Ribosomal Intergenic Spacer Analysis Research Articles

Vertical stratification of bacterial communities driven by multiple environmental factors in the waters (0–5000 m) off the Galician coast (NW Iberian margin)

The processes mediated by microbial planktonic communities occur along the entire water column, yet the microbial activity and composition have been studied mainly in surface waters. This research examined the vertical variation in bacterial abundance, activity and community composition and structure from surface down to 5000m depth following a longitudinal transect off the Galician coast (NW Iberian margin, from 43°N, 9°W to 43°N, 15°W). Community activity and composition changed with depth. The leucine incorporation rates decreased from the euphotic layer to the bathypelagic waters by three orders of magnitude, whereas prokaryotic abundance decreased only by one order of magnitude. The relative abundance of SAR11 and Alteromonas, determined by catalyzed reported deposition fluorescence in situ hybridization (CARD-FISH), decreased with depth. Meanwhile, the contribution of SAR 202 and SAR324 was significantly higher in the deeper layers (i.e. NEADW, North East Atlantic Deep Water and LDW, Lower Deep Water) than in the euphotic zone. Bacterial community structure, assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was depth-specific. A distance based linear model (DistLM) revealed that the variability found in bacterial community structure was mainly explained by temperature nitrate, phosphate, dissolved organic matter (DOM) fluorescence, prokaryotic abundance, leucine incorporation and to a lesser extent salinity, oxygen, CDOM absorbance and dissolved organic carbon concentration. Our results displayed a bacterial community structure shaped not only by depth-related physicochemical features but also by DOM quality, indicating that different prokaryotic taxa have the potential to metabolize particular DOM sources.

Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea

In the present study, the ecological distribution of marine Actinobacteria isolated from seamount and non-seamount stations in the Tyrrhenian Sea was investigated. A collection of 110 isolates was analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and 16S rRNA gene sequencing of representatives for each ARISA haplotype (n=49). Phylogenetic analysis of 16S rRNA sequences showed a wide diversity of marine isolates and clustered the strains into 11 different genera, Janibacter, Rhodococcus, Arthrobacter, Kocuria, Dietzia, Curtobacterium, Micrococcus, Citricoccus, Brevibacterium, Brachybacterium and Nocardioides. Interestingly, Janibacter limosus was the most encountered species particularly in seamounts stations, suggesting that it represents an endemic species of this particular ecosystem. The application of BOX-PCR fingerprinting on J. limosus sub-collection (n=22), allowed their separation into seven distinct BOX-genotypes suggesting a high intraspecific microdiversity among the collection. Furthermore, by screening the biotechnological potential of selected actinobacterial strains, J. limosus was shown to exhibit the most important biosurfactant activity. Our overall data indicates that Janibacter is a major and active component of seamounts in the Tyrrhenian Sea adapted to low nutrient ecological niche.

Combination of complex adsorption and anammox for nitric oxide removal

High-efficiency Fe(II)EDTA (approximately 80%) was selected to remove nitric oxide (NO) in a complex adsorption process; subsequently, this Fe(II)EDTA was combined with the anammox process to eliminate the NO in flue gas. The Fe(II)EDTA–NO solution negatively affected the conventional nitrite-dependent anammox bacteria when the solution concentration exceeded 0.5mM. Fe(II)EDTA–NO-cultivated anammox bacteria removed the ammonium coupled to complex NO reduction (≤3.5mM). The batch test results demonstrated that NH4+ was eliminated through Fe(II)EDTA–NO reduction via anammox. The removal of complex NO and NH4+ exhibited high relativity relevance, and the Fe(II)EDTA–NO/NH4+ molar ratio was approximately 0.97. The complex NO-dependent process generates lesser nitrate than that generated by conventional anammox. Moreover, Candidatus Kuenenia stuttgartiensitiensis became the dominant anammox bacterial community when the biomass is cultivated using the inoculated bacteria, and the proportion of the former increased to 90% from the initial 38% for ribosomal intergenic spacer analysis and library construction.

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility.

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms.

Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012.

Information on recent photosynthetic biomass distribution and biogeography of Arctic marine pico-eukaryotes (0.2–3 μm) is needed to better understand consequences of environmental change for Arctic marine ecosystems. We analysed pico-eukaryote biomass and community composition in Fram Strait and large parts of the Central Arctic Ocean (Nansen Basin, Amundsen Basin) using chlorophyll a (Chl a) measurements, automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. Samples were collected during summer 2012, the year with the most recent record sea ice minimum. Chl a concentrations were highest in eastern Fram Strait and pico-plankton accounted for 60–90% of Chl a biomass during the observation period. ARISA-patterns and 454-pyrosequencing revealed that pico-eukaryote distribution is closely related to water mass distribution in the euphotic zone of the Arctic Ocean. Phaeocystaceae, Micromonas sp., Dinophyceae and Syndiniales constitute a high proportion of sequence reads, while sequence abundance of autotrophic Phaeocystaceae and mixotrophic Micromonas sp. was inversely correlated. Highest sequence abundances of Phaeocystaceae were observed in the warm Atlantic Waters in Fram Strait, while Micromonas sp. dominated the abundant biosphere in the arctic halocline. Our results are of particular interest considering existing hypotheses that environmental conditions in Nansen Basin might become more similar to the current conditions in Fram Strait. We propose that in response, biodiversity and biomass of pico-eukaryotes in Nansen Basin could resemble those currently observed in Fram Strait in the future. This would significantly alter biogeochemical cycles in a large part of the Central Arctic Ocean.

Contrasting factors drive within-lake bacterial community composition and functional traits in a large shallow subtropical lake

Lakes are considered as “islands” for assessing microbial biogeography, but bacterial community composition (BCC) and function may vary significantly within lakes, with the roles of scale and connectivity still unclear. This study investigated the spatial and temporal heterogeneity of the BCC (automated ribosomal intergenic spacer analysis) and functional traits (FT, carbon-source utilization), and the contribution of: (i) environmental variables, (ii) phytoplankton, (iii) season, and (iv) space, through variance partitioning in the large and well-mixed Lake Mangueira. The BCC and FT differed in time and space, with BCC being explained by environmental variables and phytoplankton, whereas FT was explained only by space. The smallest scale of variability detected by the BCC and FT (~49 km) was larger than scales found in the other studies, suggesting an effect of lake size (fetch and connectivity). Our results indicate that barriers to bacterial dispersal due to long distances are overcome by high connectivity, reinforcing the role of species sorting for BCC. FT were probably driven by gene dispersal and/or the effects of local conditions on migrant bacterial taxa and resuspended bacteria. Our results highlight the role of within-lake heterogeneity for ecosystem functioning and the implications for the appropriate scale to use in sampling bacterial communities.

Impact of the biocide Irgarol on meiofauna and prokaryotes from the sediments of the Bizerte lagoon-an experimental study.

The biocide Irgarol 1051 has been reported to have negative effects on a large number of living components including non-target organisms, but information on its impact on the marine meiofauna and benthic prokaryotes is completely lacking. Here, we report the results of long-term experimental studies in which we determined the effects of increasing Irgarol concentrations (from 11.5 to 315ngg(-1) sediment dry weight) on meiofauna and benthic prokaryotes. We found that this biocide had a significant impact on meiofauna abundance, even at the lowest concentrations, causing a drastic decline in the abundance of nematodes (the dominant meiofaunal taxon) and an increase of the relative importance of oligochaetes. Even if no direct effects of Irgarol were found on prokaryotic abundance and biomass, the molecular fingerprinting analyses (automated ribosomal intergenic spacer analysis) showed that the prokaryotic diversity was significantly altered by the biocide. The results of the present study indicate that Irgarol 1051 in marine sediments has a significant impact on the smallest eukaryotic and microbial components also at very low concentrations (ca 12ngg(-1)).

Spatial and temporal variability of bacterial communities in high alpine water spring sediments

Water springs are complex, fragile and taxa-rich environments, especially in highly dynamic ecosystems such as glacier forefields experiencing glacier retreat. Bacterial communities are important actors in alpine water body metabolism, and have shown both high seasonal and spatial variations. Seven springs from a high alpine valley (Matsch Valley, South Tyrol, Italy) were examined via a multidisciplinary approach using both hydrochemical and microbiological techniques. Amplified ribosomal intergenic spacer analysis (ARISA) and electric conductivity (EC) measurements, as well as elemental composition and water stable isotopic analyses, were performed. Our target was to elucidate whether and how bacterial community structure is influenced by water chemistry, and to determine the origin and extent of variation in space and time. There existed variations in both space and time for all variables measured. Diversity values more markedly differed at the beginning of summer and then at the end; the extent of variation in space was prevalent over the time scale. Bacterial community structural variation responded to hydrochemical parameter changes; moreover, the stability of the hydrochemical parameters played an important role in shaping distinctive bacterial communities.

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals.

Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.

Develop and Demonstrate Fundamental Basis for Selectors to Improve Activated Sludge Settleability: Phase II Lab Investigation

The primary objective of this research was to compare dilute sludge volume index (DSVI) control in equally-sized single- and multi-stage anoxic and anaerobic selectors relative to a control aerobic reactor without a selector, using a synthetic wastewater feed containing both readily biodegradable and slowly biodegradable substrates. A further objective was to compare filamentous microorganism populations and microbial community composition for the different systems by an automated ribosomal intergenic spacer analysis (ARISA) (Fisher and Triplett, 1999) method. This title belongs to WERF Research Report Series ISBN: 9781843397939 (eBook)

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

Increasing concentrations of phenol progressively affect anaerobic digestion of cellulose and associated microbial communities.

Performance stability is a key issue when managing anaerobic digesters. However it can be affected by external disturbances caused by micropollutants. In this study the influence of phenol on the methanization of cellulose was evaluated through batch toxicity assays. Special attention was given to the dynamics of microbial communities by means of automated ribosomal intergenic spacer analysis. We observed that, as phenol concentrations increased, the different steps of anaerobic cellulose digestion were unevenly and progressively affected, methanogenesis being the most sensitive: specific methanogenic activity was half-inhibited at 1.40 g/L of phenol, whereas hydrolysis of cellulose and its fermentation to VFA were observed at up to 2.00 g/L. Depending on the level of phenol, microbial communities resisted either through physiological or structural adaptation. Thus, performances at 0.50 g/L were maintained in spite of the microbial community's shift. However, the communities' ability to adapt was limited and performances decreased drastically beyond 2.00 g/L of phenol.

The effects of entombment on water chemistry and bacterial assemblages in closed cryoconite holes on Antarctic glaciers.

Closed cryoconite holes (CCHs) are small aquatic ecosystems enclosed in glacier surface ice, and they collectively contribute substantial aquatic habitat to inland Antarctica. We examined the morphology, geochemistry and bacterial diversity of 57 CCHs, spread over seven sites, located on five glaciers, covering a range of latitudes, elevations and distance from open seawater. Isotopes confirmed glacial ice as the initial water source, with water chemistry evolving through freeze concentration and photosynthetic processes to have conductivities ranging from <0.005 to >4 mS cm(-1) and pH from <5 to >11. Nitrate concentrations were more elevated in inland, higher altitude sites. Bacterial communities were characterized by Automated Ribosomal Intergenic Spacer Analysis and high-throughput sequencing. The dominant phyla were Cyanobacteria, Bacteroides, Proteobacteria and Actinobacteria. CCH bacterial communities predominantly grouped by geographic location, suggesting initial wind-borne inocula from local and regional sources play a role in structuring assemblages. However, multivariate multiple regression analysis indicated that internal CCH conditions also influenced community structure, particularly the ion content and pH of the liquid water. This highlights the importance of founder bacterial populations, isolation and water chemistry in the evolution of CCH bacterial communities.

Asymmetrical response of anaerobic digestion microbiota to temperature changes.

In natural settings, anaerobic digestion can take place in a wide temperature range, but industrial digesters are usually operated under either mesophilic (~35°C) or thermophilic (~55°C) conditions. The ability of anaerobic digestion microbiota to switch from one operating temperature to the other remains poorly documented. We therefore studied the effect of sudden temperature changes (35°C/55°C) in lab-scale bioreactors degrading 13C-labelled cellulose. An asymmetric behaviour was observed. In terms of methane production, after an adaptation period, mesophilic inoculum exhibited a functional resistance to temperature increase but no functional resilience when temperature was reset to 35°C, while thermophilic inoculum methanogenic activity strongly decreased under mesophilic conditions but partially recovered when temperature was reset to 55°C. Automated ribosomal intergenic spacer analysis community fingerprints evidenced a strong influence of temperature on microbial diversity, particularly pronounced and persistent for Archaea. Key phylotypes involved in 13C-cellulose degradation were identified with a coupled stable isotope probing (SIP)-16S rDNA pyrotag sequencing approach, suggesting that the hydrolytic and fermentative metabolic functions could be maintained thanks to functional redundancy between members of the class Clostridia, whereas methanogenic activity primarily relied on specialized groups affiliated either to genus Methanosarcina (mesophilic conditions), Methanothermobacter or Methanoculleus (thermophilic conditions) that were irreversibly modified by temperature increase.

Dynamics of bacterial community structure on intertidal sandflat inhabited by the ghost shrimp Nihonotrypaea harmandi (Decapoda: Axiidea: Callianassidae) in Tomioka Bay, Amakusa, Japan

Callianassid (ghost) shrimp has been claimed as an ecosystem engineer, as it is one of the most powerful bioturbating macrobenthos in intertidal sandflats. However, our knowledge about the relationship between areal distribution of bottom-dwelling ghost shrimps and dynamics of sediment microbial community structure remains obscured. We used automated ribosomal intergenic spacer analysis (ARISA) to reveal the bacterial community dynamics in the sediment of intertidal sandflat of Tomioka Bay, Kyushu, Japan, which is predominantly inhabited by a burrow-dwelling callianassid shrimp Nihonotrypaea harmandi. We found that the bacterial community structures of high and middle shrimp population areas were significantly differentiated from those of low population area (ANOSIM, R=0.10–0.18, p<0.01), while the former two areas were statistically indistinguishable (ANOSIM, R=−0.015, p>0.1). These results illustrated the potential importance of shrimp population density as a key factor in shaping the bacterial community structure and interpreting their dynamics in the sandflat. Furthermore, greater similarity between burrow and non-burrow communities was found in samples taken in autumn through winter than in those in summer (one-way ANOVA, p<0.05), whereas the phylotype richness was not simply differentiated by seasons. These results suggest not only that environmental variables including water temperature and salinity of the water column overlying the sandflat could exert notable impacts on the sediment bacterial community dynamics, but that the bio-irrigation and mixing by the ghost shrimp in permeable sandflat would strongly homogenize sediment particles, enhance solute transport surrounding the burrow and ambient subsurface substrate, and therefore reduce spatial differentiation of the bacterial community structure between the two sites. A comparison between present and previous studies of axiidean (former taxonomic group name, thalassinidean) ghost shrimps provides us with a comprehensive understanding of the shrimps' impacts on bacterial community dynamics, highlighting the importance of sediment permeability, a characteristic determined by the type of sediment, as a key controlling factor to shape spatial heterogeneity of bacterial community structure around burrow.

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans.

The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu(-1) and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean.

Effects of ruminal dosing of Holstein cows with Megasphaera elsdenii on milk fat production, ruminal chemistry, and bacterial strain persistence

Megasphaera elsdenii is a lactate-utilizing bacterium whose ruminal abundance has been shown to be greatly elevated during milk fat depression (MFD). To further examine this association, a total of 23 cannulated multiparous Holstein cows were examined in 3 experiments in which strains of M. elsdenii were directly dosed into the rumen (~2×1012 cells/dose); control cows were dosed with sterile lactate-free culture medium. Cows were fed a total mixed ration (292g of starch/kg of dry matter) that contained primarily corn silage, alfalfa silage, finely ground high-moisture corn, supplemental protein, and corn oil (3g/kg of dry matter). Experiments differed in stage of lactation of the cows (early or late), dosing events (single dose, or 4 doses over a 5-d period), timing of dose (prefeed or 4h postfeed), and M. elsdenii strain (laboratory strain YI9 or 3 strains isolated from cows in the same herd). Dry matter intake and milk yield and composition were measured from 5 to 0d before dosing and 1 to 7d after first dosing, plus later time points that varied by experiment. Milk yield and composition were not affected by dosing. Megasphaera elsdenii was quantified in the liquid phase of ruminal contents by automated ribosomal intergenic spacer analysis, or by PCR with relative quantification (M. elsdenii 16S rRNA gene copy number as a percentage of total bacterial 16S rRNA gene copies). Neither the M. elsdenii-dosed or control cows displayed MFD after dosing, and in almost all cases M. elsdenii populations returned to low baseline levels (<0.02% of 16S rRNA gene copy number) within 24h of dosing. This rapid decline in M. elsdenii also occurred in several cows that were dosed with a strain of M. elsdenii that had been isolated from that particular cow during a previous bout of MFD. Ruminal pH and total millimolar volatile fatty acids and lactate did not differ between dosed and control cows, although acetate-to-propionate ratio declined in both groups and butyrate increased after dosing with M. elsdenii. The results confirm that establishing exogenously added bacterial strains in the rumen is difficult, even for strains previously isolated from the recipient cow. The potential role of M. elsdenii as an agent of MFD remains unclear in the absence of successful establishment of the dosed strains.

Potassium permanganate elicits a shift of the external fish microbiome and increases host susceptibility to columnaris disease.

The external microbiome of fish is thought to benefit the host by hindering the invasion of opportunistic pathogens and/or stimulating the immune system. Disruption of those microbial communities could increase susceptibility to diseases. Traditional aquaculture practices include the use of potent surface-acting disinfectants such as potassium permanganate (PP, KMnO4) to treat external infections. This study evaluated the effect of PP on the external microbiome of channel catfish and investigated if dysbiosis leads to an increase in disease susceptibility. Columnaris disease, caused by Flavobacterium columnare, was used as disease model. Four treatments were compared in the study: (I) negative control (not treated with PP nor challenged with F. columnare), (II) treated but not challenged, (III) not treated but challenged, and (IV) treated and challenged. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze changes in the external microbiome during the experiment. Exposure to PP significantly disturbed the external microbiomes and increased catfish mortality following the experimental challenge. Analysis of similarities of RISA profiles showed statistically significant changes in the skin and gill microbiomes based on treatment and sampling time. Characterization of the microbiomes using 16S rRNA gene pyrosequencing confirmed the disruption of the skin microbiome by PP at different phylogenetic levels. Loss of diversity occurred during the study, even in the control group, but was more noticeable in fish subjected to PP than in those challenged with F. columnare. Fish treated with PP and challenged with the pathogen exhibited the least diverse microbiome at the end of the study.

River bacterioplankton community responses to a high inflow event

Microbes drive chemical cycling and productivity within river ecosystems, but their influence may shift when intense allochthonous inputs accompany high freshwater inflow (flood) events. Investigating how floods influence microbial processes is fundamentally important for our understanding of river ecology, but is generally overlooked. We analysed bacterioplankton com- munity composition (BCC) and abundance over 4 mo following an enormous flood event in the Hunter River, Australia, that resulted in a major fish kill. Concentrations of dissolved organic car- bon (DOC) and inorganic nutrients (N and P) were up to 3 times higher during the flood event compared to prior and subsequent months. Bacterial cell abundances were up to 10 times higher at impacted sites during the flood event. Using Automated Ribosomal Intergenic Spacer Analysis we found significant shifts in BCC between the flood impacted month and subsequent months (p < 0.05). Distance linear modelling indicated that DOC and dissolved N and P correlated most strongly with BCC patterns during the high inflow, whereas community dynamics correlated most strongly with nitrogen oxides and ammonium during the river's recovery phase. 16S rRNA ampli- con pyrosequencing revealed that common soil-associated and facultative anaerobic genera of Proteobacteria were most dominant during the flood period, suggesting that a proportion of the bacterial community observed during this event were potentially inactive soil microbes trans- ported into the river via terrestrial runoff. During the recovery period, Cyanobacteria and fresh- water-associated genera of Actinobacteria and Proteobacteria became dominant in 16S rRNA pyrosequencing profiles. These observations indicate that allochthonous nutrients delivered via floods can significantly stimulate bacterial growth, underpinning substrate-controlled succession of bacterial communities and ultimately shaping the ecology within river ecosystems.

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep-silled fjord.

We investigated the relationship between viruses and co-occurring bacterial communities in the Sognefjord, a deep-silled fjord in Western Norway. A combination of flow cytometry and automated ribosomal intergenic spacer analysis (ARISA) was used to assess prokaryote and viral abundances, and bacterial diversity and community composition, respectively, in depth profiles and at two different sampling seasons (November and May). With one exception, bacterial diversity did not vary between samples regardless of depth or season. The virus and prokaryote abundances as well as bacterial community composition, however, varied significantly with season and depth, suggesting a link between the Sognefjord viral community and potential bacterial host community diversity. To our knowledge, these findings provide the first description of microbial communities in the unique Sognefjord ecosystem, and in addition are in agreement with the simple model version of the 'Killing the Winner' theory (KtW), which postulates that microbial community diversity is a feature that is essentially top-down controlled by viruses, while community composition is bottom-up controlled by competition for limiting growth substrates.