long Island Sound, where scup spawn, in situ levels of pCO2 are already at levels ranging from 689 to 1828 µatm due to primary productivity, microbial activity, and anthropogenic inputs. These results demonstrate that ocean acidification is not likely to cause adverse effects on the growth and survivability of every species of marine fish. X-ray analysis of the fish revealed a slightly higher incidence of hyperossification in the vertebrae of a few scup from the highest treatments compared to fish from the control treatments. Our results show that juvenile scup are tolerant to increases in seawater pCO2, possibly due to conditions this species encounters in their naturally variable environment and their well-developed pH control mechanisms.

Data base on pelagic ciliates grazing and growth rate as a function of size, prey size and type compiled from the literature

Microzooplankton (the 20 to 200 µm size class of zooplankton) is recognised as an important part of marine pelagic ecosystems. In terms of biomass and abundance pelagic ciliates are one of the important groups of organism in microzooplankton. However, their rates - grazing and growth - , feeding behaviour and prey preferences are poorly known and understood. A set of data was assembled in order to derive a better understanding of pelagic ciliates rates, in response to parameters such as prey concentration, prey type (size and species), temperature and their own size. With these objectives, literature was searched for laboratory experiments with information on one or more of these parameters effect studied. The criteria for selection and inclusion in the database included: (i) controlled laboratory experiment with a known ciliates feeding on a known prey; (ii) presence of ancillary information about experimental conditions, used organisms - cell volume, cell dimensions, and carbon content. Rates and ancillary information were measured in units that meet the experimenter need, creating a need to harmonize the data units after collection. In addition different units can link to different mechanisms (carbon to nutritive quality of the prey, volume to size limits). As a result, grazing rates are thus available as pg C/(ciliate*h), µm**3/(ciliate*h) and prey cell/(ciliate*h); clearance rate was calculated if not given and growth rate is expressed as the growth rate per day.

Microbial iron transport via a siderophore shuttle: A membrane ion transport paradigm

A mechanism of ion transport across membranes is reported. Microbial transport of Fe3+ generally delivers iron, a growth-limiting nutrient, to cells via highly specific siderophore-mediated transport systems. In contrast, iron transport in the fresh water bacterium Aeromonas hydrophila is found to occur by means of an indiscriminant siderophore transport system composed of a single multifunctional receptor. It is shown that (i) the siderophore and Fe3+ enter the bacterium together, (ii) a ligand exchange step occurs in the course of the transport, and (iii) a redox process is not involved in iron exchange. To the best of our knowledge, there have been no other reports of a ligand exchange mechanism in bacterial iron transport. The ligand exchange step occurs at the cell surface and involves the exchange of iron from a ferric siderophore to an iron-free siderophore already bound to the receptor. This ligand exchange mechanism is also found in Escherichia coli and seems likely to be widely distributed among microorganisms.

Effects of phytase supplementation of phosphorus-adequate, lysine-deficient, wheat-based diets on growth performance of weaner pigs

The effects of microbial phytase supplementation of phosphorus-adequate, wheat-based diets with available lysine : energy density ratios ranging from 0.75 to 0.90 g available lysine/MJ DE on growth performance of weaner pigs were investigated in 3 studies. In the first study, increasing levels of dietary phytate depressed growth rates (P<0.08) and efficiency of feed conversion (P<0.01) and phytase supplementation enhanced growth rates (P<0.05) and tended to improve feed efficiency (P<0.15). There were no significant interactions between dietary phytate and phytase inclusion to support the hypothesis that dietary substrate levels of phytate govern responses to phytase. However, in this and other studies, percentage increases in efficiency of feed conversion generated by phytase were positively correlated to dietary phytate concentrations to a significant extent (P<0.005), so it is possible that dietary substrate levels are of importance to the magnitude of responses following phytase supplementation. Diets with 3 levels of protein, expressed as 0.80, 0.85, and 0.90 g available lysine/MJ DE, were offered to pigs without and with phytase in the second study. Protein/amino acid levels or lysine : energy density ratios did not influence growth performance, which was not expected. However, phytase tended to increase growth rates (P<0.08) and improved feed efficiency (P<0.01). Although it is believed that phytase may have a positive influence on protein utilisation, this was not demonstrated in this experiment. In the third study, the simultaneous inclusion of phytase and xylanase feed enzymes in wheat-based weaner diets did not increase growth performance responses in comparison with phytase alone. Individually, phytase improved feed efficiency (P<0.05) and numerically increased growth rates (P<0.25). Although responses in growth performance of weaner pigs following phytase supplementation lacked consistency, they were generally positive and indicative of anti-nutritive properties of phytate that are unrelated to P availability. That these positive responses were observed in diets with suboptimal available lysine : energy density ratios is consistent with the possibility that phytate has a negative influence on protein utilisation, which is ameliorated by phytase. However, these antinutritive effects and their underlying mechanisms need to be better defined if full advantage of the potential protein-sparing effects of microbial phytase is to be taken.

Effects of phytase supplementation of diets with two tiers of nutrient specifications on growth performance and protein efficiency ratios of broiler chickens

in two feeding experiments male and mixed-sex broiler chicks were offered diets based on sorghum and a wheat-sorghum blend with two tiers of nutrient specifications, without and with microbial phytase (600 and 800 FTU/kg), from 7-25 and 1-42 days post-hatch, respectively. The nutrient specifications for protein, amino acids, energy density and phosphorus (P) of standard diets were reduced to formulate the modified diets on a least-cost basis. Calculated differences in nutrient specifications between standard and modified diets ranged from 14.3 to 17.1 g/kg crude protein, 0.24 to 0.40 MJ/kg apparent metabolisable energy (AME) and 1.06 to 1.20 g/kg available P. In both experiments, reduced nutrient specifications had a negative impact on growth rates and feed efficiency and phytase supplementation had a positive influence on growth performance and protein efficiency ratios (PER). Phytase addition to the less expensive, modified diets either partially or entirely compensated for reduced growth performance and, consequently, feed costs per kg of live weight gain were reduced. In Experiment 1, phytase increased (p<0.001) nitrogen-corrected AME (AMEn) from 15.39 to 15.89 MJ/kg dry matter. For nitrogen (N) retention there was an interaction (p<0.05) between diet type and phytase as the effects of phytase on N retention were more pronounced in the modified diets, with an increase from 0.512 to 0.561. These results demonstrate the positive effects of phytase on protein and energy utilisation, in addition to its established liberation of phytate-bound P and illustrate the feasibility of assigning nutrient replacement values to the feed enzyme for consideration in least-cost ration formulations. Further work is, however, required to define the most appropriate reductions in nutrient specifications in association with phytase supplementation.

Influence of phytase and xylanase supplementation on growth performance and nutrient utilisation of broilers offered wheat-based diets

Individual and combined supplementation of phosphorus-adequate, wheat-based broiler diets with exogenous phytase and xylanase was evaluated in three experiments. The effects of the enzyme combination in lysine-deficient diets containing wheat and sorghum were more pronounced than those of the individual feed enzymes. The inclusion of phytase plus xylanase improved (p<0.05) weight gains (7.3%) and feed efficiency (7.0%) of broilers (7-28 days post-hatch) and apparent metabolisable energy (AME) by 0.76 MJ/kg DM. Phytase plus xylanase increased (p<0.05) the overall, apparent ileal digestibility of amino acids by 4.5% (0.781 to 0.816); this was greater than the responses to either phytase (3.6%; 0.781 to 0.809) or xylanase (0.7%; 0.781 to 0.784). Absolute increases in amino acid digestibility with the combination exceeded the sum of the individual increases generated by phytase and xylanase for alanine, aspartic acid, glutamic acid, glycine, histidine, isoleucine, phenylalanine, threonine, tyrosine and valine. These synergistic responses may have resulted from phytase and xylanase having complementary modes of action for enhancing amino acid digestibilities and/or facilitating substrate access. The two remaining experiments were almost identical except wheat used in Experiment 2 had a higher phytate concentration and a lower estimated AME content than wheat used in Experiment 3. Individually, phytase and xylanase were generally more effective in Experiment 2, which probably reflects the higher dietary substrate levels present. Phytase plus xylanase increased (p<0.05) gains (15.4%) and feed efficiency (7.0%) of broiler chicks from 4-24 days post-hatch in Experiment 2; whereas, in Experiment 3, the combination increased (p<0.05) growth to a lesser extent (5.6%) and had no effect on feed efficiency. This difference in performance responses appeared to be 'protein driven' as the combination increased (p<0.05) nitrogen retention in Experiment 2 but not in Experiment 3; whereas phytase plus xylanase significantly increased AME in both experiments. In Experiments 2 and 3 the combined inclusion levels of phytase and xylanase were lower that the individual additions, which demonstrates the benefits of simultaneously including phytase and xylanase in wheat-based poultry diets.

Ultrastructure, aggregation-state, and crystal growth of biogenic nanocrystalline sphalerite and wurtzite

In this study, we investigated the size, submicrometer-scale structure, and aggregation state of ZnS formed by sulfate-reducing bacteria (SRB) in a SRB-dominated biofilm growing on degraded wood in cold (Tsimilar to8degreesC), circumneutral-pH (7.2-8.5) waters draining from an abandoned, carbonate-hosted Pb-Zn mine. High-resolution transmission electron microscope (HRTEM) data reveal that the earliest biologically induced precipitates are crystalline ZnS nanoparticles 1-5 nm in diameter. Although most nanocrystals have the sphalerite structure, nanocrystals of wurtzite are also present, consistent with a predicted size dependence for ZnS phase stability. Nearly all the nanocrystals are concentrated into 1-5 mum diameter spheroidal aggregates that display concentric banding patterns indicative of episodic precipitation and flocculation. Abundant disordered stacking sequences and faceted, porous crystal-aggregate morphologies are consistent with aggregation-driven growth of ZnS nanocrystals prior to and/or during spheroid formation. Spheroids are typically coated by organic polymers or associated with microbial cellular surfaces, and are concentrated roughly into layers within the biofilm. Size, shape, structure, degree of crystallinity, and polymer associations will all impact ZnS solubility, aggregation and coarsening behavior, transport in groundwater, and potential for deposition by sedimentation. Results presented here reveal nanometer- to micrometer-scale attributes of biologically induced ZnS formation likely to be relevant to sequestration via bacterial sulfate reduction (BSR) of other potential contaminant metal(loid)s, such as Pb2+, Cd2+, As3+ and Hg2+, into metal sulfides. The results highlight the importance of basic mineralogical information for accurate prediction and monitoring of long-term contaminant metal mobility and bioavailability in natural and constructed bioremediation systems. Our observations also provoke interesting questions regarding the role of size-dependent phase stability in biomineralization and provide new insights into the origin of submicrometer- to millimeter-scale petrographic features observed in low-temperature sedimentary sulfide ore deposits.

The influence of substrate kinetics on the microbial community structure in granular anaerobic biomass

The development of a strong, active granular sludge bed is necessary for optimal operation of upflow anaerobic sludge blanket reactors. The microbial and mechanical structure of the granules may have a strong influence on desirable properties such as growth rate, settling velocity and shear strength. Theories have been proposed for granule microbial structure based on the relative kinetics of substrate degradation, but contradict some observations from both modelling and microscopic studies. In this paper, the structures of four granule types were examined from full-scale UASB reactors, treating wastewater from a cannery, a slaughterhouse, and two breweries. Microbial structure was determined using fluorescence in situ hybridisation probing with 16S rRNA-directed oligonucleotide probes, and superficial structure and microbial density (volume occupied by cells and microbial debris) assessed using scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The granules were also modelled using a distributed parameter biofilm model, with a previously published biochemical model structure, biofilm modelling approach, and model parameters. The model results reflected the trophic structures observed, indicating that the structures were possibly determined by kinetics. Of particular interest were results from simulations of the protein grown granules, which were predicted to have slow growth rates, low microbial density, and no trophic layers, the last two of which were reflected by microscopic observations. The primary cause of this structure, as assessed by modelling, was the particulate nature of the wastewater, and the slow rate of particulate hydrolysis, rather than the presence of proteins in the wastewater. Because solids hydrolysis was rate limiting, soluble substrate concentrations were very low (below Monod half saturation concentration), which caused low growth rates. (C) 2003 Elsevier Ltd. All rights reserved.

Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3-.N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO3-.N mg of MLVSS-1 h(-1) over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [C-13] methanol to biomark the DNA of the denitrifiers. The extracted [C-13]DNA and [C-12]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [C-13]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [C-12]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [C-14] methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.