Composition Of Bacterial Assemblages Research Articles

Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures

Abstract. Microbial communities are recognized as major drivers of the biogeochemical processes in the oceans. However, the genetic diversity and composition of those communities is poorly understood. The aim of this study is to investigate the composition of bacterial assemblages in three different water layer habitats: surface (2–20 m), deep chlorophyll maximum (DCM; 28–90 m), and deep (100–4600 m) at nine stations along the eastern Atlantic Ocean from 42.8° N to 23.7° S. The sampling of three discrete, predefined habitat types from different depths, Longhurstian provinces, and geographical locations allowed us to investigate whether marine bacterial assemblages show spatial variation and to determine if the observed spatial variation is influenced by current environmental conditions, historical/geographical contingencies, or both. The PCR amplicons of the V6 region of the 16S rRNA from 16 microbial assemblages were pyrosequenced, generating a total of 352 029 sequences; after quality filtering and processing, 257 260 sequences were clustered into 2871 normalized operational taxonomic units (OTU) using a definition of 97% sequence identity. Community ecology statistical analyses demonstrate that the eastern Atlantic Ocean bacterial assemblages are vertically stratified and associated with water layers characterized by unique environmental signals (e.g., temperature, salinity, and nutrients). Genetic compositions of bacterial assemblages from the same water layer are more similar to each other than to assemblages from different water layers. The observed clustering of samples by water layer allows us to conclude that contemporary environments are influencing the observed biogeographic patterns. Moreover, the implementation of a novel Bayesian inference approach that allows a more efficient and explicit use of all the OTU abundance data shows a distance effect suggesting the influence of historical contingencies on the composition of bacterial assemblages. Surface bacterial communities displayed a general congruency with the ecological provinces as defined by Longhurst with modest exceptions usually associated with unique hydrographic and biogeochemical features. Collectively, our findings suggest that vertical (habitat) and latitudinal (distance) biogeographic signatures are present and that both environmental parameters and ecological provinces drive the composition of bacterial assemblages in the eastern Atlantic Ocean.

High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments.

Bacterial water quality and network hydraulic characteristics: a field study of a small, looped water distribution system using culture-independent molecular methods

To determine the spatial and temporal variability in the abundance, structure and composition of planktonic bacterial assemblages sampled from a small, looped water distribution system and to interpret results with respect to hydraulic conditions. Water samples were collected from five sampling points, twice a day at 06:00 h and 09:00 h on a Monday (following low weekend demand) and a Wednesday (higher midweek demand). All samples were fully compliant with current regulated parameter standards. This study did not show obvious changes in bacterial abundance (DAPI count) or community structure Denaturing gradient gel electrophoresis analysis with respect to sample site and hence to water age; however, the study did show temporal variability with respect to both sampling day and sample times. Data suggests that variations in the bacterial assemblages may be associated with the local system hydraulics: the bacterial composition and numbers, over short durations, are governed by the interaction of the bulk water and the biofilm influenced by the hydraulic conditions. This study demonstrates general stability in bacterial abundance, community structure and composition within the system studied. Trends and patterns supporting the transfer of idealized understanding to the real world were evident. Ultimately, such work will help to safeguard potable water quality, fundamental to public health.

Minimal and dynamic bacterial diversity in grease trap revealed by molecular analysis

Grease traps are widely used in restaurants and food industry to reduce oil and grease discharge into public sewers. Although enhancement of grease trap performance often use microbial biomasses, yet little is known about the natural microbial assemblages that colonize and settle inside grease trap and may be used for grease degradation processes. This study evaluates the diversity and composition of bacterial assemblages colonizing the greasy layer in a public restaurant grease trap. Using a culture-independent approach, the dynamic of these assemblages have been studied before (Monday) and after (Friday) a week of restaurant activity. Bacterial diversity was quite low: 16S rRNA gene clones were affiliated with only three phyla, of which Firmicutes, Proteobacteria, and Bacteroidetes were represented in all libraries. Anaerobes, facultative anaerobes and microaerophilic taxa dominated the clone libraries. Sequences similar to Selenomonas spp., Lactobacillus spp. and Dialister spp. represented respectively 23.2%, 13.0% and 8.7% of the two libraries together. The Monday and Friday libraries were quite similar (70% similarity), however diversity indices showed that bacterial diversity seemed greater at the end of the week. Several taxa were only detected on Friday, including Acetobacter spp., Gulbenkiania spp., Aeromonas spp., Petrobacter sp., Escherichia sp. and Desulfovibrio sp. The description of metabolic capabilities of surveyed species is beyond the range of the clone libraries, however several taxa were fermenting or anaerobic-respiring organisms which could be likely involved in lipid degradation.

Short‐term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution

SummaryThe changes caused by diesel oil pollution in the metabolically active bacterioplankton from an oligotrophic coastal location were analysed in laboratory microcosms (44 l) using 16S ribosomal RNA (16S rRNA) as molecular marker. The aim was to simulate typical hydrocarbon pollution events in a coastal area exploited for seasonal touristic activities. The experiment consisted in addition of low amounts of diesel oil without nutrients to seawater collected at different times (winter and summer). Bacterial diversity was analysed by terminal‐restriction fragment length polymorphism (T‐RFLP) profiling of 16S rRNAs after reverse transcription polymerase chain reaction (RT‐PCR), and by generation of 16S rRNA clone libraries in control and diesel‐polluted microcosms. Diesel addition caused a twofold increase in prokaryotic numbers in comparison with controls at the end of the experiment, both in winter and summer microcosms. Bacterioplankton composition, determined by 16S rRNA T‐RFLP data, changed rapidly (within 17 h) in response to treatment. The resulting communities were different in microcosms with water collected in summer and winter. A reduction in diversity (Shannon index, calculated on the basis of T‐RFLP data) was observed only in summer microcosms. This was due to the rapid increase of phylotypes affiliated to the Oceanospirillaceae, not observed in winter microcosms. After diesel treatment there was a reduction in the number of phylotypes related to SAR11, SAR86 and picocyanobacteria, while phylotypes of the Roseobacter clade, and the OMG group seemed to be favoured. Our results show that diesel pollution alone caused profound effects on the bacterioplankton of oligotrophic seawater, and explained many of the differences in diversity reported previously in pristine and polluted sites in this coastal area.

Ricerche sulla biodiversità delle comunità batteriche in tre laghi antartici

The bacterial diversity in three Antarctic lakes located at Crater Cirque (CC), Inexpressible Island (INI) and Luther Peak (LH) in the Victoria Land was investigated by a combination of culture-dependent and culture-independent techniques. The in situ abundance of different bacterial groups was determined by fluorescent in situ hybridization (FISH), while bacterial diversity among the cultivable microflora was investigated by culturing and genetic fingerprinting. Differences in the composition of bacterial assemblages were observed among the lakes investigated, when using the two approaches reported above. Overall, the detection rate by FISH of DAPI-stained cells varied from 48.4% to 68.9% with the general bacterial probe EUB338. Bacteria hybridizing with the group-specific probe CF319a were found to be abundant in the three lakes. A total of 478 strains were isolated from R2A agar plates and grouped by restriction analysis technique; sequencing of representative 16S rDNAs was performed to elucidate the taxonomic positions of isolates. Overall, isolates were placed within five different taxa: ?-Proteobacteria (39%), Bacteroidetes (35%), ?-Proteobacteria (8%), Actinobacteria (7%) and ?-Proteobacteria (5%). Finally, the 5.8% of total isolates shared the highest degree of sequence identity with unclassified bacteria. Members of the ?-Proteobacteria predominated at INI, whereas isolates from CC and LH mainly belonged to the Bacteroidetes. Among the ?-Proteobacteria, the genus Pseudomonas was predominant, whereas Flavobacterium spp. were very common among the Bacteroidetes. Finally, several Actinobacteria were closely related to unknown Antarctic bacteria.

Composition of diazotrophic bacterial assemblages in bean-planted soil compared to unplanted soil

The effect of common bean ( Phaseolus vulgaris L.) on the composition of nitrogen fixing bacterial assemblages in soil was studied by comparing planted and unplanted soil. The community composition was studied by terminal restriction fragment length polymorphism (T-RFLP) of the nitrogenase reductase gene ( nifH). Principal component analysis (PCA) of T-RFLP profiles showed the separation of profiles from planted and unplanted soil. Terminal restriction fragments (T-RFs) corresponding to rhizobial bacteria were identified preferentially in planted soil; however most nifH T-RFs in soil could not be assigned to T-RFs simulated from a database of known diazotrophs. To specifically study rhizobial bacteria in the soil and nodules, PCR products from the alpha subunit of the nitrogenase enzyme ( nifD) were analyzed by denaturing gradient gel electrophoresis (DGGE). DGGE results showed the specific stimulation of the rhizobial microsymbionts in planted soil.

Structural and functional patterns of bacterial communities in response to protist predation along an experimental productivity gradient

Substrate supply and protist grazing are two of the most important forces that determine the composition and properties of bacterial assemblages. General ecological theory predicts that the relative importance of these factors is changing with the environmental productivity. In the present study, the interplay between bottom-up and top-down control was studied in a productivity gradient simulated in one-stage chemostats containing natural assemblages of freshwater bacteria and heterotrophic nanoflagellates. Bacterial assemblages in the chemostats differed strongly with respect to their morphological, physiological and compositional properties in the presence versus the absence of predators. However, theses differences were modified by the productivity gradient. Whereas in predator-free chemostats the mean abundance and biomass of bacteria increased proportionally with increasing substrate supply, in treatments that included flagellates bacterial production was largely channelled into predator biomass. The bacterial morphological diversity increased along the productivity gradient with increasing substrate input but even more so with predators. Proportional to the increasing substrate supply, predation shifted the remaining bacteria towards morphologically inedible forms. Predation also caused shifts in bacterial substrate-utilization profiles, and in bacterial community composition, as analysed by terminal restriction fragment length polymorphism of PCR-amplified 16S-rRNA genes. Without predators, bacterial richness increased along the productivity gradient whereas with predators bacterial richness was higher at intermediate substrate levels. In accordance with ecological theory, these results demonstrated that predators influence all of the major characteristics of bacterial assemblages but the magnitude of this effect is modulated by the productivity of the system.

Interactive effects of solar radiation and dissolved organic matter on bacterial activity and community structure

We studied the interactive effects of dissolved organic matter (DOM) and solar radiation on the activity and community structure of bacteria from an alpine lake. Activity was assessed both at the community level as leucine incorporation rates and at the single-cell level by microautoradiography. Fluorescent in situ hybridization and signal amplification by catalysed reporter deposition (CARD-FISH) was used to track changes in the bacterial community composition. Bacteria-free filtrates of different DOM sources (lake, algae or soil) were incubated either in the dark or exposed to solar radiation. Afterwards, the natural bacterial assemblage was inoculated and the cultures incubated in the dark for 24–48 h. Bacterial activity was enhanced in the first 24 h in the soil and algal DOM amendments kept in the dark. After 48 h, the enhancement effect was greatly reduced. The initial bacterial community was dominated by Betaproteobacteria followed by Actinobacteria. The relative abundance (expressed as a percentage of DAPI-stained cells) of Betaproteobacteria increased first in dark incubated DOM amendments, but after 48 h no significant differences were detected among treatments. In contrast, the relative abundance of Actinobacteria increased in pre-irradiated DOM treatments. Although Betaproteobacteria dominated at the end of the experiment, the relative abundance of their R-BT subgroup differed among treatments. Changes in bacterial community activity were significantly correlated with those of the relative abundance and activity of Betaproteobacteria, whereas the contribution of Actinobacteria to the bulk activity was very modest. Our results indicate a negative effect of DOM photoalteration on the bulk bacterial activity. The magnitude of this effect was time-dependent and related to rapid changes in the bacterial assemblage composition.

Multiple carbon substrate utilization by bacteria at the sediment–water interface: seasonal patterns in a stratified eutrophic reservoir

Sediment–water interfaces (SWIs) in lakes and reservoirs harbor diverse assemblages of heterotrophic bacteria that influence organic matter cycling. Seasonal reservoir mixing and stratification affect the rate and type of dissolved organic carbon (DOC) utilized by SWI bacteria, however these seasonal carbon utilization dynamics remain poorly understood. We conducted an exploratory multi-seasonal study using Biolog EcoPlates to measure SWI bacterial carbon substrate utilization rates (CSURs) and patterns in a monomictic eutrophic reservoir. Principal components analysis (PCA) was used to elucidate seasonal CSUR variation. Carbohydrate utilization was greatest during early (onset of) stratification and also was high during winter mixing. Amino acid utilization was greatest during late (prolonged) stratification. Carboxylic acids had greatest utilization during late stratification, but also had moderate to high utilization during all other seasons. Amines and polymers exhibited moderate utilization during all seasons. We related seasonal variation in these CSURs to SWI bacterial abundance, temperature, dissolved oxygen, and redox potential. Collectively these environmental variables accounted for 49.4–62.3% of the total substrate utilization variance by season. Several individual substrate CSURs were significantly (P < 0.05) positively and/or negatively correlated with individual environmental variables, with l-asparagine and putrescine exhibiting significant positive and negative correlations with every measured environmental variable. Lastly, seasonal changes in CSURs corresponded to various changes in SWI bacterial assemblage composition, with highest similarities among early stratification and autumnal overturn assemblages and lowest similarities among late stratification and winter mixing assemblages.

Modulation of microbial predator–prey dynamics by phosphorus availability: Growth patterns and survival strategies of bacterial phylogenetic clades

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga-Flavobacterium-Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints.

Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH

We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (>20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.

Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands

Sediment bacteria play important roles in the biogeochemistry of ocean sediments; however, factors influencing assemblage composition have not been extensively studied. We examined extractable sediment bacterial abundance, the composition of bacterial assemblages using a high-throughput molecular fingerprinting approach, and several sediment biogeochemical parameters (organic matter content and alkaline phosphatase activity), along a 35 km transect from Point Fermin, Southern California, to Santa Catalina Island, across the approximately 900-m-deep San Pedro Basin. Automated rRNA intergenic spacer analysis (ARISA) demonstrated that in two spatially isolated shallow (approximately < 60 m, on opposite sides of the channel) sediment environments, assemblages were more similar to each other than to deeper communities. Distinct communities existed in deeper and shallower sediments, and stations within the deep basin over 2 km apart contained remarkably similar assemblage fingerprints. The relative contribution to total amplified DNA fluorescence of operational taxonomic units (OTUs) was significantly correlated to that of other OTUs in few comparisons (2.7% of total), i.e. few bacterial types were found together or apart consistently. The relative proportions within assemblages of only a few OTU were significantly correlated to measured physicochemical parameters (organic matter content and wet/dry weight ratio of sediments) or enzyme (alkaline phosphatase) activities. A low percentage of shared OTU between shallow and deep sediments, and the presence of similar, but spatially isolated assemblages suggests that bacterial OTU may be widely dispersed over scales of a few kilometres, but that environmental conditions select for particular assemblages.

Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico)

Viruses are hypothesized to cause enhanced diversity in bacterial communities by regulating the outcome of intertaxon competition. However, concomitant documentation of viral and bacterial assemblage composition in oligotrophic waters are rare, particularly in situ over time, and there is almost no information on the temporal variability in virioplankton assemblage composition in oligotrophic water masses. Assemblage composition of viruses (via pulsed-field gel electrophoresis, PFGE) and bacteria (via automated rRNA intergenic spacer analysis, ARISA) was compared during surface lagrangian drifter deployments in the oligotrophic Gulf of Mexico during summer 2001, 2002, and 2003. In vertical profile, viruses and bacteria both had maximum abundances in surface waters, which decreased with depth; however, the richness of their assemblages was not significantly different between depths, suggesting independence of biomass and diversity. Viral assemblages changed rapidly (0.17–0.32 Jaccard index d−1), which was similar to the rate of change in bacterial assemblages reported in surface waters. Patterns of viral and bacterial assemblage composition were significantly related (P&lt;0.001, r=0.58 between node ranks), and both assemblages clustered primarily by year and then by depth. These cultivation-independent observations demonstrate relationships between viral and bacterial assemblages, which are dynamic in patches of open ocean water. Even at the relatively low phylogenetic resolution of the ARISA and PFGE methods, the results support the idea that viruses may influence the species composition of host assemblages.

Viral impacts upon marine bacterioplankton assemblage structure

This study examined the relationship between viral infection and the richness, diversity and composition of bacterial assemblages in the water column. Viruses were enriched by ultrafiltration, added to water column incubation experiments at 15 locations in the North Atlantic, North Pacific, Gulf of Mexico and Southern California. In a separate experiment, viruses were removed from bacterioplankton by diafiltration at the San Pedro Ocean Time Series Station. Bacterial assemblage composition was observed using a high throughput and sensitive molecular fingerprinting analysis, automated rRNA intergenic spacer analysis (ARISA). Diazotrophs were used as a model functional group to represent rare organisms hypothesized to benefit from viral activity, and their richness and diversity was determined by terminal restriction fragment length polymorphism of a nitrogenase gene fragment (nifH). The enrichment and removal experiments demonstrated mixed impacts of viral pressure upon bacterial communities, and we observed significant effects of viruses on several microbial parameters in all but two experiments. However, there was no consistent response of viral enrichment on total bacterial and diazotroph assemblages at stations with similar environmental conditions, suggesting that untested variables, small spatial scale factors, or stochastic processes influence the outcome of viral activities. Across all experiments, the relative abundance of the more common operational taxonomic units (OTUs) in fingerprints were not significantly impacted compared to the abundance of rare OTUs. These data indicate that viruses may have significant influence upon community structure of bacterioplankton; however, effects were not consistent between sampling locations nor water masses.

Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities

Coral reefs are globally important marine ecosystems as sites of high biotic diversity. Reef flat sediments are reasonably homogeneous in composition. This substratum is subject to gradi- ents in water motion, grazing pressure and benthic productivity. This study used DNA fingerprinting techniques, automated rRNA intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP) to examine patterns of bacterial assemblage composition within Heron Reef flat sediments, targeting the entire bacterial community (not including Archaea) and nitrogen- fixing bacteria. ARISA fingerprints contained between 51 and 148 operational taxonomic units (OTU) per surface sediment sample. The mean whole-community similarity between adjacent sites along a transect from Heron Island to the reef crest was 0.50 ± 0.03 (mean ± SE) Whittaker Index (comparison of relative abundances) and 0.46 ± 0.03 Jaccard Index (presence/absence only). Comparison of sedi- ment community fingerprints to a water column community fingerprint collected above the reef flat at high tide indicated that sediments contained different assemblages to the water column (mean similarity between sediments and water column assemblage = 0.15 ± 0.01 Jaccard Index); however, assemblage composition did not differ significantly from that expected by random association. Verti- cal sediment cores showed dissimilarity between surface (0 to 3 cm) and deep (3 to 5 cm) community fingerprints, which was probably related to redox state. Comparison of fingerprints of fecally-derived sediments from the sea cucumber Holothuria atra and surrounding sediments indicated that the impact of metazoan grazing could not be distinguished from ambient small spatial scale variability in sediment assemblage composition. The nifH-TRFLP fingerprints of sediment prokaryotic assem- blages (amplified from all samples, but only in sufficient quantities for analysis from 7 locations) indi- cated the presence of ubiquitous, potentially diverse diazotroph communities, with little assemblage similarity between locations. Our results suggested that while bacterial assemblages (including communities of nitrogen-fixing bacteria) in sediments of a coral reef are diverse, their assemblage composition is not related to grazing pressure but may be influenced by other biotic and abiotic environmental conditions such wave energy and sediment depth.

Chitinolytic bacteria from alkaline hypersaline Mono Lake, California, USA

Chitinolytic activity was detected in sediment and water-column samples from Mono Lake, California, USA, using fluorogenic analogues. In order to learn more about chitin degradation in Mono Lake, we analyzed the phylogenetic composition of bacterial assemblages in chitin-enrich- ment cultures and associated with Artemia monica exuvia. We also isolated chitinolytic bacteria from aerobic and anaerobic water and sediment samples. We screened these isolates for their ability to hydrolyze chitin analogs, for the formation of clearing zones on chitin plates, and for growth with chitin as the sole carbon and energy source. We characterized the isolates phylogenetically by deter- mining partial sequences of their 16S rRNA genes. Three ribotypes, most closely related to Paracoc- cus sp. MBIC4036 (AB025192), Arhodomonas sp. EL-201 (AJ315984), and Psychroflexus tropicus (AF513434), were only found in Mono Lake exuvium and chitin-enrichment clone libraries. Four ribo- types, retrieved solely from chitin enrichments, were closely related to Proteobacteria. The majority (73%) of the isolates we obtained were Gram-positive bacteria, and 70% of the Gram-positive iso- lates were capable of hydrolyzing at least 1 model substrate.

Exploration of riffle-scale interactions between abiotic variables and microbial assemblages in the hyporheic zone

Molecular methods were applied to explore the composition of hyporheic bacterial assemblages and their possible interaction with interstitial physicochemical variables. Hyporheic flows on a riffle were manipulated (a downwelling zone was converted to an upwelling zone and vice versa) in order to examine the influence of vertical flow patterns on microbial assemblages. Bacterial assemblages were heterogeneously distributed throughout the riffle, the greatest similarity among them occurring at similar depths rather than in areas of similar flow regimes (upwelling versus downwelling). There was no correlation between the measured physicochemical variables and the microbial assemblages, with the exception of depth and sediment particle size. The flow manipulation in the original downwelling zone appeared to have had an effect on the microbial assemblages, although this influence may have been primarily due to a change in temperature in the manipulated region rather than an alteration of the vertical-flow direction per se.

A transplant experiment to identify the factors controlling bacterial abundance, activity, production, and community composition in a eutrophic canyon‐shaped reservoir

We performed a transplant experiment in eutrophic Sau reservoir to assess the factors that control bacterial abundance, activity, growth rate, and community composition. Samples from the lacustrine and the riverine ends of the reservoir were incubated in dialysis bags placed in situ and transplanted to the other side of the reservoir and also incubated after 1 µm filtration to measure predator effects. The bags were sampled at 12‐h intervals to estimate bacterial abundance, whole community activity, activity structure (by flow cytometry), and phylogenetic composition (by in situ hybridization with group‐specific phylogenetic probes). Bacterial production was always regulated by nutrient supply, but abundance and activity were differently regulated at both sites. The riverine bacteria were limited by predator activity, whereas the lacustrine were regulated by a combination of predation and nutrient supply. Therefore, even in the same environment, different modes of control can act simultaneously. Bacterial activity structure was also regulated in the same way. Abundance of high DNA bacteria and cells hybridizing with the universal EUB338 probe were well correlated. In the lacustrine sample, bacterial community structure did not change significantly, whereas in the riverine sample, Α‐ and Δ‐Proteobacteria reduced their growth when transplanted, whereas Β‐Proteobacteria were stimulated by the presence of predators. Members of the Cytophaga/Flavobacterium phylum grew only when incubated in situ in the absence of predators. This different behavior in the different bacterial groups resulted in strong changes in bacterial assemblage composition, evident already after 24 h. The experiment demonstrates that, together with the effect of predators, nutrient supply affects bacterial community properties and that a complex regulation involving both types of control can occur in a single heterogeneous planktonic system.

Changes in marine bacterioplankton phylogenetic composition during incubations designed to measure biogeochemically significant parameters

Bottle incubations, during which the activity and growth of prokaryotes is monitored during several days, are frequently carried out to study functional aspects of marine prokaryotic assemblages. These experiments will relate directly to in situ activities if all populations grow harmonically during the incubation. We tested whether this was the case by analyzing the composition of bacterial assemblages at the beginning and at the end of the incubation by denaturing gradient gel electrophoresis. Five experiments were done in different Antarctic regions. Bacterial assemblages north and south of the Polar Front were very different. In all cases, the final assemblages were very different from the initial ones, and these changes were often accompanied by a significant decrease of diversity indices. Our experiments included treatments with different temperature and organic matter amendments. Whereas the increase in temperature tested had a minor effect on prokaryotic growth rate and specific composition, the addition of organic matter strongly stimulated growth rate and selected a particular bacterial assemblage in some experiments but not in others. A significant component of bacterial assemblages from waters south of the Polar Front appeared to be Polaribacter franzmannii, a gas vacuolated bacterium of the CytophagaߚFlavobacteriumߚBacteroides group that was originally isolated from Antarctic sea ice. This phylotype was enriched and dominated in almost all final assemblages. Our results indicate that longߚterm bottle incubations mostly measure the activity of a few opportunistic bacteria and not that of the original assemblage. This should be taken into account if data obtained in these experiments are used for balancing whole ecosystem carbon budgets and to derive biogeochemical conclusions.