Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach

The free-living, cosmopolitan, freshwater betaproteobacterial bacterioplankton genus Polynucleobacter was detected in different years in 11 lakes of varying types and a river using the size-exclusion assay method (SEAM). Of the 350 strains isolated, 228 (65.1%) were affiliated with the Polynucleobacter subclusters PnecC (30.0%) and PnecD (35.1%). Significant positive correlations between fluorescence in situ hybridization and SEAM data were observed in the relative abundance of PnecC and PnecD bacteria to Polynucleobacter communities (PnecC?+?PnecD). Isolates were mainly PnecC bacteria in the samples with a high specific UV absorbance at 254?nm (SUVA(254) ), and a low total hydrolysable neutral carbohydrate and amino acid (THneutralCH?+?THAA) content of the dissolved organic matter (DOM) fraction, which is known to be correlated with a high humic content. In contrast, the PnecD bacteria were abundant in samples with high chlorophyll a and/or THneutralCH?+?THAA concentrations, indicative of primary productivity. With few exceptions, differences in the relative abundance of PnecC and PnecD in each sample, determined using a high-sensitivity cultivation-based approach, were due to DOM quality. These results suggest that the major DOM component in the field, which is allochthonously or autochthonously derived, is a key factor for ecological niche separation between PnecC and PnecD subclusters.     

pH Influences the Importance of Niche-Related and Neutral Processes in Lacustrine Bacterioplankton Assembly

pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.     

Role of ultraviolet-B radiation on bacterioplankton and the availability of dissolved organic matter

Attenuation of ultraviolet (UV)-radiation into the water column is highly correlated with the concentration of the dissolved organic matter (DOM). Thus UV penetrates deeper into marine waters than into freshwater systems. DOM is efficiently cleaved by solar surface radiation levels consuming more oxygen than bacterial metabolism. This photolytically cleaved DOM exhibits higher absorbance ratios (250/365 nm) than untreated DOM. Natural bacterioplankton reach higher abundance if inoculated in previously solar-exposed DOM than in untreated DOM; during bacterial growth the absorbance ratio declines steadily indicating the utilization of the photolytically cleaved DOM. On the other hand, bacterioplankton are greatly reduced in their activity if exposed to surface solar radiation levels. Photoenzymatic repair of DNA induced by UV-A radiation, however, leads to an efficient recovery of bacterial activity once the UV-B stress is released. Turbulent mixing of the upper layers of the water column leads to a continuous alteration of the UV exposure regime. Close to the surface, bacteria and DOM are exposed to high levels of UV-B leading to a reduction in bacterial activity and to photolysis of DOM. Once mixed into deeper layers where UV-B is attenuated, but sufficient UV-A is remaining to allow photoenzymatic repair, the photolytically cleaved DOM is efficiently taken up by bacterioplankton leading to even higher bacterial activity than prior to the exposure. Thus, the overall effect of UV on bacterioplankton is actually an enhancement of bacterial activity despite their lack of protective pigments.     

Chemical and optical changes in freshwater dissolved organic matter exposed to solar radiation

We studied the chemical and optical changes inthe dissolved organic matter (DOM) from twofreshwater lakes and a Sphagnum bog afterexposure to solar radiation. Stable carbonisotopes and solid-state ¹³C-NMR spectraof DOM were used together with optical andchemical data to interpret results fromexperimental exposures of DOM to sunlight andfrom seasonal observations of two lakes innortheastern Pennsylvania. Solar photochemicaloxidation of humic-rich bog DOM to smaller LMWcompounds and to DIC was inferred from lossesof UV absorbance, optical indices of molecularweight and changes in DOM chemistry. Experimentally, we observed a 1.2 enrichment in ¹³$C and a 47% loss in aromaticC functionality in bog DOM samples exposed tosolar UVR. Similar results were observed inthe surface waters of both lakes. In latesummer hypolimnetic water in humic LakeLacawac, we observed 3 to 4.5enrichments in ¹³C and a 30% increase inaromatic C relative to early spring valuesduring spring mixing. These changes coincidedwith increases in molecular weight and UVabsorbance. Anaerobic conditions of thehypolimnion in Lake Lacawac suggest thatmicrobial metabolism may be turning overallochthonous C introduced during springmixing, as well as autochthonous C. Thismetabolic activity produces HMW DOM during thesummer, which is photochemically labile andisotopically distinct from allochthonous DOM orautochthonous DOM. These results suggest bothphotooxidation of allochthonous DOM in theepilimnion and autotrophic production of DOM bybacteria in the hypolimnion cause seasonaltrends in the UV absorbance of lakes.     

Allochthonous dissolved organic matter as an energy source for pelagic bacteria and the concept of the microbial loop

Substantial evidence exists that allochthonous dissolved organic matter (DOM) can provide an important carbon source for pelagic bacteria. On the other hand, it is implicit in the concept of the ‘microbial loop’ that the degradation of recalcitrant, allochthonous DOM should be retarded in the pelagic environment, as bacteria able to utilize recalcitrant DOM compounds for slow growth would be outcompeted by faster-growing bacteria utilizing more labile DOM compounds. Several possible solutions of this apparent paradox are suggested in this paper, including formation of labile DOM from recalcitrant DOM by e.g. photochemical reactions, and mechanisms enabling the maintenance of a metabolically diverse bacterioplankton. These mechanisms include an explanation analogous to Hutchinson's classical solution to the ‘paradox of plankton’, and differential mortality of different populations within the bacterioplankton enabled by selective grazing, infections by bacteriophages and predatory bacteria, and spatial micropatchiness.     

微生物胞外电子传递效率的合成生物学强化

电活性微生物(产电微生物和亲电微生物)通过与外界环境进行双向电子和能量传递来实现多种微生物电催化过程(包括微生物燃料电池、微生物电解电池、微生物电催化等),从而实现在环境、能源领域的广泛应用,并为开发有效且可持续性生产新能源或大宗精细化学品的工艺提供了新机会。但是,电活性微生物的胞外电子传递效率比较低,这已经成为限制微生物电催化系统在工业应用中的主要瓶颈。以下综述了近年来利用合成生物学改造电活性微生物的相关研究成果,阐明了合成生物学如何用于打破电活性微生物胞外电子传递途径低效率的瓶颈,从而实现电活性微生物与环境的高效电子传递和能量交换,推动电活性微生物电催化系统的实用化进程。     

Simultaneous consumption and production of fluorescent dissolved organic matter by lake bacterioplankton

Recent evidence suggests a key role of bacterioplankton in shaping the composition of the dissolved organic matter (DOM) pool in aquatic systems, not only through consumption but also through production of specific compounds, but the latter process is still not well understood. We used a bioassay approach to assess the patterns in bacterial production and consumption of five fluorescent DOM pools in seven lakes and two streams in Southeastern Québec, Canada, and the links these patterns may have with key aspects of bacterial metabolism, DOM origin and nutrients availability. Total dissolved organic C declined by 3-15% during these incubations, whereas the specific DOM pools had very different dynamics: Two humic-like fractions accumulated in all incubations, with rates of production increasing as a function of bacterial growth efficiency, which itself increased with phosphorus concentrations. In contrast, two protein-like fractions and a third humic-like fraction either increased or declined over the course of the experiments. The net production or consumption of these pools appeared to be a function of the contribution of terrestrial C to bulk DOM (derived from δ(13) C of the DOM) and of total bacterial activity. Our results suggest that lake bacterioplankton play a dual role in DOM dynamics, as consumers and also producers, and that the interplay between DOM origin and nutrient availability appears to determine the net outcome of bacterial DOM processing, thus influencing the bulk DOM composition and its fate in these aquatic systems.     

Molecular underpinnings for microbial extracellular electron transfer during biogeochemical cycling of earth elements

Microbial extracellular electron transfer(EET) is electron exchanges between the quinol/quinone pools in microbial cytoplasmic membrane and extracellular substrates. Microorganisms with EET capabilities are widespread in Earth hydrosphere, such as sediments of rivers, lakes and oceans, where they play crucial roles in biogeochemical cycling of key elements, including carbon,nitrogen, sulfur, iron and manganese. Over the past 12 years, significant progress has been made in mechanistic understanding of microbial EET at the molecular level. In this review, we focus on the molecular mechanisms underlying the microbial ability for extracellular redox transformation of iron, direct interspecies electron transfer as well as long distance electron transfer mediated by the cable bacteria in the hydrosphere.     

Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the glacial lake agassiz peatland

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.     

Bacterial community structure in a latitudinal gradient of lakes: the roles of spatial versus environmental factors

1. We analysed the latitudinal variation of bacterioplankton in 45 freshwater environments (lakes, shallow lakes and ponds) across a transect of more than 2100 km stretching from Argentinean Patagonia (45°S) to Maritime Antarctica (63°S), to determine the factors that mainly determine bacterioplankton community structure. 2. Bacterioplankton community composition (BCC) was assessed by a fingerprinting method (denaturing gradient gel electrophoresis) followed by band sequencing, whereas the abundances of total bacteria and picocyanobacteria were estimated by epifluorescence microscopy. 3. Bacterioplankton community composition was controlled by a combination of spatial (latitude and longitude) and environmental [e.g. phosphate, light diffuse attenuation coefficient (K_d) and dissolved organic carbon] factors. Total bacterioplankton abundance declined with latitude. A multiple regression analysis showed that phosphate, K_d and latitude had significant effects on total bacterioplankton abundance. 4. Of 76 operational taxonomic units identified in the studied lakes, 45 were shared between Patagonian and Antarctic water bodies, 28 were present only in Patagonian lakes and three were restricted to the Antarctic lakes. Significant differences were found in BCC between Patagonia and Antarctica. Among the sequences, 54% were similar (>97% sequence similarity) to others reported from cold habitats elsewhere on the planet (glaciers, high mountain lakes, Arctic). 5. Our results provide new evidence that supports the hypotheses of biogeographic patterns of bacterial assemblages and suggest that both spatial and environmental factors control bacterioplankton community structure.     

Bacterio- and virioplankton in water bodies of a raised bog (Vologda oblast,Russia)

The abundance of virio-and bacterioplankton and the role of viruses in the mortality of heterotrophic bacteria have been studied in three different mire water bodies (lagg, hollow, and stream) in the Shichengskoe raised bog. The abundance of bacteria (up to 93 million cells/mL) and viruses (up to 152 million particles/mL) reached very high values. Considerable differences were found between the mire water bodies in seasonal dynamics and average values of the studied parameters. The ratio of the number of virioplankton to the number of bacterioplankton (median values from 1.3 in a hollow to 5.6 in a stream) is in low ranges of values which are available in literature sources. Viruses did not have a considerable direct effect on bacterioplankton while lysing ≤7.8% of the bacterial production.     

Potential-dependent extracellular electron transfer pathways of exoelectrogens

Exoelectrogens are distinct from other bacteria owing to their unique extracellular electron transfer (EET) abilities that allow for anaerobic respiration with various external redox-active surfaces, including electrode and metal oxides. Although the EET process is known to trigger diverse extracellular redox reactions, the reverse impact has been long overlooked. Recent evidences show that exoelectrogens can sense the potential changes of external surfaces and alter their EET strategies accordingly, which imparts them remarkable abilities in adapting to diverse and redox-variable environment. This mini-review provides a condensed overview and critical analysis about the recent discoveries on redox-dependent EET pathways of exoelectrogens, with focus on Geobacter sulfurreducens and Shewanella oneidensis. We summarize the detailed responses of various EET components, analyze the drives and mechanisms of such responses, highlight the diversity of EET dynamics among different bacterial species and under integrated effects of redox potential and surface chemistry, and discusses the future research needs.     

Bacterial Production in the Recently Flooded Sep Reservoir: Diel Changes in Relation to Dissolved Carbohydrates and Combined Amino Acids

The spatial distribution of bacterial abundance and production were measured every 4 h in a recently flooded oligo-mesotrophic reservoir (the Sep Reservoir, Puy-De-Dôme, France), in relation to concentrations of dissolved carbohydrates and combined amino acids. The concentration of dissolved organic matter (DOM) components in the recently flooded Sep Reservoir were higher than those measured in other lakes of similar trophic status. Short-term variations in the bacterial production in this new reservoir appeared cyclical and endogenous to bacterial communities. These results highlight the need for the evaluation of diel changes in bacterial production, if estimation of the daily production rate of bacteria is to be done accurately for a reliable model of carbon flow through bacterioplankton and ultimately through aquatic microbial food webs. Bacterial growth, measured over time and space, did not appear exclusively governed by DOM components from phytoplankton primary production.     

Nutrient limitation of bacterioplankton and phytoplankton in humic lakes in northern Sweden

1. Two small humic lakes in northern Sweden with concentrations of dissolved organic carbon (DOC) between 15 and 20 mg L^–1 were fertilized with inorganic phosphorus (P) and inorganic nitrogen (N), respectively. A third lake was unfertilized and served as a control. In addition to this lake fertilization experiment, data from different regional surveys were used to assess the role of different limiting factors.
2. The P fertilization had no effects on bacterioplankton or phytoplankton, while phytoplankton were significantly stimulated by N fertilization. Inorganic nutrient limitation of bacterioplankton was a function of DOC concentration in water of the investigated region and nutrient-limited bacteria were found only in lakes with DOC concentrations less than around 15 mg L^–1
3. The fertilization experiments demonstrated that the DOC-rich experimental lakes contained a bioavailable pool of P that was not utilized to its full potential under natural conditions. The overall mobilization of energy (bacterioplankton plus phytoplankton) in the experimental lakes was restricted by lack of inorganic N.     

Viral and Bacterioplankton Dynamics in Two Lakes with Different Humic Contents

Viral and bacterioplankton dynamics were investigated, together with the temporal variation of phage-infected bacterioplankton in two oligotrophic lakes, one humic and the other clearwater. Bacterial abundance was significantly higher in the humic lake, while the abundance of virus-like particles (VLP) was significantly higher in the clearwater lake. There were no differences in either the frequency of infected bacterial cells (FIC), or in burst size between the lakes. Because of the higher bacterial abundance in the humic lake, a larger number of bacteria were lyzed in this lake. FIC showed large seasonal changes, varying between 9 and 43%, which covers almost the entire range of previously published data from both lacustrine and marine environments. The temporal changes in VLP abundance and FIC were slow in both the humic and clearwater lakes. The burst size was low in both lakes (average value, nine in each case), probably because of the oligotrophic status of the lakes. The chlorophyll a concentrations were higher and positively correlated with VLP numbers in the clearwater lake, indicating that a significant proportion of the viruses in this lake may be phytoplankton viruses.     

Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes

We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes) . Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes.     

贫营养湖泊花神湖和紫霞湖浮游细菌群落结构分析

以南京市花神湖和紫霞湖两个贫营养型湖泊为研究对象,通过构建花神湖和紫霞湖16S rRNA基因克隆文库探讨了浮游细菌群落结构组成的变化。结果表明,花神湖和紫霞湖两湖泊水体中浮游细菌群落结构相似,主要隶属于放线菌门(Actinobacteria)、蓝藻门(Cyanobacteria)、α-变形菌门(Alphaproteobacteria)、β-变形菌门(Betaproteobacteria)、杆菌门(Bacteroidetes)、浮霉菌门(Planctomycetes)、疣微菌门(Verrucomicrobia)和芽单胞菌门(Gemmatimonadetes),其中放线菌门(Actinobacteria)、蓝藻门(Cyanobacteria)、β-变形菌门(Betaproteobacteria)是优势细菌类群。两个湖泊水体中75%的细菌与GenBank中已有的未培养细菌同源性高于97%,同时在两个克隆文库中还发现了6个淡水细菌新类群。通过对低纬度区域贫营养型湖泊浮游细菌群落结构的分析,加深了我们对浮游细菌多样性的了解,表明湖泊浮游细菌多样性有待进一步认识。     

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation

The Chloroflexi CL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world''s largest freshwater system, the Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that a CL500-11 population was present mostly in offshore waters along a transect in ultraoligotrophic Lake Michigan (a Laurentian Great Lake). It occurred throughout the water column in spring and only in the hypolimnion during summer stratification, contributing up to 18.1% of all cells. Genome reconstruction from metagenomic data suggested an aerobic, motile, heterotrophic lifestyle, with additional energy being gained through carboxidovory and methylovory. Comparisons to other available streamlined freshwater genomes revealed that the CL500-11 genome contained a disproportionate number of cell wall/capsule biosynthesis genes and the most diverse spectrum of genes involved in the uptake of dissolved organic matter (DOM) substrates, particularly peptides. In situ expression patterns indicated the importance of DOM uptake and protein/peptide turnover, as well as type I and type II carbon monoxide dehydrogenase and flagellar motility. Its location in the water column influenced its gene expression patterns the most. We observed increased bacteriorhodopsin gene expression and a response to oxidative stress in surface waters compared to its response in deep waters. While CL500-11 carries multiple adaptations to an oligotrophic lifestyle, its investment in motility, its large cell size, and its distribution in both oligotrophic and mesotrophic lakes indicate its ability to thrive under conditions where resources are more plentiful. Our data indicate that CL500-11 plays an important role in nitrogen-rich DOM mineralization in the extensive deep-lake hypolimnion habitat.     

Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions

Bacterioplankton community composition was studied in 12 lakes in three different geographic regions in Scandinavia using denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rDNA. Area-specific abundant taxa were found in the lakes in two of the regions. In the region of Uppland the lakes had an alpha-proteobacterium, belonging to the subgroup Alpha V in common. The Alpha V bacteria appeared to be favored by neutral or higher pH values. The lakes in Lappland were found to harbor Actinobacteria, which appeared to be favored in bog lakes. No abundant taxon was found to be in common for the lakes in Svalbard, the third region studied.     

Bacterioplankton Community Composition in Five Lakes Differing in Trophic Status and Humic Content

Abstract To investigate the relation between lake type and bacterioplankton community composition, five Swedish lakes, which differed from each other in nutrient content and water color, were studied. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA was used to examine community composition. The DGGE-patterns of the different samples were analyzed in relation to physical, chemical, and biological data from the lakes by canonical correspondence analysis (CCA). The three variables found to most strongly correlate with the DGGE patterns were biomasses of microzooplankton, cryptophytes, and chrysophytes, suggesting that these biota had an impact on bacterioplankton community structure. Two of the three factors were, in turn, significantly correlated to parameters associated with the trophic status of the lakes, indicating that the nutrient content of the lakes, at least indirectly, influenced the structure of the bacterioplankton community. The relation to water color was less pronounced. Received: 16 February 2000; Accepted: 27 April 2000; Online Publication: 18 July 2000