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PubMed2002

Studying marine microorganisms from space.

Microorganisms are but a few micrometers in diameter and are not visible to the naked eye. Yet, the large numbers of microorganisms present in the oceans and the global impact of their activities make it possible to observe them from space. Here a few examples of how microorganisms can be studied from satellites are presented. The first case is the best known: the main pigment used in photosynthesis (chlorophyll a) can be determined from satellites. These kinds of studies have contributed a tremendous amount of understanding about the distribution and dynamics of primary production in the oceans. Two other examples will concern analysis of heterotrophic prokaryotic production and estimates of dimethyl sulfide (DMS) concentration and flux to the atmosphere. These three processes are of fundamental importance for the functioning of the biosphere. Marine microbes carry out about half of the total primary production in the planet. A substantial fraction of the respiration in the oceans is due to the activity of heterotrophic prokaryotes. Finally, the flux of DMS to the atmosphere is believed to constitute one of the mechanisms by which the biota can regulate climate. The global implications of microbial processes in the oceans can only be addressed with the help of satellites.

Chlorophyll↗
PubMed2003

Adaptive control of the nitrate level in an activated sludge process.

In an activated sludge process for nitrogen removal, nitrate may be reduced to nitrogen gas by facultative heterotrophic bacteria in an anoxic environment. In order to guarantee sufficient supplies of readily biodegradable carbon compounds, an external carbon source often needs to be added. In this paper, an automatic control strategy for controlling the nitrate level using an external carbon source is presented. The external carbon source is added in the first anoxic zone to control the nitrate concentration in the last anoxic zone. Key process parameters are estimated on-line for a simplified Activated Sludge Model No 1. The estimated parameters are used for updating a linear quadratic controller. The strategy is illustrated in a simulation study with realistic influent data and is shown to perform very well.

Bioreactors↗
PubMed2002

A simple biofilm model of bacterial competition for attached surface.

A simple biofilm model of competition in bacterial growth for an attached surface is developed. Competition for the attached surface is expressed with the crowded and detachment effects. The developed model is verified by comparing simulated results with data obtained in the experiments of batch culture of nitrifier and continuous treatment of actual sewage with biofilm reactor. This model can favorably simulate the growth competition between autotrophic and heterotrophic bacteria for the attached surface. Then some parameters for nitrification process are discussed with this model. It is clarified that the effective removal of organic matter before nitrification tank is required for effective nitrification in the biofilm reactor.

Biodegradation, Environmental↗
PubMed2003

Modification of Activated Sludge Model no. 3 considering direct growth on primary substrate.

This paper provides the structural framework for the proposed modified version of Activated Sludge Model No. 3 (ASM3), where direct heterotrophic growth on readily biodegradable substrate is included as a new process and provision is made so that growth on internal storage compounds is started sequentially, after the depletion of the external primary substrate pool. The results have provided strong indication that there was a need for considering direct growth on primary substrate as a significant biological mechanism.

Biodegradation, Environmental↗
PubMed2003

Dynamic mathematical model of high rate algal ponds (HRAP).

This article presents a mathematical model to describe High-Rate Algal Ponds (HRAPs). The hydrodynamic behavior of the reactor is described as completely mixed tanks in series with recirculation. The hydrodynamic pattern is combined with a subset of River Water Quality Model 1 (RWQM1), including the main processes in liquid phase. Our aim is to develop models for WSPs and aerated lagoons, too, but we focused on HRAPs first for several reasons: Sediments are usually less abundant in HRAP and can be neglected, Stratification is not observed and state variables are constant in a reactor cross section, Due to the system's geometry, the reactor is quite similar to a plugflow type reactor with recirculation, with a simple advection term. The model is based on mass balances and includes the following processes: *Phytoplankton growth with NO3-, NO2- and death, *Aerobic growth of heterotrophs with NO3-, NH4+ and respiration, *Anoxic growth of heterotrophs with NO3-, NO2- and anoxic respiration, *Growth of nitrifiers (two stages) and respiration. The differences with regard to RWQM1 are that we included a limiting term associated with inorganic carbon on the growth rate of algae and nitrifiers, gas transfers are taken into account by the familiar Adeney equation, and a subroutine calculates light intensity at the water surface. This article presents our first simulations.

Bioreactors↗
PubMed2005

Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil.

Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the alpha-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the gamma-Proteobacteria group (genus Xanthomonas), the alpha-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the gamma-Proteobacteria group (genus Xathomonas), the beta-Proteobacteria group (genera Alcaligenes and Achromobacter), and the alpha-Proteobacteria group (genus Sphingomonas) were the dominant groups in the nutrient treatment. This study shows that specific bacterial phylotypes are associated both with different phases of PAH degradation and with nutrient addition in a preadapted PAH-contaminated soil. Our findings also suggest that there are complex interactions between bacterial species and medium conditions that influence the biodegradation capacity of the microbial communities involved in bioremediation processes.

Bacteria↗
PubMed2004

Trickling filters for upgrading low technology wastewater plants for nitrogen removal.

Previous work through the 1990s in the Thames Water region in the UK has demonstrated the ability of the trickling filter process to produce fully nitrified effluents, reliably throughout the year. The original data used for the nitrification model derivations have been reanalysed, to investigate the degree of nitrogen removal across the process. Removals of total nitrogen ranging from 0% to over 50% were observed across the trickling filter process and calculated total nitrogen removals of 26-63% were obtained when primary treatment was included. The degree of nitrogen removal and biological denitrification (excluding cellular assimilation) was found to be strongly influenced by BOD load, irrigation velocity and media size. Regression models were produced which gave good predictive relationships for the data ranges used. The models produced worked for filters used with and without a recirculation of effluent nitrate which suggests that a significant degree of nitrification occurred in areas of high heterotroph activity (BOD removal). The simplicity and energy efficiency of the trickling filter process, combined with its capacity for full nitrification and partial denitrification, make the process attractive as a combined process used with pond systems in developing countries where nitrogen removal may be required. Some of these synergies have already been developed with the PETRO process in South Africa.

Filtration↗
PubMed2000

Surface Attachment of Ammonia-Oxidizing Bacteria in Soil.

A BSTRACTIndigenous ammonia-oxidizing bacteria (AOB) in a clay loam soil were extremely difficult to release from soil particles compared to most heterotrophic bacteria; less than 1% of indigenous AOB (estimated as potential ammonia oxidation rate) were extractable by the dispersion-density-gradient centrifugation technique. This is at least 10-fold less than the extractability of heterotrophic bacteria. Urea applications to the same soil induced a 5-fold increase in the potential ammonia oxidation rate, and this resulted in a much higher percentage (8%) extractability of AOB. Thus, the newly grown AOB in the urea-treated soil were less strongly attached to the soil particles. The contrast suggests that the strong attachment of indigenous AOB is a gradual process taking place due to a long residence time (infrequent/slow cell division) compared to heterotrophic organisms. However, the contrast could also reflect differences in species composition of the original AOB community and those growing in response to urea inputs. Specific detection of AOB in extinction dilution cultures was done by PCR and sequencing of the products. Considerable diversity was found within the genus Nitrosospira, but severe problems with the specificity of the primers were observed. Two allegedly AOB specific PCR primers pairs were used: one specific for Nitrosospira (SPIRA) and one which should encompass all AOB within the beta- Proteobacteria (GAOB). Only 33% of the cultures that gave PCR products with GAOB also gave products with the SPIRA primer pair, suggesting the presence of AOB other than Nitrosospira. However, the phylogeny based on the sequencing placed all the cultures in various clusters of the Nitrosospira clade, suggesting that the SPIRA primers do not match all members of the Nitrosospira genus. The cultures obtained from the urea-treated soil were different from the others in giving PCR products only with the SPIRA primers and not with the GAOB. Since sequencing also here confirmed the presence of Nitrosospira, these observations suggest that the GAOB primers do not match all AOB species.

Journal Article↗
PubMed2004

BICT biological process for nitrogen and phosphorus removal.

An updated biological nitrogen and phosphorus removal process--BICT (Bi-Cyclic Two-Phase) biological process--is proposed and investigated. It is aimed to provide a process configuration and operation mode that has facility and good potential for optimizing operation conditions, especially for enhancing the stability and reliability of the biological nutrient removal process. The proposed system consists of an attached-growth reactor for growing autotrophic nitrifying bacteria, a set of suspended-growth sequencing batch reactors for growing heterotrophic organisms, an anaerobic biological selector and a clarifier. In this paper, the fundamental concept and operation principles of BICT process are described, and the overall performances, major operation parameters and the factors influencing COD, nitrogen and phosphorus removal in the process are also discussed based on the results of extensive laboratory experiments. According to the experimental results with municipal sewage and synthetic wastewater, the process has strong and stable capability for COD removal. Under well controlled conditions, the removal rate of TN can reach over 80% and TP over 90% respectively, and the effluent concentrations of TN and TP can be controlled below 15 mg/L and 1.0 mg/L respectively for municipal wastewater. The improved phosphorus removal has been reached at short SRT, and the recycling flow rate of supernatant between the main reactors and attached-growth reactor is one of the key factors controlling the effect of nitrogen removal.

Bacteria, Anaerobic↗
PubMed2002

A comparison of organic and inorganic carbon controls over biological denitrification in aquaria.

In aquaria and rearing tanks, nitrate accumulation as a result of organic matter degradation is inevitable and has two major negative side effects: direct toxicity to organisms, specially invertebrates, and the introduction of a reducing environment by oxygen consumption. The aim of this study was to compare two alternate methods of removing nitrogen compounds from closed systems, autotrophic columnar denitrification (ACD) and heterotrophic columnar denitrification (HCD) by following end product concentrations as reaction progressed. A pilot plant consisting of two series of 50 dm3 recirculating flow systems (each in triplicate) was used to test both methods. Absence of pH control was also useful in autotrophic denitrification systems in order to follow effects over reaction rates and pathways. Concentrations of NO(3-), NO2- and NH(4+) were followed throughout the experiment, as well as pH, temperature and salinity. Under different flow conditions results show that higher nitrate reduction rates were possible in the autotrophic systems (35.1+/-4.7 microM/day without pH control until reversal of the process and 20.6+/-7.3 microM/day after reestablishment of pH control) in comparison with heterotrophic (9.9+/-1.3 microM/day). However, pH control through calcium bicarbonate addition was found to be crucial in maintaining constant levels of total denitrification in ACD systems, just as it was necessary to closely maintain organic carbon addition to HCD systems.

Aquaculture↗
PubMed2006

Effects of acetate and nitrite addition on fraction of denitrifying phosphate-accumulating organisms and nutrient removal efficiency in anaerobic/aerobic/anoxic process.

The effects of acetate and nitrite on the performance of sequencing batch reactors (SBRs) employing an anaerobic/aerobic/anoxic (AOA) process were investigated. Three types of SBR operations were used: sodium acetate addition at the start of anoxic condition for heterotrophic denitrification (Type 1); sodium acetate addition at the start of aerobic condition for anoxic phosphate removal by denitrifying phosphate-accumulating organisms (DNPAOs) (Type 2: conventional AOA process); and nitrite addition at the start of aerobic condition for inhibition of phosphate-accumulating organisms (PAOs) (Type 3). A track experiment shows that Type 2 led to the best performance of SBRs among the three types. An analysis by fluorescence in situ hybridization (FISH) revealed that nitrite addition decreased the ratio of PAOs with a decrease in phosphorus removal efficiency. The fraction of DNPAOs in Type 2 was the highest at 13%, indicating that Type 2 is suitable for the simultaneous nitrogen and phosphorus removal in the AOA process.

Acetates↗
PubMed2006

An important pool of sucrose linked to starch biosynthesis is taken up by endocytosis in heterotrophic cells.

We have recently shown the occurrence of endocytic sucrose uptake in heterotrophic cells. Whether this mechanism is involved in the sucrose-starch conversion process was investigated by comparing the rates of starch accumulation in sycamore cells cultured in the presence or absence of the endocytic inhibitors wortmannin and 2-(4-morpholynyl-)-8-phenyl-4H-1 benzopyran-4-1 (LY294002). These analyses revealed a two-phase process involving an initial 120 min wortmannin- and LY294002-insensitive starch accumulation period, followed by a prolonged phase that was arrested by the endocytic inhibitors. Both wortmannin and LY294002 led to a strong reduction of the intracellular levels of both sucrose and the starch precursor molecule, ADPglucose. No changes in maximum catalytic activities of enzymes closely linked to starch and sucrose metabolism occurred in cells cultured with endocytic inhibitors. In addition, starch accumulation was unaffected by endocytic inhibitors when cells were cultured with glucose. These results provide a first indication that an important pool of sucrose incorporated into the cell is taken up by endocytosis prior to its subsequent conversion into starch in heterotrophic cells. This conclusion was substantiated further by experiments showing that sucrose-starch conversion was strongly prevented by both wortmannin and LY294002 in both potato tuber discs and developing barley endosperms.

Acer↗
PubMed2000

Energetics and carbon metabolism during growth of microalgal cells under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions.

Chlorella pyrenoidosa was cultivated under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions. The influence of light on the carbon and energy metabolism of microalgae was investigated by the use of metabolic flux analysis. The respiratory activity of microalgae in the light was assessed from the autotrophic flux distribution. Results showed that the glycolytic pathway, tricarboxylic acid cycle and mitochondrial oxidative phosphorylation maintained high activities during illumination, indicating little effect of light on these pathways, while the flux through the pentose phosphate pathway during illumination was very small due to the light-mediated regulation. The theoretical yields of biomass on ATP decreased in the following order: heterotrophic culture>mixotrophic culture>autotrophic culture, and a significant amount of the available ATP was required for maintenance processes in microalgal cells. The energy conversion efficiency between the supplied energy to culture, the absorbed energy by cells and the free energy conserved in ATP were analyzed for the different cultures. Analysis showed that the heterotrophic culture generated more ATP from the supplied energy than the autotrophic and mixotrophic cultures. The maximum thermodynamic efficiency of ATP production from the absorbed energy, which was calculated from the metabolic fluxes at zero growth rate, was the highest in the heterotrophic culture and as low as 16% in the autotrophic culture. By evaluating the energy economy through the energy utilization efficiency, it was found that the biomass yield on the supplied energy was the lowest in the autotrophic cultivation, and the cyclic culture gave the most efficient utilization of energy for biomass production.

Journal Article↗
PubMed2000

Producer-decomposer co-dependency influences biodiversity effects.

Producers, such as plants and algae, acquire nutrients from inorganic sources that are supplied primarily by decomposers whereas decomposers, mostly fungi and bacteria, acquire carbon from organic sources that are supplied primarily by producers. This producer-decomposer co-dependency is important in governing ecosystem processes, which implies that the impacts of declining biodiversity on ecosystem functioning should be strongly influenced by this process. Here we show, by simultaneously manipulating producer (green algal) and decomposer (heterotrophic bacterial) diversity in freshwater microcosms, that algal biomass production varies considerably among microcosms (0.0-0.67 mg ml(-1)), but that neither algal nor bacterial diversity by itself can explain this variation. Instead, production is a joint function of both algal and bacterial diversity. Furthermore, the range in algal production in microscosms in which bacterial diversity was manipulated was nearly double (1.82 times) that of microcosms in which bacterial diversity was not manipulated. Measures of organic carbon use by bacteria in these microcosms indicate that carbon usage is the mechanism responsible for these results. Because both producer and microbial diversity respond to disturbance and habitat modification, the main causes of biodiversity loss, these results suggest that ecosystem response to changing biodiversity is likely to be more complex than other studies have shown.

Bacterial Physiological Phenomena↗
PubMed2001

Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream.

We used in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes concurrently with measurements of bacterial carbon production, biomass, and extracellular polymeric substances (EPS) to describe the bacterial community in sediments along a glacial stream. The abundance of sediment-associated Archaea, as detected with the ARCH915 probe, decreased downstream of the glacier snout, and a major storm increased their relative abundance by a factor of 5.5 to 7.9. Bacteria of the Cytophaga-Flavobacterium group were also sixfold to eightfold more abundant in the storm aftermath. Furthermore, elevated numbers of Archaea and members of the Cytophaga-Flavobacterium group characterized the phylogenetic composition of the supraglacial ice community. We postulate that glacial meltwaters constitute a possible source of allochthonous bacteria to the stream biofilms. Although stream water temperature increased dramatically from the glacier snout along the stream (3.5 km), sediment chlorophyll a was the best predictor for bacterial carbon production and specific growth rates along the stream. Concomitant with an increase in sediment chlorophyll a, the EPS carbohydrate-to-bacterial-cell ratio declined 11- to 15-fold along the stream prior to the storm, which is indicative of a larger biofilm matrix in upstream reaches. We assume that a larger biofilm matrix is required to assure prolonged transient storage and enzymatic processing of allochthonous macromolecules, which are likely the major substrate for microbial heterotrophs. Bacteria of the Cytophaga-Flavobacterium cluster, which are well known to degrade complex macromolecules, were most abundant in these stream reaches. Downstream, higher algal biomass continuously supplies heterotrophs with easily available exudates, therefore making a larger matrix unnecessary. As a result, bacterial carbon production and specific growth rates were higher in downstream reaches.

Archaea↗
PubMed2006

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.

Anaerobiosis↗
PubMed2005

Effects of pulp and paper mill effluents on the microplankton and microbial self-purification capabilities of the Biobío River, Chile.

Most studies focus on the ecotoxicity of pulp and paper mill effluents, rather than on how they affect the physicochemical and biological structure and the intrinsic ecological capabilities of the receiving watercourses. We investigated the impact of such effluents on the water quality, microplankton system and microbial self-purification capacity (degradation of polymeric organic compounds via extracellular enzymes) of the Biobío River in Chile. The physicochemical impact on the water quality was indicated by raised conductivity, by the pollution of the water body with nitrate, nitrite and soluble reactive phosphorus, by the appearance of tannin and lignin, and by the steady accumulation of inorganic and organic suspended matter (SPM) along the river. From the biological structure of the microplankton system, very low and declining concentrations of chlorophyll a and heterotrophic flagellate densities were determined. The pulp and paper mill effluents introduced high bacterial abundances and biomass concentrations into the river water. This reflects the effective use made of the abundantly available inorganic and organic nutrients within this industrial and municipal process water by bacteria adapted to these extreme environments, additionally supported by concomitant low grazing pressure derivable from low heterotrophic flagellate abundances. Indeed, in one section of the river affected by a pulp mill, the plant was found to significantly contribute to the self-cleaning capacity of the river. However, this elevated degradation capacity was not enough to compensate for the additionally discharged organic material which, together with the toxic effects of the paper plant effluents, significantly interferes with the ecological status of the Biobío River.

Animals↗
PubMed1996

Photosynthate partitioning and fermentation in hot spring microbial mat communities.

Patterns of (sup14)CO(inf2) incorporation into molecular components of the thermophilic cyanobacterial mat communities inhabiting hot springs located in Yellowstone National Park and Synechococcus sp. strain C1 were investigated. Exponentially growing Synechococcus sp. strain C1 partitioned the majority of incorporated (sup14)CO(inf2) into protein, low-molecular-weight metabolites, and lipid fractions (45, 22, and 18% of total incorporated carbon, respectively). In contrast, mat cores from various hot springs predominantly accumulated polyglucose during periods of illumination (between 77 and 85% of total incorporated (sup14)CO(inf2)). Although photosynthetically active, mat photoautotrophs do not appear to be rapidly growing, since we also detected only limited synthesis of macromolecules associated with growth (i.e., protein and rRNA). To test the hypothesis that polysaccharide reserves are fermented in situ under the dark anaerobic conditions cyanobacterial mats experience at night, mat cores were prelabeled with (sup14)CO(inf2) under illuminated conditions and then transferred to dark anaerobic conditions. Radiolabel in the polysaccharide fraction decreased by 74.7% after 12 h, of which 58.5% was recovered as radiolabeled acetate, CO(inf2), and propionate. These results indicate tightly coupled carbon fixation and fermentative processes and the potential for significant transfer of carbon from primary producers to heterotrophic members of these cyanobacterial mat communities.

Journal Article↗