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

Unified understanding of intrinsic and extrinsic controls of dissolved organic carbon reactivity in aquatic ecosystems

Despite our growing understanding of the global carbon cycle, scientific consensus on the drivers and mechanisms that control dissolved organic carbon (DOC) turnover in aquatic systems is lacking, hampered by the mismatch between research that approaches DOC reactivity from either intrinsic (inherent chemical properties) or extrinsic (environmental context) perspectives. Here we propose a conceptual view of DOC reactivity in which the combination of intrinsic and extrinsic factors controls turnover rates and determines which reactions will occur. We review three major types of reactions (biological, photochemical, and flocculation) from an intrinsic chemical perspective and further define the environmental features that modulate the expression of chemically inherent reactivity potential. Finally, we propose hypotheses of how extrinsic and intrinsic factors together shape patterns in DOC turnover across the land-to-ocean continuum, underscoring that there is no intrinsic DOC reactivity without environmental context. By acknowledging the intrinsic-extrinsic control duality, our framework intends to foster improved modeling of DOC reactivity and its impact on ecosystem services.

Detection of Alternaria alternata in tomato juice and fresh fruit by the production of its biomass, respiration, and volatile compounds

Tomato is widely consumed and marketed as juice, puree, or fresh product. Nevertheless, 30% of its harvest volume is lost because of the fungus Alternaria alternata. This research aimed to provide early detection methods for this fungal decay on tomato juice and fresh fruit. Biomass content, CO₂, O₂ and volatile compounds (VOCs) during A. alternata growth in tomato juice and fruit at two ripening stages (breaker and red colour) were evaluated. Additionally, CO₂ and VOCs data set were analysed with a hierarchical cluster technique (HCA) to explore the differences between inoculated and non-inoculated samples. Biomass was determined by gravimetry, CO₂ and O₂ by gas chromatography (GC), and VOCs by GC-mass spectrometry. Biomass content was not drastically modified by tomato's ripening stage (3-6 mg of dry weight). CO₂ in tomato juice was considerably higher in the inoculated samples with A. alternata (27-63%) than in the non-inoculated ones (2.8-6.6%), regardless of the ripeness stage; while in tomato fruit CO₂ was higher at breaker stage and inoculated with A. alternata (33-41%) than the remaining treatments (9-23%). It was also observed that, except for limonene, trans-sabinene hydrate, and rhodovibrin, VOCs' release during the interaction between tomato juice and A. alternata was different from the fresh tomato and A. alternata interaction. Only the HCA based on CO₂ data showed clear differences between the inoculated and non-inoculated tomato juice and fruit at both ripening stages.

Seasonal and spatial dynamics of bacterioplankton communities in a brackish water coastal lagoon

Coastal ecosystems, one of the most productive ecosystems, are subjected to natural and anthropogenic stresses. Coastal bacterioplankton communities are highly dynamic due to spatiotemporal heterogeneity in the environmental parameters. We investigated the seasonal and spatial variation in bacterioplankton communities, their abundances and environmental drivers during one year period in Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes of bacterioplankton communities showed that they were dominated by heterotrophs namely α-Proteobacteria SAR11 and their sub-clades (SAR11_Ib, Chesapeake-Delaware_Bay, Candidatus_Pelagibacter, and SAR11_Surface_1), actinobacterial lineages (hgcI, CL500-29, and Candidatus_Aquiluna), β-Proteobacteria MWH-UniP1, β-Proteobacteria OM43, and verrucomicrobial clade Spartobacteria 'LD29'. Synechococcus was the dominant member within autotrophic cyanobacterial community. Response ratio derived from comparisons of taxon-specific absolute abundances and indicator analyses showed that SAR11_Surface_1 sub-clade occupied high-salinity environment especially during summer and winter and emerged as a strong indicator for mesohaline-polyhaline salinity regime. In contrast, Spartobacteria 'LD29', Actinobacteria hgcI, and CL500-29 preferred low-salinity freshwater environment and were strong indicators for oligohaline-mesohaline regimes. Spatiotemporal patterns were governed by 'distance-decay' and 'similarity-time' relationships. Bacterioplankton communities were mostly determined by salinity, dissolved oxygen, phosphate, and pH which resulted 'species sorting' leading to biogeographical patterns in the bacterioplankton communities. Modeling analysis revealed the characteristic shift in the indicator bacterioplankton taxa along with estuarine salinity gradient. This study has provided baseline information on the bacterioplankton communities and their environmental drivers within an anthropogenically impacted cyclone prone coastal lagoon which would be useful in assessing the impact of multiple stressors on this vulnerable ecosystem.

Recurrent seasonal changes in bacterial growth efficiency, metabolism and community composition in coastal waters

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (T_A ) and September (T_S ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before T_A and the bloom of prokaryotic phytoplankton before T_S . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.

Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area

Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

Dispersal timing and drought history influence the response of bacterioplankton to drying-rewetting stress

The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying-rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.

Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China

Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.

Fungal-bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality

Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial-aquatic C cycling in relation to environmental conditions.

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains

Microbial community assembly and microbial functions are affected by a number of different but coupled drivers such as local habitat characteristics, dispersal rates, and species interactions. In groundwater systems, hydrological flow can introduce spatial structure and directional dependencies among these drivers. We examined the importance of hydrology in structuring bacterial communities and their function within two alpine floodplains during different hydrological states. Piezometers were installed in stream sediments and surrounding riparian zones to assess hydrological flows and also were used as incubation chambers to examine bacterial community structures and enzymatic functions along hydrological flow paths. Spatial eigenvector models in conjunction with models based on physico-chemical groundwater characteristics were used to evaluate the importance of hydrologically-driven processes influencing bacterial assemblages and their enzymatic activities. Our results suggest a strong influence (up to 40% explained variation) of hydrological connectivity on enzymatic activities. The effect of hydrology on bacterial community structure was considerably less strong, suggesting that assemblages demonstrate large functional plasticity/redundancy. Effect size varied between hydrological periods but flow-related mechanisms always had the most power in explaining both bacterial structure and functioning. Changes in hydrology should be considered in models predicting ecosystem functioning and integrated into ecosystem management strategies for floodplains.

Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment

Predicted increases in runoff of terrestrial dissolved organic matter (DOM) and sea surface temperatures implicate substantial changes in energy fluxes of coastal marine ecosystems. Despite marine bacteria being critical drivers of marine carbon cycling, knowledge of compositional responses within bacterioplankton communities to such disturbances is strongly limited. Using 16S rRNA gene pyrosequencing, we examined bacterioplankton population dynamics in Baltic Sea mesocosms with treatments combining terrestrial DOM enrichment and increased temperature. Among the 200 most abundant taxa, 62 % either increased or decreased in relative abundance under changed environmental conditions. For example, SAR11 and SAR86 populations proliferated in combined increased terrestrial DOM/temperature mesocosms, while the hgcI and CL500-29 clades (Actinobacteria) decreased in the same mesocosms. Bacteroidetes increased in both control mesocosms and in the combined increased terrestrial DOM/temperature mesocosms. These results indicate considerable and differential responses among distinct bacterial populations to combined climate change effects, emphasizing the potential of such effects to induce shifts in ecosystem function and carbon cycling in the future Baltic Sea.

Toward an ecologically meaningful view of resource stoichiometry in DOM-dominated aquatic systems

Research on nutrient controls of planktonic productivity tends to focus on a few standard fractions of inorganic or total nitrogen (N) and phosphorus (P). However, there is a wide range in the degree to which land-derived dissolved organic nutrients can be assimilated by biota. Thus, in systems where such fractions form a majority of the macronutrient resource pool, including many boreal inland waters and estuaries, our understanding of bacterio- and phytoplankton production dynamics remains limited. To adequately predict aquatic productivity in a changing environment, improved standard methods are needed for determining the sizes of active (bioavailable) pools of N, P and organic carbon (C). A synthesis of current knowledge suggests that variation in the C:N:P stoichiometry of bioavailable resources is associated with diverse processes that differentially influence the individual elements across space and time. Due to a generally increasing organic nutrient bioavailability from C to N to P, we hypothesize that the C:N and N:P of bulk resources often vastly overestimates the corresponding ratios of bioavailable resources. It is further proposed that basal planktonic production is regulated by variation in the source, magnitude and timing of terrestrial runoff, through processes that have so far been poorly described.

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments

In aquatic systems, limited data exists on the impact of mortality forces such as viral lysis and flagellate grazing when seeking to explain factors regulating prokaryotic metabolism. We explored the relative influence of top-down factors (viral lysis and heterotrophic nanoflagellate grazing) on prokaryotic mortality and their subsequent impact on their community metabolism in the euphotic zone of 21 temperate freshwater lakes located in the French Massif Central. Prokaryotic growth efficiency (PGE, index of prokaryotic community metabolism) determined from prokaryotic production and respiration measurements varied from 5 to 74% across the lakes. Viral and potential grazer-induced mortality of prokaryotes had contrasting impact on PGE. Potential flagellate grazing was found to enhance PGE whereas viral lysis had antagonistic impacts on PGE. The average PGE value in the grazing and viral lysis dominated lake water samples was 35.4% (±15.2%) and 17.2% (±8.1%), respectively. Selective viral lysis or flagellate grazing on prokaryotes together with the nature of contrasted substrates released through mortality processes can perhaps explain for the observed variation and differences in PGE among the studied lakes. The influences of such specific top-down processes on PGE can have strong implications on the carbon and nutrient fluxes in freshwater pelagic environments.

Spatio-temporal patterns of major bacterial groups in alpine waters

Glacial alpine landscapes are undergoing rapid transformation due to changes in climate. The loss of glacial ice mass has directly influenced hydrologic characteristics of alpine floodplains. Consequently, hyporheic sediment conditions are likely to change in the future as surface waters fed by glacial water (kryal) become groundwater dominated (krenal). Such environmental shifts may subsequently change bacterial community structure and thus potential ecosystem functioning. We quantitatively investigated the structure of major bacterial groups in glacial and groundwater-fed streams in three alpine floodplains during different hydrologic periods. Our results show the importance of several physico-chemical variables that reflect local geological characteristics as well as water source in structuring bacterial groups. For instance, Alpha-, Betaproteobacteria and Cytophaga-Flavobacteria were influenced by pH, conductivity and temperature as well as by inorganic and organic carbon compounds, whereas phosphorous compounds and nitrate showed specific influence on single bacterial groups. These results can be used to predict future bacterial group shifts, and potential ecosystem functioning, in alpine landscapes under environmental transformation.

Effects of warming on stream biofilm organic matter use capabilities

The understanding of ecosystem responses to changing environmental conditions is becoming increasingly relevant in the context of global warming. Microbial biofilm communities in streams play a key role in organic matter cycling which might be modulated by shifts in flowing water temperature. In this study, we performed an experiment at the Candal stream (Portugal) longitudinally divided into two reaches: a control half and an experimental half where water temperature was 3 °C above that of the basal stream water. Biofilm colonization was monitored during 42 days in the two stream halves. Changes in biofilm function (extracellular enzyme activities and carbon substrate utilization profiles) as well as chlorophyll a and prokaryote densities were analyzed. The biofilm in the experimental half showed a higher capacity to decompose cellulose, hemicellulose, lignin, and peptidic compounds. Total leucine-aminopeptidase, cellobiohydrolase and β-xylosidase showed a respective 93, 66, and 61% increase in activity over the control; much higher than would be predicted by only the direct temperature physical effect. In contrast, phosphatase and lipase activity showed the lowest sensitivity to temperature. The biofilms from the experimental half also showed a distinct functional fingerprint and higher carbon usage diversity and richness, especially due to a wider use of polymers and carbohydrates. The changes in the biofilm functional capabilities might be indirectly affected by the higher prokaryote and chlorophyll density measured in the biofilm of the experimental half. The present study provides evidence that a realistic stream temperature increase by 3 °C changes the biofilm metabolism to a greater decomposition of polymeric complex compounds and peptides but lower decomposition of lipids. This might affect stream organic matter cycling and the transfer of carbon to higher trophic levels.

Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean

Marine dissolved organic carbon (DOC) encompasses one of the largest reservoirs of carbon on Earth. Heterotrophic bacteria are the primary biotic force regulating the fate of this material, yet the capacity of individual strains to significantly contribute to carbon cycling is unknown. Here we quantified the ability of a single Alteromonas strain [Alteromonas sp. strain Scripps Institution of Oceanography (AltSIO)] to drawdown ambient DOC in a coastal ecosystem. In three experiments, AltSIO alone consumed the entire pool of labile DOC, defined here as the quantity consumed by the submicron size fraction of ambient microbial assemblages within 5 d. These findings demonstrate that complete removal of the labile DOC pool in coastal surface seawater can be achieved by a single taxon. During long-term incubations (>1 y) testing semilabile DOC consumption, AltSIO entered dormancy but remained viable, while the diverse assemblages continued to consume carbon. Given that AltSIO is a large bacterium and thus subject to increased grazing pressure, we sought to determine the ecological relevance of this phenotype. Growth dynamics in natural seawater revealed that AltSIO rapidly outgrew the native bacteria, and despite intense grazing pressure, was never eliminated from the population. A survey in the California Current Ecosystem revealed that large bacteria (≥40 fg C⋅cell(-1)) were persistent, accounting for up to 12% of total bacterial abundance and 24% of total bacterial biomass. We conclude that large, rapidly growing bacteria have the potential to disproportionately alter the fate of carbon in the mesotrophic ocean and play an important role in ecosystem function.

The temporal scaling of bacterioplankton composition: high turnover and predictability during shrimp cultivation

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance-similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity-time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P = 0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w = 0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO4 (3-), and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance-similarity decay model.

Biogeography of the sediment bacterial community responds to a nitrogen pollution gradient in the East China Sea

Patterns of microbial distribution represent the integrated effects of historical and biological processes and are thus a central issue in ecology. However, there is still active debate on whether dispersal limitation contributes to microbial diversification in strongly connected systems. In this study, sediment samples were collected along a transect representing a variety of seawater pollution levels in the East China Sea. We investigated whether changes in sediment bacterial community structures would indicate the effects of the pollution gradient and of dispersal limitation. Our results showed consistent shifts in bacterial communities in response to pollution. More geographically distant sites had more dissimilar communities (r = -0.886, P < 0.001) in this strongly connected sediment ecosystem. A variance analysis based on partitioning by principal coordinates of neighbor matrices (PCNM) showed that spatial distance (dispersal limitation) contributed more to bacterial community variation (8.2%) than any other factor, although the environmental factors explained more variance when combined (11.2%). In addition, potential indicator taxa (primarily affiliated with Deltaproteobacteria and Gammaproteobacteria) were identified; these taxa characterized the pollution gradient. This study provides direct evidence that dispersal limitation exists in a strongly connected marine sediment ecosystem and that candidate indicator taxa can be applied to evaluate coastal pollution levels.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities

Metabolic plasticity and functional redundancy are fundamental properties of microbial communities, which shape their response to environmental forcing, and also mediate the relationship between community composition and function. Yet, the actual quantification of these emergent community properties has been elusive, and we thus do not know how they vary across bacterial communities, and their relationship to environmental gradients and to each other. Here we present an experimental framework that allows us to simultaneously quantify metabolic plasticity and functional redundancy in freshwater bacterioplankton communities, and to explore connections that may exists between them. We define metabolic plasticity as the rate of change in single-cell properties (cell wall integrity, cell size, single-cell activity) relative to changes in community composition. Likewise, we define functional redundancy as the rate of change in carbon substrate uptake capacities relative to changes in community composition. We assessed these two key community attributes in transplant experiments where bacterioplankton from various aquatic habitats within the same watershed were transplanted from their original water to waters from other systems that differ in their main resources. Our results show that metabolic plasticity is an intrinsic property of bacterial communities, whereas the expression of functional redundancy appears to be more dependent on environmental factors. Furthermore, there was an overall strong positive relationship between the level of functional redundancy and of metabolic plasticity, suggesting no trade-offs between these community attributes but rather a possible co-selection. The apparent continuum in the expression of both functional redundancy and plasticity among bacterial communities and the link between them, in turn suggest that the link between community diversity and function may also vary along a continuum, from being very tight, to being weak, or absent.

Alternative states drive the patterns in the bacterioplankton composition in shallow Pampean lakes (Argentina)

We assessed the influence of environmental factors in shaping the free-living bacterial community structure in a set of shallow lakes characterized by contrasting stable state patterns (clear-vegetated, inorganic-turbid and phytoplankton-turbid). Six temperate shallow lakes from the Pampa Plain (Argentina) were sampled over an annual cycle, and two fingerprinting techniques were applied: a 16S rDNA analysis was performed using denaturing gradient gel electrophoresis (DGGE) profiles, and a 16S-23S internally transcribed spacer region analysis was conducted by means of automated ribosomal intergenic spacer analysis (ARISA) profiles. Our results show that the steady state that characterized the different shallow lakes played a major role in structuring the community: the composition of free-living bacteria differed significantly between clear-vegetated, inorganic-turbid and phytoplankton-turbid shallow lakes. The state of the system was more important in determining these patterns than seasonality, geographical location or degree of hydrological connectivity. Moreover, this strong environmental control was particularly evident in the pattern observed in one of the lakes, which shifted from a clear to a turbid state over the course of the study. This lake showed a directional selection of species from a typical clear-like to a turbid-like community. The combined DGGE/ARISA approach revealed not only broad patterns among different alternative steady states, but also more subtle differences within different regimes.

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities.

Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH₃F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH₃F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH₃F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH₃F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH₃F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.

Effects of large river dam regulation on bacterioplankton community structure

Large rivers are commonly regulated by damming, yet the effects of such disruption on prokaryotic communities have seldom been studied. We describe the effects of the three large reservoirs of the Ebro River (NE Iberian Peninsula) on bacterioplankton assemblages by comparing several sites located before and after the impoundments on three occasions. We monitored the abundances of several bacterial phylotypes identified by rRNA gene probing, and those of two functional groups (picocyanobacteria and aerobic anoxygenic phototrophic bacteria-AAPs). Much greater numbers of particles colonized by bacteria were found in upstream waters than downstream sites. Picocyanobacteria were found in negligible numbers at most sites, whereas AAPs constituted up to 14% of total prokaryotes, but there was no clear effect of reservoirs on the spatial dynamics of these two groups. Instead, damming caused a pronounced decline in Betaproteobacteria, Gammaproteobacteria and Bacteroidetes from upstream to downstream sites, whereas Alphaproteobacteria and Actinobacteria significantly increased after the reservoirs. Redundancy analysis revealed that conductivity, temperature and dissolved inorganic nitrogen were the environmental predictors that best explained the observed variability in bacterial community composition. Our data show that impoundments exerted significant impacts on bacterial riverine assemblages and call attention to the unforeseen ecological consequences of river regulation.

Microbial composition affects the functioning of estuarine sediments

Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low- and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial 'cages' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short- (1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO2 production, CH4 flux, nitrification and enzyme activities) depended on both the sediment's origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments.

Prokaryotic community structure and respiration during long-term incubations

Despite the importance of incubation assays for studies in microbial ecology that frequently require long confinement times, few reports are available in which changes in the assemblage structure of aquatic prokaryotes were monitored during long-term incubations. We measured rates of dissolved organic carbon degradation and microbial respiration by consumption of dissolved oxygen (DO) in four experiments with Lake Kinneret near-surface water and, concomitantly, we analyzed the variability in prokaryotic community structure during long-term dark bottle incubations. During the first 24 h, there were only minor changes in bacterial community composition. Thereafter there were marked changes in the prokaryotic community structure during the incubations. In contrast, oxygen consumption rates (a proxy for both respiration and dissolved organic carbon degradation rates) remained stable for up to 10-23 days. This study is one of the first to examine closely the phylo-genetic changes that occur in the microbial community of untreated freshwater during long-term (days) incubations in dark, sealed containers. Novel information on the diversity of the main bacterial phylotypes that may be involved in dissolved organic matter degradation in lake Kinneret is also provided. Our results suggest that, under certain ecological settings, constant community metabolic rates can be maintained as a result of shifts in community composition.

Mechanisms determining the fate of dispersed bacterial communities in new environments

Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed 'functional overachievement'. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

Structuring of bacterioplankton communities by specific dissolved organic carbon compounds

The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis 'fingerprints' and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.

Effects of disturbance intensity and frequency on bacterial community composition and function

Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and ‘disturbed’ incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance.