Biodegradation of Poly-(beta)-Hydroxyalkanoates in a Lake Sediment Sample Increases Bacterial Sulfate Reduction

The addition of a poly-(beta)-hydroxyalkanoate (PHA) to incubation bottles containing anaerobic sediment from Lake Ciso (Banyoles, Catalonia, northeast Spain) was correlated with an increase in sulfide production. The concentration of PHA diminished to 51 to 99% of the initial amount. Sodium molybdate (1 mM) decreased the rate of PHA degradation and inhibited sulfide production, thus indicating that PHAs serve as carbon and electron sources for sulfate reduction.     

Distribution and Life Strategies of Two Bacterial Populations in a Eutrophic Lake

Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plußsee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i.e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h⁻¹) were higher than those of the entire bacterial community (0.04 to 0.08 h⁻¹) but lower than those of PU7718 (0.26 to 0.31 h⁻¹). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically versatile A. hydrophila PU7718 is an r-strategist or opportunistic population in Lake Plußsee, whereas the grazing-resistant C. acidovorans PX54 is rather a K-strategist or equilibrium population.     

Reduction of Sulfur Compounds in the Sediments of a Eutrophic Lake Basin

Concentrations of various sulfur compounds (SO₄²⁻, H₂S, S⁰, acid-volatile sulfide, and total sulfur) were determined in the profundal sediments and overlying water column of a shallow eutrophic lake. Low concentrations of sulfate relative to those of acid-volatile sulfide and total sulfur and a decrease in total sulfur with sediment depth implied that the contribution of dissimilatory sulfur reduction to H₂S production was relatively minor. Addition of 1.0 mM Na₂³⁵SO₄ to upper sediments in laboratory experiments resulted in the production of H₂³⁵S with no apparent lag. Kinetic experiments with ³⁵S demonstrated an apparent K_m of 0.068 mmol of SO₄²⁻ reduced per liter of sediment per day, whereas tracer experiments with ³⁵S indicated an average turnover time of the sediment sulfate pool of 1.5 h. Total sulfate reduction in a sediment depth profile to 15 cm was 15.3 mmol of sulfate reduced per m² per day, which corresponds to a mineralization of 30% of the particulate organic matter entering the sediment. Reduction of ³⁵S⁰ occurred at a slower rate. These results demonstrated that high rates of sulfate reduction occur in these sediments despite low concentrations of oxidized inorganic compounds and that this reduction can be important in the anaerobic mineralization of organic carbon.     

Microbial Population Dynamics in the Sediments of a Eutrophic Lake (Aydat,France) and Characterization of Some Heterotrophic Bacterial Isolates

The bacterial populations of anoxic sediments in a eutrophic lake (Aydat, Puy-de-Dôme-France) were studied by phospholipid fatty acid analysis (PLFA) and also by culturing heterotrophic bacteria under strictly anaerobic conditions. The mean PLFA concentrations of prokaryotes and microeukaryotes were 5.7 ± 2.9 mgC g^–1 DS and 9.6 ± 6.7 mgC g^–1 DS, respectively. The analysis of bacterial PLFA markers was used to determine the dynamics of the Gram-positive and Gram-negative species of anaerobic bacteria, Clostridiae, and sulfate-reducing bacteria. Throughout the sampling period the concentrations of i15:0 (from 20 nmol g^–1 DS to 130 nmol g^–1 DS), markers of Gram-positive bacteria, were higher than those for Gram-negative bacteria. The dynamics of Clostridiae (Cy15:0) paralleled those of sulfate-reducing bacteria that were marked by i17:17. Partial 16S rDNA sequencing and the physiological study of the various fermenting strains, whose abundance in the superficial sediment layer was 1.1 ± 0.4 × 10⁶ cells mL^–1, showed that all the isolates belonged to the Clostridiae and related taxa (Lactosphaera pasteurii, Clostridium vincentii, C. butyricum, C. algidixylanolyticum, C. puniceum, C. lituseburense, and C. gasigenes). All the isolates were capable of metabolizing a wide range of organic substrates.     

Bacterial Contribution to Dissolved Organic Matter in Eutrophic Lake Kasumigaura,Japan

Incubation experiments using filtered waters from Lake Kasumigaura were conducted to examine bacterial contribution to a dissolved organic carbon (DOC) pool. Bacterial abundance, bacterial production, concentrations of DOC, total dissolved amino acids (TDAA), and total dissolved neutral sugars (TDNS) were monitored during the experiments. Bacterial production during the first few days was very high (20 to 35 μg C liter⁻¹ day⁻¹), accounting for 40 to 70% of primary production. The total bacterial production accounted for 34 to 55% of the DOC loss during the experiment, indicating high bacterial activities in Lake Kasumigaura. The DOC degradation was only 12 to 15%, whereas the degradation of TDAA and TDNS ranged from 30 to 50%, suggesting the preferential usage of TDAA and TDNS. The contribution of bacterially derived carbon to a DOC pool in Lake Kasumigaura was estimated using d-amino acids as bacterial biomarkers and accounted for 30 to 50% of the lake DOC. These values were much higher than those estimated for the open ocean (20 to 30%). The ratio of bacterially derived carbon to bulk carbon increased slightly with time, suggesting that the bacterially derived carbon is more resistant to microbial degradation than bulk carbon. This is the first study to estimate the bacterial contribution to a DOC pool in freshwater environments. These results indicate that bacteria play even more important roles in carbon cycles in freshwater environments than in open oceans and also suggests that recent increases in recalcitrant DOC in various lakes could be attributed to bacterially derived carbon. The potential differences in bacterial contributions to dissolved organic matter (DOM) between freshwater and marine environments are discussed.     

Population Dynamics and Diversity of Viruses,Bacteria and Phytoplankton in a Shallow Eutrophic Lake

We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 x 10(7) and 1.3 x 10(8) virus-like particles ml(-1) and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus-host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht.     

Dynamics of the Volatile Organic Substances Associated with Cyanobacteria and Algae in a Eutrophic Shallow Lake

The volatile substances present in a eutrophic shallow lake were determined qualitatively and quantitatively during the growing season, allowing a first-time analysis of the dynamics of these compounds in a water body. The major compounds found were β-cyclocitral, α-cyclocitral, β-ionone, 1,3,3-trimethylcyclohexene, 2,2,6-trimethylcyclohexanone, 2,6,6-trimethylcyclohex-2-en-1-one, eucalyptol, geosmin, two argosmin isomers, pent-1-en-3-ol, pent-1-en-3-one, heptadec-1-ene, heptadec-cis 5-ene, heptadeca-1, cis 8-diene, decanal, and hexanal. Most of the substances have not been detected before in natural waters. The occurrence of geosmin, the argosmin isomers, heptadec-cis 5-ene, and an unknown sesquiterpene could clearly be correlated with the appearance of Aphanizomenon gracile, as could the occurrence of β-cyclocitral with the appearance of Microcystis wesenbergii. The data presented indicate that a rapid metabolism or the elimination of these compounds occurs in lake water.     

Bacterial Community Composition of Size-Fractioned Aggregates within the Phycosphere of Cyanobacterial Blooms in a Eutrophic Freshwater Lake

Bacterial community composition of different sized aggregates within the Microcystis cyanobacterial phycosphere were determined during summer and fall in Lake Taihu, a eutrophic lake in eastern China. Bloom samples taken in August and September represent healthy bloom biomass, whereas samples from October represent decomposing bloom biomass. To improve our understanding of the complex interior structure in the phycosphere, bloom samples were separated into large (>100 µm), medium (10–100 µm) and small (0.2–10 µm) size aggregates. Species richness and library coverage indicated that pyrosequencing recovered a large bacterial diversity. The community of each size aggregate was highly organized, indicating highly specific conditions within the Microcystis phycosphere. While the communities of medium and small-size aggregates clustered together in August and September samples, large- and medium-size aggregate communities in the October sample were grouped together and distinct from small-size aggregate community. Pronounced changes in the absolute and relative percentages of the dominant genus from the two most important phyla Proteobacteria and Bacteroidetes were observed among the various size aggregates. Bacterial species on large and small-size aggregates likely have the ability to degrade high and low molecular weight compounds, respectively. Thus, there exists a spatial differentiation of bacterial taxa within the phycosphere, possibly operating in sequence and synergy to catalyze the turnover of complex organic matters.     

Temporal Variation and Co-occurrence Patterns of Bacterial Communities in Eutrophic Lake Taihu,China

To understand the long-term and local variations of bacteria under the influence of annually re-occurred water bloom, bacterial community composition (BCC) was investigated monthly for 3 years (2009–2011) at four different sites located across Lake Taihu. The bacterial community composition was analyzed by 16S rRNA gene clone libraries and terminal restriction fragment length polymorphism. Co-occurrence patterns among bacterial taxa and environmental variables were determined through network analysis. Overall, strong seasonal variation patterns of BCC were observed whilst the spatial variations of BCC were slight in the long-term observation. However, core species bacteria persisted throughout the annual variations. Network analysis showed that the highly connected operational taxonomic units in bacteria-environment network included both the numerically dominant taxa and some functional groups with low abundance, such as Methylophilaceae and Nitrospira. Co-occurrence networks further revealed that the correlations of bacteria-bacteria could be more critical than those between environment and bacteria in structuring microbial communities, and would be a crucial driving factor of BCC in Lake Taihu.     

Bacterial Succession on n-Alkanes under the Conditions of Sulfate Reduction

The dynamics of species composition of a hydrocarbon-oxidizing bacteriocenosis of a ground suspension of the Mozhaisk Reservoir has been studied. The bacteriocenosis was undergoing development in a paraffin film (model association composed of sulfate-reducing bacteria and hydrocarbon-oxidizing bacteria). The type of bacterial succession did not depend on the depth, from which ground samples were collected. Two microbial species (Pseudomonas sp. andArthrobacter globiformis) were absolutely dominant. Pseudomonas sp. was dominant at the early and intermediate stages of the succession, whereas A. globiformis was present in the hydrocarbon-oxidizing bacteriocenosis throughout the whole period of the succession. There was a trend toward a gradual increase in the ratio of A. globiformis, and, by the end of the experiment, Pseudomonas sp. was replaced by A. globiformis almost completely. The bacterial species Micrococcus sp. and Rhodococcus erythropolis were minor components of the hydrocarbon-oxidizing bacteriocenosis under the conditions of sulfate reduction. The succession of species of hydrocarbon-oxidizing bacteria in the paraffin film of the model association reflects both the life strategy of the bacterial species under study and the degree of their tolerance to products of sulfate reduction.     

Seasonal Variation of Virioplankton in a Eutrophic Shallow Lake

Lake Donghu is a typical eutrophic freshwater lake in which high abundance of planktonic viruses was recently revealed. In this study, seasonal variation of planktonic viruses were observed at three different trophic sites, hypertrophic, eutrophic, and mesotrophic regions, and the correlation between their abundances and other aquatic environmental components, such as bacterioplankton, chlorophyll a, burst size, pH, dissolved oxygen, and temperature, was analyzed for the period of an year. Virioplankton abundance detected by transmission electron microscope (TEM) ranged from 5.48 × 10⁸ to 2.04 × 10⁹ ml⁻¹ in all the sites throughout the study, and the high abundances and seasonal variations of planktonic viruses were related to the trophic status at the sampled sites in Lake Donghu. Their annual mean abundances were, the highest at the hypertrophic site (1.23×10⁹ ml⁻¹), medium at the eutrophic site (1.19×10⁹ ml⁻¹), and the lowest at the mesotrophic site (1.02×10⁹ ml⁻¹). The VBR (virus-to-bacteria ratio) values were high, ranging from 49 to 56 on average at the three sampled sites. The data suggested that the high viral abundance and high VBR values might be associated with high density of phytoplankton including algae and cyanobacteria in this eutrophic shallow lake, and that planktonic viruses are important members of freshwater ecosystems.     

Production and Consumption of Hydrogen in a Eutrophic Lake

The vertical distribution of hydrogen was measured in the Loclat, a eutrophic and holomictic lake near Neuchâtel, Switzerland, before and during summer stratification. H₂ concentrations decreased with depth in the anaerobic hypolimnion and were often below the detection limit (2.5 nl of H₂ liter⁻¹) in the water adjacent to the lake sediment. H₂ was apparently not released from the lake sediment. The highest H₂ concentrations (>4 μl of H₂ liter⁻¹) were observed in the aerobic water of the epilimnion and metalimnion. There, the H₂ concentrations changed with time, indicating a turnover of H₂. The H₂ production processes could not be studied in the laboratory since incubation of water samples in light or darkness did not result in H₂ production but rather always in H₂ consumption. The possible role of cyanobacteria and algae for H₂ production is discussed. Aerobic or anaerobic H₂ consumption activities were observed at all depths of the water column, with highest activities in the hypolimnion. Aerobic H₂ consumption activity was insensitive to azide inhibition, but sensitive to heat, mercuric chloride, or cyanide. It was restricted to a particle fraction of 0.2 to 3.0 μm in size, so that it must be due to single bacterial cells. Aerobic hydrogen bacteria, on the other hand, occurred in clusters of >3.0 μm. Therefore, the hydrogen bacteria could not have caused the H₂ consumption in lake water. The aerobic H₂ consumption activity followed Michaelis-Menten kinetics, with a K_m of 67 nM H₂. This is an exceptionally low value compared with K_m values of hydrogenases in hydrogen bacteria and other species, but is similar to that for H₂-decomposing abiontic soil hydrogenases.     

Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques

Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.     

Variability in Microbiological Data from a Stratified Eutrophic Lake

A survey of a stratified eutrophic lake was undertaken to determine the degree of variability in direct counts of bacteria, electron transport system activity, ATP concentration, chlorophyll a concentration and chemiluminescence, in the water column and the sediment. Heterogeneity in the horizontal and vertical dimension was studied in detail and the scale of variability was compared with within-sample and between-sample errors, and with seasonal fluctuations. Variability was greater in the sediment samples, and the coefficient of variation of samples taken at a single site was often as large as that between sites in a transect across the lake. Although this was not an exhaustive survey, the values provided should allow rough estimates to be made of the number of samples required to achieve a given level of precision in future investigations.     

Characterization of Bacterial Communities Associated with Organic Aggregates in a Large, Shallow, Eutrophic Freshwater Lake (Lake Taihu, China)

Although organic-aggregate-associated bacteria play a pivotal role in microbial food webs and in the cycling of major elements, their community composition and diversity have not been extensively studied, especially in shallow freshwater systems. This study is among the first to explore intra-lake horizontal heterogeneity of organic-aggregate-associated bacterial community composition (OABC) in the large, shallow, and eutrophic Lake Taihu. During November 2006, samples were collected at four locations representing different trophic states and food web structures. Regional variability of OABC and diversity were studied by amplified ribosomal DNA restriction analysis and comparative analysis of four large 16S ribosomal RNA clone libraries. Our results demonstrate that OABC were numerically dominated by members of the β-proteobacteria (19.2–38.6%), Bacteroidetes (3.6–20.0%), and α-proteobacteria (11.5–19.2%) groups. The dominance of the Bacteroidetes group was related to algae-based aggregates. Horizontal heterogeneity of OABC exists within habitats, suggesting that the trophic state of the water and the physicochemical properties of organic aggregates (OA) play a key role. Diverse bacterial communities found on OA were substantially different from free-living ones. Comparative statistical analyses of the habitats of OA-associated bacteria highlight the potential ecological importance of the exchange between OABC and the surrounding planktonic community. Lastly, we found at least 45% of sequences closely related to ones previously found in soils, sludge, sediments, and other habitats. This demonstrates that microorganisms from terrestrial and sediment habitats are an important component of OA. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Thermophilic Sulfate Reduction in Hydrothermal Sediment of Lake Tanganyika, East Africa

In environments with temperatures above 60°C, thermophilic prokaryotes are the only metabolically active life-forms. By using the ³⁵SO₄^2- tracer technique, we studied the activity of sulfate-reducing microorganisms (SRM) in hot sediment from a hydrothermal vent site in the northern part of freshwater Lake Tanganyika (East Africa). Incubation of slurry samples at 8 to 90°C demonstrated meso- and thermophilic sulfate reduction with optimum temperatures of 34 to 45°C and 56 to 65°C, respectively, and with an upper temperature limit of 80°C. Sulfate reduction was stimulated at all temperatures by the addition of short-chain fatty acids and benzoate or complex substrates (yeast extract and peptone). A time course experiment showed that linear thermophilic sulfate consumption occurred after a lag phase (12 h) and indicated the presence of a large population of SRM in the hydrothermal sediment. Thermophilic sulfate reduction had a pH optimum of about 7 and was completely inhibited at pH 8.8 to 9.2. SRM could be enriched from hydrothermal chimney and sediment samples at 60 and 75°C. In lactate-grown enrichments, sulfide production occurred at up to 70 and 75°C, with optima at 63 and 71°C, respectively. Several sporulating thermophilic enrichments were morphologically similar to Desulfotomaculum spp. Dissimilatory sulfate reduction in the studied hydrothermal area of Lake Tanganyika apparently has an upper temperature limit of 80°C.     

Sulfate Reduction Dynamics and Enumeration of Sulfate-Reducing Bacteria in Hypersaline Sediments of the Great Salt Lake (Utah, USA)

Bacterial sulfate reduction activity (SRA) was measured in surface sediments and slurries from three sites in the Great Salt Lake (Utah, USA) using radiolabeled 35S-sulfate. High rates of sulfate reduction (363 ± 103 and 6,131 ± 835 nmol cm-3 d-1) were measured at two sites in the moderately hypersaline southern arm of the lake, whereas significantly lower rates (32 ± 9 nmol cm-3 d-1) were measured in the extremely hypersaline northern arm. Bacterial sulfate reduction was strongly affected by salinity and showed an optimum around 5-6% NaCl in the southern arm and an optimum of around 12% NaCl in the more hypersaline northern arm of the lake. High densities of sulfate-reducing bacteria (SRB) ranging from 2.2 × 107 to 6.7 × 108 cells cm-3 were determined by a newly developed tracer MPN-technique (T-MPN) employing sediment media and 35S-sulfate. Calculation of specific sulfate reduction rates yielded values comparable to those obtained in pure cultures of SRB. However, when using a conventional MPN technique with synthetic media containing high amounts of Fe(II), the numbers of SRB were underestimated by 1-4 orders of magnitude as compared to the T-MPN method. Our results suggest that high densities of slightly to moderately halophilic and extremely halotolerant SRB are responsible for the high rates of sulfate reduction measured in Great Salt Lake sediments.     

Dynamics of Methane Production, Sulfate Reduction, and Denitrification in a Permanently Waterlogged Alder Swamp

The dynamics of sulfate reduction, methane production, and denitrification were investigated in a permanently waterlogged alder swamp. Molybdate, an inhibitor of sulfate reduction, stimulated methane production in soil slurries, thus suggesting competition for common substrates between sulfate-reducing and methane-producing bacteria. Acetate, hydrogen, and methanol were found to stimulate both sulfate reduction and methane production, while trimethylamine mainly stimulated methane production. Nitrate addition reduced both methane production and sulfate reduction, either as a consequence of competition or poisoning of the bacteria. Sulfate-reducing bacteria were only slightly limited by the availability of electron acceptors, while denitrifying bacteria were seriously limited by low nitrate concentrations. Arrhenius plots of the three processes revealed different responses to temperature changes in the slurries. Methane production was most sensitive to temperature changes, followed by denitrification and sulfate reduction. No significant differences between slope patterns were observed when comparing summer and winter measurements, indicating similar populations regarding temperature responses.     

Use of Metabolic Inhibitors to Estimate Protozooplankton Grazing and Bacterial Production in a Monomictic Eutrophic Lake with an Anaerobic Hypolimnion

Inhibitors of eucaryotes (cycloheximide and amphotericin B) and procaryotes (penicillin and chloramphenicol) were used to estimate bacterivory and bacterial production in a eutrophic lake. Bacterial production appeared to be slightly greater than protozoan grazing in the aerobic waters of Lake Oglethorpe. Use of penicillin and cycloheximide yielded inconsistent results in anaerobic water and in aerobic water when bacterial production was low. Production measured by inhibiting eucaryotes with cycloheximide did not always agree with [³H]thymidine estimates or differential filtration methods. Laboratory experiments showed that several common freshwater protozoans continued to swim and ingest bacterium-size latex beads in the presence of the eucaryote inhibitor. Penicillin also affected grazing rates of some ciliates. We recommend that caution and a corroborating method be used when estimating ecologically important parameters with specific inhibitors.