Coupling Nutrient Uptake and Energy Flow in Headwater Streams

Nutrient cycling and energy flow in ecosystems are tightly linked through the metabolic processes of organisms. Greater uptake of inorganic nutrients is expected to be associated with higher rates of metabolism [gross primary production (GPP) and respiration (R)], due to assimilatory demand of both autotrophs and heterotrophs. However, relationships between uptake and metabolism should vary with the relative contribution of autochthonous and allochthonous sources of organic matter. To investigate the relationship between metabolism and nutrient uptake, we used whole-stream and benthic chamber methods to measure rates of nitrate–nitrogen (NO₃–N) uptake and metabolism in four headwater streams chosen to span a range of light availability and therefore differing rates of GPP and contributions of autochthonous carbon. We coupled whole-stream metabolism with measures of NO₃–N uptake conducted repeatedly over the same stream reach during both day and night, as well as incubating benthic sediments under both light and dark conditions. NO₃–N uptake was generally greater in daylight compared to dark conditions, and although day-night differences in whole-stream uptake were not significant, light–dark differences in benthic chambers were significant at three of the four sites. Estimates of N demand indicated that assimilation by photoautotrophs could account for the majority of NO₃–N uptake at the two sites with relatively open canopies. Contrary to expectations, photoautotrophs contributed substantially to NO₃–N uptake even at the two closed-canopy sites, which had low values of GPP/R and relied heavily on allochthonous carbon to fuel R.     

Ingestion and inactivation of bacteriophages by Tetrahymena

Abiotic factors are thought to be primarily responsible for the loss of bacteriophages from the environment, but ingestion of phages by heterotrophs may also play a role in their elimination. Tetrahymena thermophila has been shown to ingest and inactivate bacteriophage T4 in co-incubation experiments. In this study, other Tetrahymena species were co-incubated with T4 with similar results. In addition, T. thermophila was shown to inactivate phages T5 and lambda in co-incubations. Several approaches, including direct visualization by electron microscopy, demonstrated that ingestion is required for T4 inactivation. Mucocysts were shown to have no role in the ingestion of T4. When (35)S-labeled T4 were fed to T. thermophila in a pulse-chase experiment, the degradation of two putative capsid proteins, gp23(*) and hoc, was observed. In addition, a polypeptide with the apparent molecular mass of 52 kDa was synthesized. This suggests that Tetrahymena can use phages as a minor nutrient source in the absence of bacteria.     

Floridosides in unicellular hot spring algae

Cyanidium caldarium strains RK-1, KS-1 and 001 are probably obligate autotrophs, while Chroococcidiopsis sp. strains M-8 and 002 (formerly named Cyanidium caldarium) are facultative autotrophs. The Cyanidium strains contain floridoside (2-O-glycerol-α-d-galactopyranoside) and a small amount of iso-floridoside (1-O-glycerol-α-d-galactopyranoside), both of which are known to be distributed in Rhodophyta. The Chroococcidiopsis strains also contain floridoside, but no iso-floridoside, under various culture conditions. These results indicate that Cyanidium is clearly distinguishable from Chroococcidiopsis in iso-floridoside content and nutritional properties, and suggest that all strains tested may be closely related to Rhodophyta.     

Heterotrophic nitrification and aerobic denitrification inAlcaligenes faecalis strain TUD

Heterotrophic nitrification and aerobic and anaerobic denitrification byAlcaligenes faecalis strain TUD were studied in continuous cultures under various environmental conditions. Both nitrification and denitrification activities increased with the dilution rate. At dissolved oxygen concentrations above 46% air saturation, hydroxylamine, nitrite and nitrate accumulated, indicating that both the nitrification and denitrification were less efficient. The overall nitrification activity was, however, essentially unaffected by the oxygen concentration. The nitrification rate increased with increasing ammonia concentration, but was lower in the presence of nitrate or nitrite. When present, hydroxylamine, was nitrified preferentially. Relatively low concentrations of acetate caused substrate inhibition (K_I=109 M acetate). Denitrifying or assimilatory nitrate reductases were not detected, and the copper nitrite reductase, rather than cytochrome cd, was present. Thiosulphate (a potential inhibitor of heterotrophic nitrification) was oxidized byA. faecalis strain TUD, with a maximum oxygen uptake rate of 140–170nmol O₂·min^-1·mg prot^-1. Comparison of the behaviour ofA. faecalis TUD with that of other bacteria capable of heterotrophic nitrification and aerobic denitrification established that the response of these organisms to environmental parameters is not uniform. Similarities were found in their responses to dissolved oxygen concentrations, growth rate and ammonia concentration. However, they differed in their responses to externally supplied nitrite and nitrate.     

Costs, benefits and characteristics of mixotrophy in marine oligotrichs

1. Oligotrich ciliates are an important part of most marine plankton communities. Mixotrophic (chloroplast-sequestering) oligotrichs, a common component of marine oligotrich communities, obtain fixed carbon from both photosynthesis as well as the ingestion of particulate food. Mixotrophy, in general, is often considered an adaptation permitting exploitation of food-poor environments. We examined the hypothesis that, among oligotrichs, mixotrophs may be at a disadvantage relative to heterotrophs in food-rich conditions in a nutrient-enrichment experiment. We compared growth responses of mixotrophic and heterotrophic oligotrichs in natural communities from the N.W. Mediterranean Sea in microcosms with daily nutrient additions resulting in increases in nanoflagellates and Synechococcus populations. The results indicated that both mixotrophic and heterotrophic oligotrichs respond to prey increases with rapid growth (μ=1.2 d−1).
2. To examine the hypothesis that the proportion of mixotrophic to heterotrophic oligotrichs changes with the trophic status of a system, increasing with oligotrophy, we examined data from a variety of marine systems. Across systems ranging in chlorophyll concentration from about 0.1 to 40 μg L−1, oligotrich cell concentrations are correlated with chlorophyll concentrations, and mixotrophs are a consistent component of oligotrich communities, averaging about 30% of oligotrich cell numbers.
3. We discuss the costs, benefits and possible uses of mixotrophy in marine oligotrichs and suggest that mixotrophy in marine oligotrichs is not closely linked to the exploitation of food-poor environments, but probably serves a variety of purposes.     

Complete genome sequence of Rhodothermus marinus type strain (R-10)

Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Isolation and characterization of sulfur-utilizing denitrifiers from the sulfur-oxidizing denitrification process

Of 14 potential sulfur-oxidizing strains, Pseudomonas sp. B21 and Agrobacterium sp. B19 were considered as denitrifiers. Under aerobic conditions, with S⁰ as electron donor, maximum cell growth rates were 0.022 (B21) and 0.043 h^–1 (B19). Both grew optimally at pH 7.5 and 28 °C. When NO₃-N was increased from 10 to 200 mg l^–1 the efficiency of nitrate removal of each strain gradually decreased, from 60 to 40%. Addition of suitable organic compounds (C/N < 4.2) increased the nitrate removal efficiencies of both strains, indicating their mixotrophic characters.     

Planktonic nitrate-reducing bacteria and sulfate-reducing bacteria in some western Canadian oil field waters

Oil fields that use water flooding to enhance oil recovery may become sour because of the production of H₂S from the reduction of sulfate by sulfate-reducing bacteria (SRB). The addition of nitrate to produced waters can stimulate the activities of nitrate-reducing bacteria (NRB) and control sulfide production. Many previous studies have focused on chemolithotrophic bacteria that can use thiosulfate or sulfide as energy sources while reducing nitrate. Little attention has been given to heterotrophic NRB in oil field waters. Three different media were used in this study to enumerate various types of planktonic NRB present in waters from five oil fields in western Canada. The numbers of planktonic SRB and bacteria capable of growth under aerobic conditions were also determined. In general, microbial numbers in the produced waters were very low (<10 ml⁻¹) in samples taken near or at wellheads. However, the numbers increased in the aboveground facilities. No thiosulfate-oxidizing NRB were detected in the oil field waters, but other types of NRB were detected in 16 of 18 produced water samples. The numbers of heterotrophic NRB were equal to or greater than the number of sulfide-oxidizing, chemolithotrophic NRB in 12 of 15 samples. These results showed that each of the oil fields contained NRB, which might be stimulated by nitrate amendment to control H₂S production by SRB. Journal of Industrial Microbiology & Biotechnology (2002) 29, 83–92 doi:10.1038/sj.jim.7000274 Received 20 February 2002/ Accepted in revised form 14 May 2002     

Combined heterotrophic nitrification and aerobic denitrification in Thiosphaera pantotropha and other bacteria

Reports of the simultaneous use of oxygen and denitrification by different species of bacteria have become more common over the past few years. Research with some strains (e.g. Thiosphaera pantotropha) has indicated that there might be a link between this aerobic denitrification and a form of nitrification which requires rather than generates energy and is therefore known as heterotrophic nitrification. This paper reviews recent research into heterotrophic nitrification and aerobic denitrification, and presents a preliminary model which, if verified, will provide at least a partial explanation for the simultaneous occurrence of nitrification and denitrification in some bacteria.     

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney

Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1(T) was the first isolate within the phylum "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1(T) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.