Effects of Resources and Trophic Interactions on Freshwater Bacterioplankton Diversity

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Variations in bacterioplankton communities in aquaculture ponds and the influencing factors during the peak period of culture

An increase in nutrient input may disturb the bacterioplankton communities in freshwater aquaculture ponds during the peak period of culture. Water samples were collected from ponds of three cultivated species. After the samples were filtered and total DNA was extracted, Illumina high-throughput sequencing was used to profile the spatiotemporal distributions in bacterioplankton communities, the belt diversity, and the influencing factors during this period of time. The results showed that Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla. Biological differences in cultivated species were the main influencing factors that shaped bacterioplankton communities. Monthly variations and thermal stratification provided little and no contribution to bacterioplankton communities, respectively. CODmn, Chla, and TN were the most appropriate parameters to describe the environmental interpretation of bacterial ordinations, and CODmn was the predominant factor. In addition, the higher similarity between CODmn and Chla, shown by clustering analysis, indicated that the algae-bacteria symbiotic system may have an important role in material circulation in freshwater aquaculture pond water during the peak period of culture. The present study has helped to elucidate the biological characteristics of aquaculture tail water, and enriched the basic data provided by bacterioplankton studies.

Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca²⁺–Mg²⁺–HCO₃⁻–SO₄²⁻ water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

Community Composition and Diversity of Coastal Bacterioplankton Assemblages in Lakes Michigan, Erie, and Huron

The Laurentian Great Lakes, including Lakes Superior, Michigan, Huron, Erie, and Ontario, located in the eastern part of North America are considered the largest of freshwater lakes in the world; however, very little is known about the diversity and distribution of indigenous microbial assemblages within these vast bodies of freshwater systems. Therefore, to delineate the microbial structure and community composition in these aquatic environments, combinations of high-throughput sequencing and fluorescent in situ hybridization (FISH) approaches were utilized to quantitatively characterize the occurrence, diversity, and distribution of bacterioplankton assemblages in six different sites located along the coastal regions of Lakes Michigan, Huron, and Erie. Phylogenetic examination showed a diverse bacterial community belonging to 11 different taxonomic groups. Pyrosequencing results revealed that the majority of the sequences were clustered into four main groups, i.e., Proteobacteria, Bacteriodetes, Actinobacteria, and Cyanobacteria, while fluorescent in situ hybridization also showed the numerical dominance of members of the Gammaproteobacteria and the Cytophaga-Flavobacterium in the six lake sites examined. Overall, the assemblages were shown to be quite diverse in distribution among the lake sites examined, comprising mostly of various heterotrophic populations, with the exception of the Lake Erie-Sandusky Bay site with more than 50% domination by autotrophic Cyanobacteria. This indicates that combinations of factors including water chemistry and various anthropogenic disturbances as well as the lake morphometric characteristics are probably influencing the community structure and diversity of the bacterial assemblages within the systems.

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a result of nutrient importation from the surrounding watershed.

Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

The bacterioplankton community composition's (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao'an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

Within-lake heterogeneity of environmental factors structuring bacterial community composition in Lake Dongting, China

Within-lake heterogeneity of bacterial community composition (BCC) was investigated in the large and shallow regulating Lake Dongting. Samples were collected at 13 sites located in different areas of the lake. PCR-denaturing gradient gel electrophoresis (DGGE) and redundancy analysis (RDA) were used for revealing spatial distribution of BCC and the relationships between BCC and environmental variables. The DGGE banding patterns revealed a remarkable spatial heterogeneity which was closely related to their geographical positions. RDA result demonstrated that TP and TN, as well as Secchi depth, were the three most influential factors, responsible for a major part of the observed variation in BCC. Total bacterial abundances were significantly higher in Eastern Dongting due to high TP and suspended solids. In conclusion, bacterial community diversity in Lake Dongting was mainly shaped by within-lake heterogeneity of nutrient and transparency.

Planctomycetes in lakes: poor or strong competitors for phosphorus?

Experiments were conducted with water samples from two perialpine lakes with differing eutrophication status in order to examine the effects of inorganic-nutrient amendments (nitrogen as NO3(-) or NH4(+) and phosphorus as PO4(3-)) on the dynamics, structure, and composition of Planctomycetes and to test the hypothesis that the community structure of Planctomycetes members and that of the other bacteria (without Planctomycetes, here referred to as bacteria-wP, the most represented groups within the community) would be similarly impacted by nutrient additions. Initial samples were characterized by high total nitrogen-to-total phosphorus ratios (range, 39 to 55), suggesting P rather than N was the limiting nutrient for microbial communities. Consistent with this, P additions stimulated phytoplankton growth and affected the community structure of bacteria-wP but, surprisingly, not that of Planctomycetes. N additions did not significantly affect the community structures of bacteria-wP and Planctomycetes or the Planctomycetes phylotype composition. The estimated generation time of Planctomycetes was 123 h. These findings could suggest that the generally well-accepted statement that bacteria (as a whole) are superior to phytoplankton in the ability to obtain phosphorus under P limitation might actually not hold for Planctomycetes. Planctomycetes might be poor competitors for P that do not respond quickly to the nutrient supply, which may help explain why their abundance is low in aquatic systems. The alternative view that Planctomycetes could be strong competitors for P (storing it) is also discussed. Our findings highlight the need for further studies examining Planctomycetes-phosphorus relationships in aquatic ecosystems.

Impacts of labile organic carbon concentration on organic and inorganic nitrogen utilization by a stream biofilm bacterial community

In aquatic ecosystems, carbon (C) availability strongly influences nitrogen (N) dynamics. One manifestation of this linkage is the importance in the dissolved organic matter (DOM) pool of dissolved organic nitrogen (DON), which can serve as both a C and an N source, yet our knowledge of how specific properties of DOM influence N dynamics are limited. To empirically examine the impact of labile DOM on the responses of bacteria to DON and dissolved inorganic nitrogen (DIN), bacterial abundance and community composition were examined in controlled laboratory microcosms subjected to various combinations of dissolved organic carbon (DOC), DON, and DIN treatments. Bacterial communities that had colonized glass beads incubated in a stream were treated with various glucose concentrations and combinations of inorganic and organic N (derived from algal exudate, bacterial protein, and humic matter). The results revealed a strong influence of C availability on bacterial utilization of DON and DIN, with preferential uptake of DON under low C concentrations. Bacterial DON uptake was affected by the concentration and by its chemical nature (labile versus recalcitrant). Labile organic N sources (algal exudate and bacterial protein) were utilized equally well as DIN as an N source, but this was not the case for the recalcitrant humic matter DON treatment. Clear differences in bacterial community composition among treatments were observed based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes. C, DIN, and DON treatments likely drove changes in bacterial community composition that in turn affected the rates of DON and DIN utilization under various C concentrations.

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships

A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22,669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few 'laws' in ecology.

Composition influences the pathway but not the outcome of the metabolic response of bacterioplankton to resource shifts

Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations.

From structure to function: the ecology of host-associated microbial communities

In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

IS-pro: high-throughput molecular fingerprinting of the intestinal microbiota

The human intestinal microbiota is known to play an important role in human health and disease, and with the advent of novel molecular techniques, disease-specific variations in its composition have been found. However, analysis of the intestinal microbiota has not yet been applicable in large-scale clinical research or routine diagnostics because of the complex and expensive nature of the techniques needed. Here, we describe a new PCR-based profiling technique for high-throughput analysis of the human intestinal microbiota, which we have termed IS-pro. This technique combines bacterial species differentiation by the length of the 16S-23S rDNA interspace region with instant taxonomic classification by phylum-specific fluorescent labeling of PCR primers. We validated IS-pro in silico, in vitro, and in vivo, on human colonic biopsies and feces, and introduced a standardized protocol for data analysis. IS-pro is easy to implement in general clinical microbiological laboratories with access to capillary gel electrophoresis, and the high-throughput nature of the test makes analysis of large numbers of samples feasible. This combination renders IS-pro ideally suited for use in clinical research and routine diagnostics.

Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons

Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon throughout the year were best related to salinity and concentrations of NO (3) (-) , dissolved phosphorus and chlorophyll-a, while changes in BCC between lagoons were best related to salinity and dissolved phosphorus concentration. Salinity has a direct impact on the integrity of the bacterial cell, and it was previously observed that phosphorus is the main limiting nutrient to bacterial growth in these lagoons. Therefore, we conclude that great variations in limnological conditions of coastal lagoons throughout time and space resulted in different BCCs and salinity and nutrient concentration, particularly dissolved phosphorus, are the main limnological factors influencing BCC in these tropical coastal lagoons.

Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics

Yuan Yang Lake (YYL), Taiwan, experiences both winter and typhoon-initiated mixing, and each type of mixing event is characterized by contrasting environmental conditions. Previous work suggested that after typhoon mixing, bacterial communities in YYL reset to a pioneer composition and then follow a predictable trajectory of change until the next typhoon. Our goal was to continue this investigation by observing bacterial community change after a range of mixing intensities, including seasonal winter mixing. We fingerprinted aquatic bacterial communities in the epilimnion and hypolimnion using automated ribosomal intergenic spacer analysis and then assessed community response using multivariate statistics. We found a significant linear relationship between water column stability and the epilimnion to hypolimnion divergences. In comparison to the summer, we found the winter community had a distinct composition and less variation. We divided the bacterial community into population subsets according to abundance (rare, common, or dominant) and occurrence (transient or persistent) and further explored the contribution of these subsets to the overall community patterns. We found that transient taxa did not drive bacterial community patterns following weak typhoon mixing events, but contributed substantially to patterns observed following strong events. Common taxa generally did not follow the community trajectory after weak or strong events. Our results suggest intensity, frequency, and seasonality jointly contribute to aquatic bacterial response to mixing disturbance.

Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial beta diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive beta diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and alpha- and beta-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.

Resource availability influences the diversity of a functional group of heterotrophic soil bacteria

Resource availability is a key factor regulating biodiversity and ecosystem functioning, but the relationship between resource availability and diversity has only been rarely investigated in microbial communities. The aim of this study was to determine how diversity and community structure of a functional group of soil bacteria are influenced by resource concentration. To achieve this, we used soil microcosms to investigate degradation of benzoate, which served as a model compound, by soil bacterial communities. Microcosms were supplied with (13)C-labelled benzoate at four concentrations and RNA-stable isotope probing followed by molecular fingerprinting analysis of 16S rRNA genes was employed to identify bacteria able to assimilate benzoate at different concentrations. The composition of the benzoate degrader community differed at different concentrations and there was a significant decrease in taxa evenness at the highest substrate concentration. Active organisms could be grouped into generalists, occurring at all substrate concentrations, specialists, active at one particular benzoate concentration only, and taxa that were active at either the two lowest or two highest concentrations. The study comprises the first explicit demonstration that resource availability has an effect on the diversity of a functional group of heterotrophic soil bacteria.

Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray

The distribution of nitrogen-fixing microorganisms in the Chesapeake Bay was investigated using fingerprints from a nifH microarray comprised of 706 60-mer oligonucleotide nifH probes representing cultivated organisms and environmental clones from different nifH clusters. Diverse nifH targets, amplified from samples using degenerate nifH primers, were detected in water column and sediment samples collected in April and October, 2001-2002. Total nifH richness and diversity (Simpson's and Shannon indices) were highest at the most riverine, oligohaline North Bay station. In most samples, the highest diversity was in nifH Cluster 3, which includes many anaerobes, while Cluster 1 (alpha-, beta- gamma- Proteobacteria, Cyanobacteria) targets had the greatest microarray signal intensities. In a multidimensional scaling analysis, deep water communities from April and October were similar within each of the sampling sites, while the surface communities had more variability. Diazotroph communities in the water column in the North Bay were distinct from the Mid- and South Bay communities, and there was a gradual change in sediment diazotroph assemblages from the North to the South Bay. Diazotrophic assemblages from the majority of the water column samples from the Mid- and South Bay clustered with the sediment assemblage in Mid-Bay. Dissolved inorganic nitrogen, salinity, dissolved organic carbon and dissolved organic phosphorus had a significant relationship with the diazotrophic bacterioplankton community. Higher diversity in the freshwater end of the system may reflect variability in disturbance rates and environmental conditions such as forms and concentrations of organic matter, nutrients and oxygen.

Nutrients and other abiotic factors affecting bacterial communities in an Ohio River (USA)

Nitrogen and phosphorus additions from anthropogenic sources can alter the nutrient pool of aquatic systems, both through increased nutrient concentrations and changes in stoichiometry. Because bacteria are important in nutrient cycling and aquatic food webs, information about how nutrients affect bacterial communities enhances our understanding of how changes in nutrient concentrations and stoichiometry potentially affect aquatic ecosystems as a whole. In this study, bacterial communities were examined in biofilms from cobbles collected across seasons at three sites along the Mahoning River (Ohio) with differing levels of inorganic nutrient inputs. Members of the alpha-, beta-, and gamma-proteobacteria, the Cytophaga-Flavobacteria cluster, and the Domain Bacteria were enumerated using fluorescent in situ hybridization. Detrended canonical correspondence analysis (DCCA) revealed that stoichiometric ratios, especially the dissolved inorganic nitrogen (DIN):soluble reactive phosphorus (SRP) molar ratio (NO(2)/NO(3) + NH(4):soluble reactive phosphorus), were correlated with abundance of the various bacterial taxa. However, the patterns were complicated by correlations with single nutrient concentrations and seasonal changes in temperature. Seasonal cycles appeared to play an important role in structuring the community, as there were distinct winter communities and temperature was negatively correlated with abundance of both alpha-proteobacteria and Cytophaga-Flavobacteria. However, nutrients and stoichiometry also appeared to affect the community. Numbers of cells hybridizing the Domain Bacteria probe were correlated with the DOC:DIN ratio, the beta-proteobacteria had a negative correlation with soluble reactive phosphorus concentrations and a positive correlation with the DIN:SRP ratio, and the Cytophaga-Flavobacteria had a significant negative partial correlation with the DIN:SRP ratio. Abundances of the alpha- or gamma-proteobacteria were not directly correlated to nutrient concentrations or stoichiometry. It appears that nutrient stoichiometry may be an important factor structuring bacterial communities; however, it is one of many factors, such as temperature, that are interlinked and must be considered together when studying environmental bacteria.

Strong coupling between natural Planctomycetes and changes in the quality of dissolved organic matter in freshwater samples

Dilution-regrowth experiments coupled to fluorescence in situ hybridization were conducted with samples from two humic reservoirs in order to examine how inorganic nutrients (N, P) affect free-living bacterioplankton phylogenetic groups and subsequently the quality of dissolved organic matter (DOM). The experiments were complemented by analyses of the empirical relationships between the targeted bacteria, nutrients, DOM and grazers. The ratio of absorbance of waters (A) at 250 and 365 nm (A(250 nm):A(365 nm)), which has been found to increase with the proportion of small molecules in the DOM pool in other humic waters, was used as an index of DOM quality. When nutrient stimulated bacteria, both the responses of bacterial groups (in the absence of grazers) and the ratio A(250 nm):A(365 nm) were generally different between treatments (+N, +P, +NP), suggesting that in nutrient-poor systems, differences in the type of inorganic nutrient supply will ultimately cause differences in DOM quality. The ratio A(250 nm),:A(365 nm) peaked in the +N treatments where members of the Planctomycetes (PLA) were the most stimulated group, and across treatments, PLA best explained (positive relationship) variations in this ratio. Consistent with this, the in situ data showed that the removal of the negative effects of flagellates on PLA yielded the highest R(2) in attempts to use bacterial groups to explain variations in A(250 nm):A(365 nm). These findings provide lines of evidence, not previously demonstrated in natural waters, that Planctomycetes may be an important factor changing the DOM quality, particularly in nutrient-poor systems when supplied with inorganic N.

High predictability of the seasonal dynamics of a species-like Polynucleobacter population in a freshwater lake

One of the key questions in microbial ecology is if seasonal patterns of bacterial community composition (BCC) observed in one year repeat in the following years. We have investigated if the recorded annual dynamics of a species-like Polynucleobacter (subcluster PnecB) population allowed the prediction of the population dynamics in another year. The abundance of PnecB bacteria in the pelagic of temperate Lake Mondsee was investigated by fluorescence in situ hybridization (FISH) over three consecutive years. The PnecB bacteria formed a persistent population, and were present in the entire water body of the lake. Two of the three investigated years differed strongly in summer temperatures and precipitation, which resulted in markedly different growth conditions. But despite of these different environmental conditions, the PnecB population demonstrated remarkably similar seasonal dynamics in the three investigated years. Water temperature was the best predictor of the population dynamics during the first half of the annual cycles. Statistical analysis also indicated influences of phytoplankton and metazooplankton successions on the PnecB population dynamics. Furthermore, 65 lakes and ponds were investigated for the presence of PnecB bacteria. They were detected in the majority (78%) of circum-neutral and alkaline freshwater habitats, but not in any investigated acidic or saline habitat.

Dissolved organic matter concentration and quality influences upon structure and function of freshwater microbial communities

Past studies have suggested that the concentration and quality of dissolved organic matter (DOM) may influence microbial community structure. In this study, we cross-inoculated the bacterial communities from two streams and a dystrophic lake that varied in DOM concentration and chemistry, to yield nine fully crossed treatments. We measured dissolved organic carbon (DOC) concentration and heterotrophic microbial community productivity throughout a 72-h incubation period, characterized DOM quality by molecular weight, and determined microbial community structure at the initial and final time points. Our results indicate that all bacterial inoculate sources had similar effects upon DOC concentration and DOM quality, regardless of the DOM source. These effects included an overall decrease in DOM M (W) and an initial period of DOC concentration variability between 0-24h. In contrast, microbial communities and their metabolic rates converged to profiles that reflected the DOM source upon which they were growing, regardless of the initial bacterial inoculation. The one exception was that the bacterial community from the low-concentration and low-molecular-weight DOM source exhibited a greater denaturing gradient gel electrophoresis (DGGE) band richness when grown in its own DOM source than when grown in the highest concentration and molecular weight DOM source. This treatment also exhibited a higher rate of productivity. In general, our data suggest that microbial communities are selected by the DOM sources to which they are exposed. A microbial community will utilize the low-molecular-weight (or labile) DOM sources as well as parts of the high-molecular-weight (refractory) DOM, until a community develops that can efficiently metabolize the more abundant high-molecular-weight source. This experiment examines some of the complex interactions between microbial community selection and the combined factors of DOM quality and concentration. Our data suggest that the roles of aerobic aquatic heterotrophic bacteria in carbon cycling, as well as the importance of high-molecular-weight DOM as a carbon source, may be more complex than is conventionally recognized.

Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure

A previous multiyear study observed correlations between bacterioplankton community composition (BCC) and abundance and the dynamics of phytoplankton populations and bacterivorous grazers in a humic lake. These observations generated hypotheses about the importance of trophic interactions (both top-down and bottom-up) for structuring bacterial communities in this lake, which were tested using two multifactorial food web manipulation experiments that separately manipulated the intensity of grazing and the composition of the phytoplankton community. Our results, combined with field observations, suggest that a hierarchy of drivers structures bacterial communities in this lake. While other studies have noted links between aggregate measures of phytoplankton and bacterioplankton communities, we demonstrate here correlations between succession of phytoplankton assemblages and BCC as assessed by automated ribosomal intergenic spacer analysis (ARISA). We used a novel approach linking community ARISA data to phylogenetic assignments from sequence analysis of 16S rRNA gene clone libraries to examine the responses of specific bacterial phylotypes to the experimental manipulations. The synchronous dynamics of these populations suggests that primary producers may mediate BCC and diversity through labile organic matter production, which evolves in quality and quantity during phytoplankton succession. Superimposed on this resource-mediated control of BCC are brief periods of intense bacterivory that impact bacterial abundance and composition.

Influence of dissolved organic matter source on lake bacterioplankton structure and function--implications for seasonal dynamics of community composition

It has been suggested that autochthonous (internally produced) organic carbon and allochthonous (externally produced) organic carbon are utilized by phylogenetically different bacterioplankton. We examined the relationship between the source of organic matter and the structure and function of lake bacterial communities. Differences and seasonal changes in bacterial community composition in two lakes differing in their source of organic matter were followed in relation to environmental variables. We also performed batch culture experiments with amendments of various organic substrates, namely fulvic acids, leachates from algae, and birch and maple leaves. Differences in bacterial community composition between the lakes, analysed by terminal restriction fragment length polymorphism, correlated with variables related to the relative loading of autochthonous and allochthonous carbon (water colour, dissolved organic carbon, nutrients, and pH). Seasonal changes correlated with temperature, chlorophyll and dissolved organic carbon in both lakes. The substrate amendments led to differences in both structure and function, i.e. production, respiration and growth yield, of the bacterial community. In conclusion, our results suggest that the source of organic matter influences community composition both within and among lakes and that there may be a coupling between the structure and function of the bacterial community.

Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments

The effect of nutrient resources (N and P enrichment) and of different grazing communities on the prokaryotic community composition (PCC) was investigated in two freshwater ecosystems: Sep reservoir (oligomesotrophic) and lake Aydat (eutrophic). An experimental approach using microcosms was chosen, that allowed control of both predation levels, by size fractionation of predators, and resources, by nutrient amendments. Changes in PCC were monitored by fluorescent in situ hybridization (FISH) and terminal-restriction fragment length polymorphism (T-RFLP). The main mortality agents were (i) heterotrophic nanoflagellates and virus-like particles in Aydat and (ii) cladocerans in Sep. All the nutritional elements assayed (N-NO3, P-PO4 and N-NH4) together with prokaryotic production (PP) always accounted for a significant part of the variations in PCC. Overall, prokaryotic diversity was mainly explained by resources in Sep, by a comparable contribution of resources and mortality factors in lake Aydat and, to a lesser extent, by the combined action of both.

Effect of nutrient loading on bacterioplankton community composition in lake mesocosms

Changes in bacterioplankton community composition were followed in mesocosms set up in the littoral of Lake Vesijärvi, southern Finland, over two summers. Increasing nitrogen and phosphorus concentrations in the mesocosms represented different trophic states, from mesotrophic to hypertrophic. In 1998, the mesocosms were in a turbid state with a high biomass of phytoplankton, whereas in 1999, macrophytes proliferated and a clear-water state prevailed. The bacterial communities in the mesocosms also developed differently, as shown by denaturing gradient gel electrophoresis profiling of partial 16S rRNA gene fragments and by nonmetric multidimensional scaling analysis. In 1998, nutrient treatments affected the diversity and clustering of bacterial communities strongly, but in 1999, the bacterial communities were less diversified and not clearly affected by treatments. Canonical correspondence analysis indicated that bacterioplankton communities in the mesocosms were influenced by environmental physicochemical variables linked to the increasing level of eutrophication. Nitrogen concentration correlated directly with the bacterioplankton composition. In addition, the high nutrient levels had indirect effects through changes in the biomass and composition of phyto- and zooplankton. Sequencing analysis showed that the dominant bacterial divisions remained the same, but the dominant phylotypes changed during the 2-year period. The occurrence of Verrucomicrobia correlated with more eutrophic conditions, whereas the occurrence of Actinobacteria correlated with less eutrophic conditions.

Molecular approaches to the assessment of biodiversity in aquatic microbial communities

For the past 20 years, the increased development and routine application of molecular-based techniques has made it possible to carry out detailed evaluations of the biodiversity of aquatic microbial communities. It also offers great opportunities for finding out how this parameter responds to various environmental stresses. Most of these approaches involve an initial PCR amplification of a target, which is generally located within the ribosomal operon. The amplification is achieved by means of primers that are specific to the organisms of interest. The second step involves detecting sequence variations in the PCR fragments either by a cloning/sequencing analysis, which provides a complete characterization of the fragments, or by an electrophoretic analysis, which provides a visual separation of the mixture of fragments according to sequence polymorphism (denaturing or temperature gradient gel electrophoresis, single strand conformation polymorphism) or length polymorphism (terminal-restriction fragment length polymorphism, automated ribosomal intergenic spacer analysis). Other non-PCR-based methods are also commonly used, such as fluorescence in-situ hybridization and DNA re-association analysis. Depending on the technique used, the information gained can be quite different. Moreover, some of these analyses may be rather onerous in terms of time and money, and so not always suitable for screening large numbers of samples. The most widely used techniques are discussed in this paper to illustrate the principles, advantages and shortcomings of each of them. Finally, we will conclude by evaluating the techniques and discussing some emerging molecular techniques, such as real-time PCR and the microarray technique.

Geographic and environmental sources of variation in lake bacterial community composition

This study used a genetic fingerprinting technique (automated ribosomal intergenic spacer analysis [ARISA]) to characterize microbial communities from a culture-independent perspective and to identify those environmental factors that influence the diversity of bacterial assemblages in Wisconsin lakes. The relationships between bacterial community composition and 11 environmental variables for a suite of 30 lakes from northern and southern Wisconsin were explored by canonical correspondence analysis (CCA). In addition, the study assessed the influences of ARISA fragment detection threshold (sensitivity) and the quantitative, semiquantitative, and binary (presence-absence) use of ARISA data. It was determined that the sensitivity of ARISA was influential only when presence-absence-transformed data were used. The outcomes of analyses depended somewhat on the data transformation applied to ARISA data, but there were some features common to all of the CCA models. These commonalities indicated that differences in bacterial communities were best explained by regional (i.e., northern versus southern Wisconsin lakes) and landscape level (i.e., seepage lakes versus drainage lakes) factors. ARISA profiles from May samples were consistently different from those collected in other months. In addition, communities varied along gradients of pH and water clarity (Secchi depth) both within and among regions. The results demonstrate that environmental, temporal, regional, and landscape level features interact to determine the makeup of bacterial assemblages in northern temperate lakes.

Effects of decreased resource availability, protozoan grazing and viral impact on a structure of bacterioplankton assemblage in a canyon-shaped reservoir

We conducted a transplant experiment to elucidate the effects of different levels of grazing pressure, nutrient availability, especially phosphorus, and the impact of viruses on the changes in the structure of bacterioplankton assemblage in a meso-eutrophic reservoir. A sample taken from the nutrient-rich inflow part of the reservoir was size-fractionated and incubated in dialysis bags in both inflow and dam area. The structure of bacterial assemblage was examined by fluorescence in situ hybridization using oligonucleotide probes with different levels of specificity. In terms of the relative proportions of different bacterial groups, we found very few significant changes in the bacterioplankton composition after transplanting the treatments to the nutrient-poor dam area. However, we observed marked shifts in morphology and biomass towards the development of filaments, flocs and "vibrio-like" morphotypes of selected probe-defined groups of bacteria induced by increased grazing pressure. Despite the very high abundances of viruses in all the treatments, their effects on bacterioplankton were rather negligible.

Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities

ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the facade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxic basin in the Mediterranean Sea were analyzed with the three primer sets. The number of peaks in the ARISA profiles, the range of peak size (width of the profile), and the reproducibility of results were used as indices to evaluate the efficiency of the three primer sets. The overall data showed that ITSF and ITSReub generated the most informative (in term of peak number) and reproducible profiles and yielded a wider range of spacer sizes (134 to 1,387) than the other primer sets, which were limited in detecting long fragments. The minimum amount of DNA template and sensitivity in detection of minor DNA populations were evaluated with artificial mixtures of defined bacterial species. ITSF and ITSReub amplified all the bacteria at DNA template concentrations from 280 to 0.14 ng microl(-1), while the other primer sets failed to detect the spacers of one or more bacterial strains. Although the primer set consisting of ITSF and ITSReub and that of S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 showed similar sensitivities for the DNA of Allorhizobium undicula mixed with the DNA of other species, the S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 primer set failed to detect the DNA of Pseudomonas stutzeri.

Annual patterns in bacterioplankton community variability in a humic lake

Bacterioplankton community composition (BCC) was monitored in a shallow humic lake in northern Wisconsin, USA, over 3 years using automated ribosomal intergenic spacer analysis (ARISA). Comparison of ARISA profiles of bacterial communities over time indicated that BCC was highly variable on a seasonal and annual scale. Nonmetric multidimensional scaling (MDS) analysis indicated little similarity in BCC from year to year. Nevertheless, annual patterns in bacterioplankton community diversity were observed. Trends in bacterioplankton community diversity were correlated to annual patterns in community succession observed for phytoplankton and zooplankton populations, consistent with the notion that food web interactions affect bacterioplankton community structure in this humic lake. Bacterioplankton communities experience a dramatic drop in richness and abundance each year in early summer, concurrent with an increase in the abundance of both mixotrophic and heterotrophic flagellates. A second drop in richness, but not abundance, is observed each year in late summer, coinciding with an intense bloom of the nonphagotrophic dinoflagellate Peridinium limbatum. A relationship between bacterial community composition, size, and abundance and the population dynamics of Daphnia was also observed. The noted synchrony between these major population and species shifts suggests that linkages across trophic levels play a role in determining the annual time course of events for the microbial and metazoan components of the plankton.

Seasonal dynamics of phytoplankton and planktonic protozoan communities in a northern temperate humic lake: diversity in a dinoflagellate dominated system

Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups' diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4', 6'-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 x 10(6) cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day(-1) and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon-Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion followed very similar seasonal patterns in this lake, supporting the hypothesis that in freshwaters, diversity patterns of these groups are linked.

Impact of resource availability on species composition and diversity in freshwater nematodes

This study investigates the long-term effects of resource availability in a freshwater nematode community. We carried out a mesocosm experiment where natural nematode communities were exposed to nutrient addition/depletion over 2 years. Compared to the nutrient-addition treatment, species richness and diversity were strongly reduced upon nutrient depletion. The functional group of bacterial feeders particularly suffered severely from nutrient depletion. The decrease in diversity of bacterial feeders was linked to reduced species richness and diversity of large omnivorous species, as predicted by trophic-dynamic models. Tilman's (1976) statement, that under low nutrient levels the best competitor dominates the system, was applicable in our system. Upon nutrient depletion, resource depletion led to a monoculture of 1 small bacterial feeder, but even after 2 years of resource depletion, up to 16 species still coexisted. Our results provide strong evidence that freshwater nematode systems can be regulated by nutrient competition.

Microbial communities and their interactions in soil and rhizosphere ecosystems

Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.