Bacteria In Lakes Research Articles

Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.

Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method.

In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling.

Molecular characterization of the planktonic microorganisms in water of two mountain brackish lakes

The prokaryotic diversity in two brackish lakes (Sayram Lake and Chaiwopu Lake) was investigated by constructing bacterial and archaeal clone libraries of 16S rRNA genes. Bacterial clones from Sayram Lake were classified into six phyla (Proteobacteria, Verrucomicrobia, Bacteroidetes, Planctomycetes, Acidobacteria, Actinobacteria). Of these, Proteobacteria and Verrucomicrobia were the most dominant, representing 50.4 and 16.8% of the clone library, respectively. Sequences related to Proteobacteria (58.1%), Cyanobacteria (17.2%), Bacteroidetes (15%), Verrucomicrobia (4.3%), Actinobacteria (3.2%) constituted over 97% of the bacterial clone library from Chaiwopu Lake. In addition, 58.8% (Sayram Lake) and 48% (Chaiwopu Lake) of bacterial clones showed high sequence identity to pure cultures. The composition of Archaea was obviously different between the two lakes. Only the Crenarchaeota phylum was found in the Sayram Lake, whereas Archaeal sequences from Chaiwopu Lake were classified into three phyla: Crenarchaeota (5.8%), Thaumarchaeota (81.2%), and Euryarchaeota (13%). Among the archaeal sequences, 94.2% were highly related to cultivable species of the genus Nitrosopumilus, Methanoculleus, and Methanobacterium. These results showed a high diversity of potential cultivable heterotrophic bacteria in Sayram Lake and Chaiwopu Lake. Chaiwopu Lake was a source of potentially novel, cultivable archaea.

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment.

Different diversity-functioning relationship in lake and stream bacterial communities

Biodiversity patterns have been successfully linked to many ecosystem functions, and microbial communities have been suspected to harbour a large amount of functionally redundant taxa. We manipulated the diversity of stream and lake water column bacterial communities and investigated how the reduction in diversity affects the activities of extracellular enzymes involved in dissolved organic carbon degradation. Dissimilar communities established in cultures inoculated with stream or lake bacteria and utilized different organic matter compounds as indicated by the different extracellular enzyme activities. Stream bacterial communities preferentially used plant-derived organic material such as cellulose and hemicellulose. Communities obtained from the lake, where the longer residence time might permit the organic matter to age, efficiently degraded lignin-like material and also showed higher peptide degradation capacities. The results highlight a stronger negative effect of decreasing diversity on ecosystem multifunctionality for stream than for lake bacterial communities. We found a relatively higher multifunctional redundancy in the lake as compared to the stream-derived cultures and suggest that community assembly might shape diversity-functioning relationships in freshwater bacterial communities.

Salinity Impact on Bacterial Community Composition in Five High-Altitude Lakes from the Tibetan Plateau, Western China

The influence of salinity and geographical distance on bacterial community composition (BCC) in five freshwater, oligosaline or polysaline lakes located at altitudes higher than 4400 m on the central and southern Tibetan Plateau were investigated using the 16S rRNA gene clone library approach together with multivariate analysis of environmental variables. A total of 10 clone libraries were constructed with two libraries in each lake, one in the epilimnion and the other in the hypolimnion. Geographical distance was not found to impact BCC significantly, but salinity, chl a and lake hydraulic retention time were significant factors influencing the BCC. Bacteria in lakes located on the central and southern Plateau owned the same community composition as that observed from the eastern Tibetan lakes. They were both predominated by Bacteroidetes and Cyanobacteria, had low taxon richness, and similar typical freshwater clusters and distributed characteristics. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.

Grazing resistant freshwater bacteria profit from chitin and cell‐wall‐derived organic carbon

The rise of grazing resistant planktonic bacteria in freshwater lakes during vernal phytoplankton blooms is favoured by predation of heterotrophic nanoflagellates (HNF). The spring period is also characterized by increased availability of organic carbon species that are in parts derived from cellular debris generated during bacterivory or viral lysis, such as peptidoglycan, chitin and their subunit N-acetylglucosamine (NAG). We tested the hypothesis that two dominant grazing resistant bacterial taxa, the ac1 tribe of Actinobacteria (ac1) and filamentous bacteria from the LD2 lineage (Saprospiraceae), profit from such carbon sources during periods of intense HNF predation. The abundances of ac1 and LD2 rose in parallel with HNF, and disproportionally high fractions of cells from both lineages were involved in NAG uptake. Members of ac1 and LD2 were significantly more enriched after NAG addition to lake water. However, highest growth rates of both bacterial lineages were found on chitin and peptidoglycan. Moreover, the direct or indirect transfer of organic carbon from peptidoglycan to LD2 filaments could be demonstrated. We thus provide evidence that these taxa may benefit twofold from protistan predation: by removal of their competitors, and by specific physiological adaptations to utilize carbon sources that are released during grazing or viral lysis.

Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes usingsoxB as a functional molecular marker

The diversity of soxB gene encoding a key enzyme of the Sox pathway sulfate thiohydrolase has been investigated in pure cultures of various halophilic and haloalkaliphilic sulfur-oxidizing bacteria (SOB) and in salt and soda lakes in southwestern Siberia and Egypt. The gene was detected in the majority of strains belonging to eleven SOB genera excluding members of genera Thiohalospira and Thioalkalimicrobium. The uncultured diversity of soxB in salt and soda lakes was low with a majority of detected sequences belonging to autotrophic SOB from the Gammaproteobacteria. In addition, the soxB analysis allowed detection of putative heterotrophic Gamma- and Alphaproteobacterial SOB yet unknown in culture. All clone libraries obtained from soda lakes contained soxB belonging to the genus Thioalkalivibrio in agreement with the cultivation results. Besides, representatives of the genera Halothiobacillus, Marinobacter, and Halochromatium and of the family Rhodobacteraceae have been detected in both type of saline lakes.

Bacterial community dominance of particle-attached bacteria in lakes of the Mackenzie River Delta: transparent exopolymer particle contribution

Bacterial community dominance of particle-attached bacteria in lakes of the Mackenzie River Delta: transparent exopolymer particle contribution

Analysis of nestedness in freshwater assemblages—patterns across species and trophic levels

Nestedness measures the degree to which species assemblages are proper subsets of larger assemblages within a metacommunity. We analyzed nestedness in 20 freshwater data sets, each for a single metacommunity within a drainage basin. First, we examined the degree of nestedness across local assemblages and identified major environmental correlates of nestedness at sites. Second, we examined whether nestedness showed concordance among trophic levels. Third, we examined whether nested and idiosyncratic species (i.e., species that have unpredictable gaps in their distribution) differed ecologically and showed dissimilar distribution patterns along geographical and environmental gradients. Degrees of nestedness, obtained using a metric by Almeida-Neto et al. (2008), ranged from 22.9 to 57.0, with 11 matrices showing significant nestedness. Lake bacteria had a higher degree of nestedness than did phyto- or zooplankton. The degree of nestedness was related mainly to water temperature, conductivity, and trophic status of the water, results suggesting that habitat quality may be an important predictor of nestedness, but was only weakly concordant among trophic levels within metacommunities. However, averaged across all metacommunities, nestedness values between phytoplankton and zooplankton and between phytoplankton and bacteria were positively correlated. Nested and idiosyncratic species did not differ in their spatial and environmental distribution patterns. Freshwater planktonic assemblages were characterized by a relatively low degree of nestedness. The low congruence in nestedness among trophic levels suggests that assemblages typically show independent gradients of nestedness. This result indicates that assemblages respond dissimilarly to driving forces, such as habitat quality, or that nestedness in freshwaters might be related to stochastic colonization. Conserving only the most diverse sites may not protect rare species because of the relatively low degree of nestedness in fresh waters.

What could arsenic bacteria teach us about life?

In this paper, I discuss the recent discovery of alleged arsenic bacteria in Mono Lake, California, and the ensuing debate in the scientific community about the validity and significance of these results. By situating this case in the broader context of projects that search for anomalous life forms, I examine the methodology and upshots of challenging biochemical constraints on living things. I distinguish between a narrower and a broader sense in which we might challenge or change our knowledge of life as the result of such a project, and discuss two different kinds of projects that differ in their potential to overhaul our knowledge of life. I argue that the arsenic bacteria case, while potentially illuminating, is the kind of constraint-challenging project that could not—in spite of what was said when it was presented to the public—change our knowledge of life in the deeper sense.

Denitrification by sulfur-oxidizing bacteria in a eutrophic lake

Understanding the mechanistic controls of microbial denitrification is of central importance to both environmental microbiology and ecosystem ecology. Loss of nitrate (NO3 � ) is often attributed to carbon-driven (heterotrophic) denitrification. However, denitrification can also be coupled to sulfur (S) oxidation by chemolithoautotrophic bacteria. In the present study, we used an in situ stable isotope ( 15 NO3 � ) tracer addition in combination with molecular approaches to understand the contribution of sulfur-oxidizing bacteria to the reduction of NO3 � in a eutrophic lake. Samples were incubated across a total dissolved sulfide (H2S) gradient (2 to 95 µM) between the lower epilimnion and the upper hypolimnion. Denitrification rates were low at the top of the chemocline (4.5 m) but increased in the deeper waters (5.0 and 5.5 m), where H2S was abundant. Concomitant with increased denitrification at depths with high sulfide was the production of sul- fate (SO4 2� ), suggesting that the added NO3 � was used to oxidize H2S to SO4 2� . Alternative nitrate removal pathways, including dissimilatory nitrate reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox), did not systematically change with depth and accounted for 1 to 15% of the overall nitrate loss. Quantitative PCR revealed that bacteria of the Sulfurimonas genus that are known denitrifiers increased in abundance in response to NO3 � addition in the treatments with higher H2S. Stoichiometric estimates suggest that H2S oxidation accounted for more than half of the denitrification at the depth with the highest sulfide concentration. The present study pro- vides evidence that microbial coupling of S and nitrogen (N) cycling is likely to be important in eutrophic freshwater ecosystems.

Distribution of aerobic anoxygenic phototrophic bacteria in glacial lakes of northern Europe

Distribution of aerobic anoxygenic phototrophic bacteria in glacial lakes of northern Europe

Seasonal biogeochemical and microbiological studies of small lakes in taiga zone of northwestern Russian (Arkhangelsk Province)

The results of biogeochemical and microbiological studies of three small lakes in southwestern Arkhangelsk province are presented. The lakes differ in their morphometric characteristics, thermal and oxygen regimes, and the extent of anthropogenic impact they experience. In the periods of summer and winter stratification, anaerobic water layers with higher phosphates, ammonium, and sulfide sulfur (hydrogen sulfide) are found to form in the bottom horizon of deep-water zones of the lakes. The highest concentrations of sulfide sulfur (150–210 μg dm−3) were recorded in the shallow Beloe Lake during winter low-water period, while in summer, sulfide concentration did not differ from those obtained in other lakes (∼10 μg dm−3). The abundance of sulfate-reducing bacteria in lake bottom sediments varied from 10 to 100000 cell cm−3, and the rate of sulfate reduction process varied from 29 to 3746 μg S dm−3 day−1. Seasonal variations were revealed in hydrogen sulfide distribution over the water column and in the rate of sulfate reduction process in the upper horizons of bottom sediments in the examined lakes.

Isolation and characterization of halophilic bacteria from Urmia Lake in Iran

Urmia Lake is one of the most permanent hypersaline lakes in the world which is threatened by hypersalinity and serious dryness. In spite of its importance no paper has been published regarding bacterial community of this lake. Accordingly, the present study aimed to investigate the halophilic bacteria in the aforementioned lake. In so doing, thirty seven strains were isolated on six different culture media. The isolated strains were characterized using phenotypic and genotypic methods. Growth of the strains occurred at 2535 degrees C, pH 6-9 and 7 to 20% (w/v) NaCl indicating that most of the isolates were moderately halophiles. Catalase, oxidase and urease activities were found to be positive for the majority of the isolates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolated bacteria belonged to two major taxa: Gammaproteobacteria (92%, including Salicola [46%], Pseudomonas [13.5%], Marinobacter [ 11%], Idiomarina [11%], and Halomonas [8%]) and Firmicutes (8%, including Bacillus [5%] and Halobacillus [3%]). In addition, a novel bacterium whose 16S rRNA gene sequence showed almost 98% sequence identity with the taxonomically troubled DSM 3050T, Halovibrio denitrificans HGD 3T and Halospina denitrificans HGD 1-3T, each, was isolated. 16S rRNA gene similarity levels along with phenotypic characteristics suggest that some of the isolated strains could be regarded as potential type strain for novel species, on which further studies are recommended.

Rhodoferax‐related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes

The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha- and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south-west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria-related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas- and Rhodobacter-like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter-rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium-related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.

Methane-oxidizing and photoautotrophic bacteria are major producers in a humic lake with a large anoxic hypolimnion

Heterotrophic processes are considered to prevail in lakes with high terrestrial loading and a high content of dissolved organic carbon. However, previous studies have shown abundant methanotrophic bacteria (MOB) and photoautotrophic green sulphur bacteria (GSB) in some boreal lakes. We used genetic and lipid biomarkers to follow the seasonal succession of the abundance and carbon biomass of the major bacterial groups in Lake Mekkojarvi, a small Finnish polyhumic lake with a large anoxic hypolimnion. Biomarkers were based on length heterogeneity analysis of 16S rRNA gene amplification by polymerase chain reaction (PCR) (LH-PCR) and on phospholipid fatty acid (PLFA) analysis. Representative strains closely affiliated to the dominant bacterial groups in the lake were cultured and their characteristic PLFA biomarkers were selected. According to these bio- markers, the relative abundance and biomass of the anaerobic photo autotrophic bacteria (e.g. GSB) were extremely high in the pelagial during summer stratification (on average 47% of the bacterial rRNA genes and 77% of the total particulate organic carbon). Type I MOB were especially abundant during autumn mixing, forming on average 32% — but occasionally up to 73% — of the carbon bio- mass. Heterotrophic bacteria affiliated to Actinobacteria and Poly nucleobacter spp. together con- tributed 1 to 8% of the seasonal carbon biomass in the lake, although their genetic biomarkers were much more common. The results indicate that a significant proportion of the bacterial biomass was formed through methanotrophic and photoautotrophic production, both being comparable with the summer primary production rates of phytoplankton. These findings challenge the current model of the heterotrophic microbial pathway as the principal basis for microbial mobilisation of carbon and energy in freshwater food webs in oxygen-stratified lakes.

Carbon and phosphorus regulating bacterial metabolism in oligotrophic boreal lakes

This study focused on how phosphorus and carbon control pelagic bacteria in lakes over a gradient of dissolved organic carbon (DOC from 6.7 to 29.5 mg C L-1) and phosphorus (P-tot from 5 to 19 mu g L-1). Five oligotrophic lakes in southern Sweden were sampled in late autumn. Phosphate-P and glucose-C alone or in combination (0.01 and 0.3 mg L-1, respectively) was added to 1.0 mu m filtered lake water and incubated in darkness at 20 degrees C. Additions of glucose (C) and phosphorus (P) alone did not lead to changes in the rates of bacterial metabolic processes, whereas bacterial respiration and bacterial production responded positively to C + P enrichment for most of the lakes sampled. Bacterial growth efficiency showed a wide range (2.5-28.7%) and low mean value (12%). These variations were not correlated with the DOC concentration. Our results show that heterotrophic bacterial carbon mineralization in this kind of system during autumn is conditioned by the combined availability of labile carbon and phosphorus, with the assimilated carbon mainly transformed to inorganic carbon in respiration, contributing to CO2 supersaturation in these systems. (Less)

Mercury uptake by biogenic silica modified with L‐cysteine

Contaminated sediments provide the main source of mercury for methylation by bacteria in lakes and waterways. In situ capping has been used to remediate these sediments, but traditional reactive materials have very low affinity for Hg(II). This study investigated the mercury uptake by biogenic silica modified with L‐cysteine, as a potential material to be used for in situ remediation technologies. The adsorbent was obtained from rice hull ash by extraction as sodium silicate and acid hydrolysis through the sol–gel process; it was then modified with L‐cysteine by impregnation from aqueous solution. The unmodified and modified biogenic silica showed structural and chemical properties suitable for mercury sorption from aqueous medium. The cysteine affected the structural properties of the unmodified silica, decreasing the specific surface area and pore volume by eightfold. On the other hand, cysteine increased the silica adsorption capacity, resulting in mercury uptake similar to that of the unmodified silica. The Hg(II) specific adsorption by unmodified and modified silica was 0.20 mmol/g and 0.19 mmol/g SiO2, respectively, from an aqueous solution of 1 mmol/L Hg(II). The pH range of 3–7did not have an effect on Hg(II) adsorption. However, the presence of chlorine, added as HgCl2, seems to have limited the mercury adsorption, especially at high concentrations of Hg(II). The mercury adsorbed on the silica surface could not be recovered using HCl even from concentrated solutions.

Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov.

Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H2 and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00792-011-0370-7) contains supplementary material, which is available to authorized users.