Freshwater Bacterial Communities Research Articles

Functional Diversity of Bacterioplankton in Three North Florida Freshwater Lakes over an Annual Cycle

The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.

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.

Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake

We examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic Lake Mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). Microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (BCC) change or community activity response (assessed via alkaline phosphatase activity, APA) relative to the controls during any season. Treatments enriched with carbon- and nitrogen-containing compounds resulted in a dramatic BCC change and a large APA increase in the autumn and spring seasons, but only treatments receiving carbon, nitrogen and phosphorus (CNP) exhibited similar responses in the summer season. Despite the fact that the amendments created similar CNP concentration conditions across seasons, the BCC following amendment greatly varied among seasons. 16S rRNA gene sequence analysis indicated that many common freshwater bacterial lineages from the Alpha- and Betaproteobacteria class and Bacteroidetes phylum were favoured following nutrient (CNP) addition, but individual taxa were generally not favoured across all seasons. Targeted quantitative PCR analysis revealed that the abundance of the Actinobacteria acIB1 cluster decreased in all microcosms during all three seasons, while the Flavobacterium aquatile (spring) and ME-B0 (summer) clusters of Bacteroidetes increased following CNP addition. These results suggest a particular bacterial group is not universally favoured by increased nutrient loads to a lake; therefore, efforts to predict which bacteria are involved in nutrient cycling during these periods must take into account the seasonality of freshwater bacterial communities.

Function-specific response to depletion of microbial diversity

Recent meta-analyses suggest that ecosystem functioning increases with biodiversity, but contradictory results have been presented for some microbial functions. Moreover, observations of only one function underestimate the functional role of diversity because of species-specific trade-offs in the ability to carry out different functions. We examined multiple functions in batch cultures of natural freshwater bacterial communities with different richness, achieved by a dilution-to-extinction approach. Community composition was assessed by molecular fingerprinting of 16S rRNA and chitinase genes, representing the total community and a trait characteristic for a functional group, respectively. Richness was positively related to abundance and biomass, negatively correlated to cell volumes and unrelated to maximum intrinsic growth rate. The response of chitin and cellulose degradation rates depended on the presence of a single phylotype. We suggest that species identity and community composition rather than richness matters for specific microbial processes.

Species‐sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics

Long distance atmospheric transport of bacterial cells is often implied as a driver of the apparent cosmopolitan distribution of bacterial taxa. Surprisingly, efforts to measure immigration in bacterial communities are rare. An 8-week time series of within-lake bacterial community composition and atmospheric deposition rates and composition were used to estimate the influence of immigration on bacterial community dynamics in two north temperate lakes. Characterization of bacterial community dynamics using automated ribosomal intergenic spacer analysis suggested moderate overlap in composition between the lakes and atmospherically deposited cells. However, taxa that appeared to be delivered by atmospheric deposition had a relatively minor influence on lake bacterial community dynamics. The weak influence of immigrating bacterial taxa suggests that a species-sorting concept best describes aquatic bacterial metacommunity dynamics.

Potential for atmospheric deposition of bacteria to influence bacterioplankton communities

Biogeographic patterns in microbial communities are an exciting but controversial topic in microbial ecology. Advances in theory pertaining to assembly of microbial communities have made strong assumptions about dispersal of bacteria without exploration. For this reason, we investigated rates of atmospheric bacterial deposition and compared the taxonomic composition of bacteria in rain with that of common freshwater bacterial communities. Our findings suggest that it is not appropriate to take for granted that atmospheric deposition of bacteria is a significant vector of immigration to freshwater ecosystems.

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.

A multiphasic characterization of the impact of the herbicide acetochlor on freshwater bacterial communities

Acetochlor is the third most frequently detected herbicide in natural waters; however, it is unknown if exposure to environmentally relevant concentrations of acetochlor will impact bacterial community structure and function. This study examined the impact of acetochlor on freshwater heterotrophic bacteria number, and community structure and function using direct counting, community level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) analysis. Acetochlor concentration did not appear to correlate with the number of total (P=0.69) and viable (P=0.80) bacteria, even at concentrations up to 500 microg l(-1). However, CLPP indicated that acetochlor increased functional diversity as shown by (i) an increase in the number of carbon sources utilized by the microbial community, relative to nonexposed controls and (ii) increased functional evenness within the heterotrophic bacterial community. Conversely, DGGE fingerprints suggested that exposure to acetochlor generally decreased the community complexity, as the average number of DGGE bands in most treatments was significantly less than in the control treatment. Cluster analysis of DGGE fingerprints revealed three distinct, dose-dependent clusters (i) communities exposed to 0, 1 and 5 microg l(-1); (ii) 50 and 100 microg l(-1) and (iii) 500 microg l(-1), indicating a relationship between acetochlor concentration bacterial community changes. This study indicated that while exposure to environmentally relevant concentrations of acetochlor resulted in no significant impact to the number of freshwater bacteria, impacts to the function and structure of the community were revealed by adopting a multiphasic approach.

Quantification of the Filterability of Freshwater Bacteria through 0.45, 0.22, and 0.1 μm Pore Size Filters and Shape-Dependent Enrichment of Filterable Bacterial Communities

Micro-filtration is a standard process for sterilization in scientific research, medical, and industrial applications, and to remove particles in drinking water or wastewater treatment. It is generally assumed, and confirmed by quantifying filtration efficiency by plating, that filters with a 0.1-0.45 microm pore size can retain bacteria. In contrast to this assumption, we have regularly observed the passage of a significant fraction of natural freshwater bacterial communities through 0.45, 0.22, and 0.1 microm pore size filters. Flow cytometry and a regrowth assay were applied in the present study to quantify and cultivate filterable bacteria. Here we show for the first time a systematic quantification of their filterability, especially their ability to pass through 0.1 microm pore size filters. The filtered bacteria were subsequently able to grow on natural assimilable organic carbon (AOC) with specific growth rates up to 0.47 h(-1). We were able to enrich bacteria communities that pass preferentially through all three pore size filters at significantly increased percentages using successive filtration-regrowth cycles. In all instances, the dominant microbial populations comprised slender spirillum-shaped Hylemonella gracilis strains, suggesting shape-dependent selection during the filtration process. This quantification of the omnipresence of microfilterable bacterial in natural freshwater and their regrowth characteristics demand a change in the sterile filtration practice used in industrial and engineering applications as well as scientific research.

Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 47:1-10 (2007) - doi:10.3354/ame047001 Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities Katalin É. Szabó1,2, Paul O. B. Itor1, Stefan Bertilsson1, Lars Tranvik1, Alexander Eiler1,* 1Department of Ecology and Evolution, Limnology, Uppsala University, Husargatan 3 Box 573, Uppsala 75237, Sweden 2Hungarian Danube Research Station of the Hungarian Academy of Sciences, Jávorka Sándor utca 14, Göd 2131, Hungary *Corresponding author. Email: alexander.eiler@ebc.uu.se ABSTRACT: Lakewater microcosms were inoculated with freshwater bacterioplankton, to determine how the elimination of less abundant populations affects the structure and basic functional features (growth) of microbial communities. The number of bacteria added to individual microcosms varied from <1 to 2.6 × 107 cells. Cultures amended with 11 mg C l–1 of either isolated humic substances or phenol, as well as unamended controls, were studied in parallel. All cultures inoculated with 260 cells or more showed vigorous growth, whereas an inoculum size of 2.6 to 26 cells resulted in growth in the control and humic enrichment cultures only. All cultures were harvested at steady state within 14 d of inoculation. The biomass yield was only slightly affected by the dilution factor. The catechol 2,3-dioxygenase gene (encoding the enzyme responsible for starting the meta pathway of aromatic compound degradation) was detected in all phenol and in the least diluted humic enrichment cultures. Dominant members of the emerging bacterial communities were detected by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA genes. The number of detected community members was much higher in the humic treatment than in the phenol and control treatments. Based on the T-RFLP data, dilution of the inoculum significantly affected the resulting community composition (p < 0.0001). Rare, opportunistic populations were apparently able to exploit the humic enrichment cultures. Phenol appeared to be detrimental to the most abundant members of the original inoculum, but promoted the growth of relatively rare species carrying the catechol 2,3-dioxygenase gene. Thus, community functioning following an environmental perturbation can depend on the presence of rare as well as abundant species. Bacterioplankton · Dilution · 16S rRNA · T-RFLP · Catechol 2,3-dioxygenase · Bacterial growth potential Full text in pdf format NextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 47, No. 1. Online publication date: April 03, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.

Interannual dynamics and phenology of bacterial communities in a eutrophic lake

We investigated patterns of intra‐ and interannual change in pelagic bacterial community composition (BCC, assessed using automated ribosomal intergenic spacer analysis) over six years in eutrophic Lake Mendota, Wisconsin. A regular phenology was repeated across years, implying that freshwater bacterial communities are more predictable in their dynamics than previously thought. Seasonal events, such as water column mixing and trends in water temperature, were most strongly related to BCC variation. Communities became progressively less similar across years between the months of May and September, when the lake was thermally stratified. Dissolved oxygen and nitrate + nitrite concentrations were highly correlated to BCC change within and across seasons. The relationship between BCC and seasonal drivers suggests that trajectories of community change observed over long time series will reflect large‐scale climate variation.

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

In the article ‘Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes’ (Eiler and Bertilsson, 2004), the wrong GenBank accession numbers were cited in the Experimental procedures section, page 1240. The correct text is as follows: All sequences were deposited in GenBank under accession numbers AY496976–AY497004 and AY509261–AY509524. We apologize for this error.

Protein Extraction and Fingerprinting Optimization of Bacterial Communities in Natural Environment

Recent development in molecular approaches allows access to genetic structure and diversity of indigenous microbial communities. In contrast, the functional analysis of microorganisms in their environment is still hampered by methodological limitations. Analysis of total proteins expressed at the whole community level (metaproteome) has been proposed to characterize the functional structure of microbial communities in their environment. However, developments are still required to perform such analysis. Our aim was to optimize methods to extract and characterize metaproteome of indigenous microbial communities. Experiments were first conducted in monoxenic bacterial cultures, and various methods were examined to define a procedure of protein extraction ensuring an efficient recovery regardless of the taxonomic affiliation of the cells. These developments were next applied to characterize the metaproteome from indigenous bacterial communities in freshwater samples. Bacterial cells were recovered from water using a high-speed density gradient centrifugation method before protein extraction and fingerprinting. The reactivity and sensitivity of this metaproteomic approach were tested by analyzing the variations of protein fingerprints according to perturbations (cadmium or mercury contamination). The genetic structure of the corresponding communities was also characterized by automated ribosomal spacer analysis (ARISA) DNA fingerprinting. Both protein and DNA fingerprints were statistically analyzed. Results obtained showed that the method developed for protein recovery and fingerprinting was efficient, sensitive, and reproducible. Both the functional and genetic structures of the freshwater bacterial community were complex and varied with perturbations. These variations occurred at both population and protein expression levels and were specific to the perturbation applied.

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.

Changes in freshwater bacterial community composition during measurements of microbial and community respiration

The respiration rates of a pelagic community and of its microbial fraction (< 1.2 μm) were measured at two depths in the oxic layer of a meromictic alpine lake (Cadagno, Switzerland) using the oxygen technique. The duration of the incubations were 12, 24 and 55 h. Bacterioplankton abundance (DAPI counts) and composition (whole cell hybridization using 11 group-specific rRNA-targeted oligonucleotide probes) were measured during the incubations. Respiration generally increased with time, especially in the microbial fraction, or remained similar. This result was not always consistent with changes in bacterial abundance and cell volume. The composition of the community also changed during the incubations. The abundance of β-Proteobacteria increased during the course of all the experiments. These results extend the previous conclusions drawn in marine environments to fresh waters and demonstrate that, in addition to changes in bacterial abundance, cell volume and biomass, changes in the taxonomic composition of the bacterial community can occur during discrete incubations of freshwater planktonic communities.

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition.

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4-6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (delta BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48-72 h and A BCC showed that delta BCC was positively and tightly correlated (r2 = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. bacterial community composition

Effects of Resources and Trophic Interactions on Freshwater Bacterioplankton Diversity

In a study of bacterioplankton in an oligotrophic lake in northern Wisconsin, a community fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used to determine the effect of resources and trophic interactions on bacterioplankton diversity. Inorganic nitrogen and phosphorus (NP), carbon in the form of glucose (G) or dissolved organic matter extracted from peat (DOM), and carbon and NP in combination were added to two types of experimental systems. Ten-liter mesocosms contained all components of the original aquatic community except for large zooplankton. One-liter dilution cultures were prepared so that the effects of grazers and phytoplankton were removed. During a 3-day incubation, bacterial production showed the greatest response to the carbon plus NP treatment in both experimental systems, but bacterial diversity was strikingly different between them. In the mesocosms, the number of ARISA-PCR fragments averaged 41 per profile, whereas the dilution culture communities were highly reduced in complexity, dominated in most cases by a single PCR fragment. Further analysis of the mesocosm data suggested that whereas the NPDOM addition caused the greatest aggregate bacterial growth response, the addition of NP alone caused the largest shifts in community composition. These results suggest that the measurement of aggregate responses, such as bacterial production, alone in studies of freshwater bacterial communities may mask the effects of resources on bacterioplankton.

Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.

An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.

Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes

The bacterial communities of seven freshwater lakes in the Adirondack Mountains of New York state were examined using culture‐independent methods. β‐Proteobacteria 16S rRNA sequences were recovered from all seven lakes and their presence was confirmed by direct DNA hybridization The results are consistent with phylogenetic and in situ hybridization‐based studies in other freshwater environments, but are significantly different than the results of marine oceanic studies, where β‐Proteobacteria are noticeably absent. This relationship between evolutionary history and environmental distribution is striking, since these phylogenetic clades have not been correlated with consistent physiological features or biochemical capabilities, and there is no a priori reason to expect differences in phylogenetic composition between the environments. In contrast, freshwater relatives to marine phylogenetic clusters, in particular the SAR 11 cluster of the α‐Proteobacteria, were identified. The data imply an underlying physiological distinction between the β‐ and other Proteobacteria groups and potentially an important difference between the composition of bacterial communities in marine and freshwater environments.

Response of a freshwater bacterial community to mercury contamination (HgCl2 and CH3HgCl) in a controlled system

An experimental study was made on the effects of inorganic mercury (HgCl2) and methylmercury (CH3HgCl) on freshwater aerobic heterotrophic bacterial population. The experimental system was based on two-compartment biotopes: natural sediment, from the Garonne River, and dechlorinated tap water. The response of bacterial communities to mercury additions (to the water column) was monitored by determining total Hg in water and enumerating the total number of bacteria and the evolution of the mercury resistant community. Isolation was carried out by plate count method. Enumeration of mercury resistant strains was made with a general medium (Iron-Tryp-tone agar) amended with 10 μg Hg/ml of HgCl2. The response to 2 μg Hg/L (HgCl2) was fast approximately 50% of the maximum percentage of mercury resistant bacteria being reached after one hour (21.7% after 17 h exposure). Spikes of CH3HgCl (2 μg Hg/L) in the water column caused an initial inhibition of growth of Hg-resistant and sensitive bacteria followed by a complete recovery of the background microbial population after 84 h. Seven mercury resistant bacterial strains were isolated from the experimental systems and each of them was checked for HgCl2 and CH3HgCl transformation. All were able to volatilize HgCl2 by producing elemental mercury, but none was able to degrade methylmercury. Additions of different concentrations of HgCl2 (0.02 μg Hg/L to 2 μg Hg/L) to the water column caused a proportional increase in the percentage of mercury-resistant bacteria. Low concentrations (<0.6 μg Hg/L) of CH3HgCl also induced the Hg-resistant community, whereas 2 μg Hg/L of CH3HgCl inhibited the growth of both Hg-sensitive and Hg-resistant heterotrophic bacteria.