Bacterial Community Composition of Stream Biofilms in Spatially Variable-Flow Environments

Streams are highly heterogeneous ecosystems, in terms of both geomorphology and hydrodynamics. While flow is recognized to shape the physical architecture of benthic biofilms, we do not yet understand what drives community assembly and biodiversity of benthic biofilms in the heterogeneous flow landscapes of streams. Within a metacommunity ecology framework, we experimented with streambed landscapes constructed from bedforms in large-scale flumes to illuminate the role of spatial flow heterogeneity in biofilm community composition and biodiversity in streams. Our results show that the spatial variation of hydrodynamics explained a remarkable percentage (up to 47%) of the variation in community composition along bedforms. This suggests species sorting as a model of metacommunity dynamics in stream biofilms, though natural biofilm communities will clearly not conform to a single model offered by metacommunity ecology. The spatial variation induced by the hydrodynamics along the bedforms resulted in a gradient of bacterial beta diversity, measured by a range of diversity and similarity indices, that increased with bedform height and hence with spatial flow heterogeneity at the flume level. Our results underscore the necessity to maintain small-scale physical heterogeneity for community composition and biodiversity of biofilms in stream ecosystems.Biofilms (attached and matrix-enclosed microbial communities) are an important form of microbial life in streams and rivers, where they can greatly contribute to ecosystem functions and even large-scale carbon fluxes (1, 3). Streams are inherently heterogeneous and are characterized by a largely unidirectional downstream flow of water that controls the dispersal of suspended microorganisms (21), biofilm community composition (7), architecture (2), and metabolism (13), for instance. However, we do not understand how diverse microorganisms assemble into biofilm communities based on flow heterogeneity and related dispersal in these ecosystems.Dispersal, as the propagation and immigration of biota, can have important consequences for biodiversity and ecosystem functioning in heterogeneous landscapes (18, 25). Landscape topography and turbulent transport affect dispersal, a relationship that is well studied in the dispersal of plant seeds (31) but not in the microbial world. Only recently have microbial ecologists begun to understand the role of dispersal in large-scale biogeographic patterns (29) and metacommunity ecology (24, 44). This growing body of research on microbial dispersal and its consequences for spatial patterns of community assembly and composition rests entirely on free-living bacteria, while no comparable data exist for microbial biofilms. The confirmation of detachment as an intrinsic behavior in many biofilms has led to the appreciation of dispersal as an insurance policy for these microbial communities to seed new habitats during resource limitation or aging of the parental biofilm (4). However, microbial ecology lacks conceptual models to predict postemigration processes, such as cell propagation, immigration, and community assembly during colonization of new surfaces. The perception of biofilms as microbial landscapes and, at the same time, as integrated parts of the landscape they inhabit offers the possibility to test models for habitat selection by dispersal cells (4). In this study, we focused on the assembly of biofilm communities by dispersal cells in spatially variable-flow environments; we did not measure dispersal as the emigration of cells from established biofilms. We adopted metacommunity ecology as a framework that encapsulates environmental heterogeneity and dispersal (18) to illuminate the mechanisms underlying community assembly.If the effects of microbial diversity on ecosystem functions are to be understood, we need to address the proper spatial resolution at which microorganisms assemble into communities and at which their functioning becomes manifest. In streams, this is typically at the level of habitats and microhabitats ranging from meters to centimeters, where characteristic geomorphological features (e.g., bedforms) and induced hydrodynamic fields develop and where spatial variations in biofilm metabolism become apparent (13). The ensemble of these small-scale variations translates into the landscape heterogeneity of the streambed.The aim of this study was to test whether spatial flow heterogeneity generating diverse microhabitats induces spatial species turnover and increases the biodiversity of microbial biofilms. Microbial metacommunity ecology predicts mass effects rather than species sorting to drive community composition in ecosystems with low residence time, such as streams (14, 18, 24). To test this prediction, we constructed six streambed landscapes from bedforms of defined dimensions differing in height; the mean flow (at flume scale) was kept constant, whereas the spatial heterogeneity of flow increased across the gradient of the six landscapes. The inoculum (i.e., the stream water and naturally contained microorganisms) and water chemistry were equal in all flumes. This allowed us to isolate flow heterogeneity as a potential driver of biofilm community composition in a high-energy ecosystem. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA gene sequences from winter and summer communities and related bacterial community composition and microbial biomass to the hydrodynamics in representative microhabitats using causal modeling and forward selection of explanatory variables (9, 23).     

Bacterial Community Composition of Size-Fractioned Aggregates within the Phycosphere of Cyanobacterial Blooms in a Eutrophic Freshwater Lake

Bacterial community composition of different sized aggregates within the Microcystis cyanobacterial phycosphere were determined during summer and fall in Lake Taihu, a eutrophic lake in eastern China. Bloom samples taken in August and September represent healthy bloom biomass, whereas samples from October represent decomposing bloom biomass. To improve our understanding of the complex interior structure in the phycosphere, bloom samples were separated into large (>100 µm), medium (10–100 µm) and small (0.2–10 µm) size aggregates. Species richness and library coverage indicated that pyrosequencing recovered a large bacterial diversity. The community of each size aggregate was highly organized, indicating highly specific conditions within the Microcystis phycosphere. While the communities of medium and small-size aggregates clustered together in August and September samples, large- and medium-size aggregate communities in the October sample were grouped together and distinct from small-size aggregate community. Pronounced changes in the absolute and relative percentages of the dominant genus from the two most important phyla Proteobacteria and Bacteroidetes were observed among the various size aggregates. Bacterial species on large and small-size aggregates likely have the ability to degrade high and low molecular weight compounds, respectively. Thus, there exists a spatial differentiation of bacterial taxa within the phycosphere, possibly operating in sequence and synergy to catalyze the turnover of complex organic matters.     

Structure and Dynamics of Anaerobic Bacterial Aggregates in a Gas-Lift Reactor

Anaerobic mixed-culture aggregates, which converted glucose to acetic, propionic, butyric, and valeric acids, were formed under controlled conditions of substrate feed (carbon limitation) and hydraulic regimen. The continuous-flow system used (anaerobic gas-lift reactor) was designed to retain bacterial aggregates in a well-mixed reactor. Carrier availability (i.e., liquid-suspended sand grains) proved necessary for bacterial aggregate formation from individual cells during reactor start-up. Electron microscopic examination revealed that incipient colonization of sand grains by bacteria from the bulk liquid occurred in surface irregularities, conceivably reflecting local quiescence. Subsequent confluent biofilm formation on sand grains proved to be unstable, however. Substrate depletion in the bulk liquid is assumed to weaken deeper parts of the biofilm due to cellular lysis, after which production of gas bubbles and liquid shearing forces cause sloughing. The resulting fragments, although sand free, were nevertheless large enough to be retained in the reactor and gradually grew larger through bacterial growth and by clumping together with other fragments. In the final steady state, high cell densities were maintained in the form of aggregates, while sand had virtually disappeared due to sampling losses and wash-out. Numerical cell densities within aggregates ranged from 10¹²/ml at the periphery to very low values in the center. The cells were enmeshed in a polymer matrix containing polysaccharides; nevertheless, carbon sufficiency was not a prerequisite to sustain high hold-up ratios.     

Bacterial Community Structure in Patagonian Andean Lakes Above and Below Timberline: From Community Composition to Community Function

Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.     

156 Effects of Light and Nutrients on Periphyton Community Composition in a Hawaiian Stream

The commercial harvest of floating kelps has promise as a business opportunity that could be especially valuable for small communities in southeast Alaska. The giant kelp, Macrocystis , is harvested mainly for the commercial herring roe-on-kelp harvest in Alaska. In addition, in southeast Alaska the two other species of floating kelps, Nereocystis luetkeana and Alaria fistulosa , have been commercially harvested since 1992 for use as agrochemicals by the Alaska KelpCo. The continued existence of this company and others that may wish to harvest seaweeds on a commercial basis is threatened by the lack of a kelp harvest management system in Alaska. The objective of this research is to develop a reliable and cost effective method for estimating the aerial extent and the standing crop biomass of the floating kelps in SE Alaska. We are employing an aerial multispectral imaging system that can be flown at varying altitudes to achieve spatial resolutions ranging from 0.5 to 2 meters. We are investigating whether the three species have unique spectral or textural characteristics in the multispectral imagery that can be used to differentiate the populations. The end products for this project will be kelp resource maps that delineate the spatial extent and biomass of kelp populations within the beds and a methodology for assessing kelp beds with mixed species composition. These products will find use by resource managers such as the Alaska Department of Fish and Game and the Department of Natural Resources.     

Flagellate Predation on a Bacterial Model Community: Interplay of Size-Selective Grazing, Specific Bacterial Cell Size, and Bacterial Community Composition

The influence of grazing by the bacterivorous nanoflagellate Ochromonas sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day⁻¹ when nongrazed) and low substrate concentration (9 mg liter⁻¹). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by Pseudomonas sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.     

Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom

Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment (≈24 μg of chlorophyll a liter⁻¹). At this time bacterial abundance abruptly decreased from 2.8 × 10⁶ to 0.75 × 10⁶ ml⁻¹, and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-μm size fraction towards the >1.0-μm size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized α-Proteobacteria- and Cytophagales-related phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, β-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.     

Considerable Bacterial Community Structure Coupling with Extracellular Electron Transfer at Karst Area Stone in Yunnan,China

Nearly all karst stones have partial dark and light color sections under the same condition. In this study, 24662 operational taxonomic units (OTUs) were examined from karst stones surface samples. Dark samples showed higher abundance of 18,115 OTUs (73.5%) and containing clustered bacterial communities, as indicated by the results of principal component and cluster analyses. Additionally, heatmap analysis showed microorganisms distinction between different color samples and 19 genera of electroactive microorganisms gathered in the dark samples. Furthermore, iron manganese oxides were detected as the main mineral composition difference. Notably, dark samples exhibited remarkable photoelectrochemical activity in response to visible light. Under sunlight, both microorganisms and minerals displayed close relationship with extracellular electron transfer process, which enhanced the understanding for microorganism-–mineral interactions in natural karst environments.     

Bacterial Community Structure and Location in Stilton Cheese

The microbial diversity occurring in Stilton cheese was evaluated by 16S ribosomal DNA analysis with PCR-denaturing gradient gel electrophoresis. DNA templates for PCR experiments were directly extracted from the cheese as well as bulk cells harvested from a variety of viable-count media. The variable V3 and V4-V5 regions of the 16S genes were analyzed. Closest relatives of Lactococcus lactis, Enterococcus faecalis, Lactobacillus plantarum, Lactobacillus curvatus, Leuconostoc mesenteroides, Staphylococcus equorum, and Staphylococcus sp. were identified by sequencing of the DGGE fragments. Fluorescently labeled oligonucleotide probes were developed to detect Lactococcus lactis, Lactobacillus plantarum, and Leuconostoc mesenteroides in fluorescence in situ hybridization (FISH) experiments, and their specificity for the species occurring in the community of Stilton cheese was checked in FISH experiments carried out with reference cultures. The combined use of these probes and the bacterial probe Eub338 in FISH experiments on Stilton cheese sections allowed the assessment of the spatial distribution of the different microbial species in the dairy matrix. Microbial colonies of bacteria showed a differential location in the different parts of the cheese examined: the core, the veins, and the crust. Lactococci were found in the internal part of the veins as mixed colonies and as single colonies within the core. Lactobacillus plantarum was detected only underneath the surface, while Leuconostoc microcolonies were homogeneously distributed in all parts observed. The combined molecular approach is shown to be useful to simultaneously describe the structure and location of the bacterial flora in cheese. The differential distribution of species found suggests specific ecological reasons for the establishment of sites of actual microbial growth in the cheese, with implications of significance in understanding the ecology of food systems and with the aim of achieving optimization of the fermentation technologies as well as preservation of traditional products.     

Geographic and Environmental Sources of Variation in Lake Bacterial Community Composition

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

Bacterial Community Structure and Function along a Heavy Metal Gradient

The response of the planktonic, sediment, and epilithic bacterial communities to increasing concentrations of heavy metals was determined in a polluted river. None of the communities demonstrated a pollution-related effect on bacterial numbers (viable and total), heterotrophic activity, resistance to Pb or Cu, or species diversity as determined by either the Shannon-Wiener diversity index or rarefaction. The lack of correlation between concentrations of heavy metals and resistance in the sediment bacterial community was investigated and found to be due at least in part to the high pH of the river water and the resultant reduction in heavy metal toxicity. The three different communities demonstrated characteristic profiles based on the relative abundances of bacterial strains grouped according to functional similarities.     

Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity

Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of the Cyanobacteria, Actinobacteria, Nitrospirae, green nonsulfur bacteria, and Firmicutes divisions and the Gamma- and Deltaproteobacteria subdivisions. The BCC in the lake displayed both vertical and latitudinal variation. Vertical changes in BCC were related to the thermal water column stratification, which influences oxygen and nutrient concentrations. Latitudinal variation was related to upwelling of deep water and increased primary production in the south of the lake. The number of bands per sample increased with bacterial production in the epilimnion of the lake, suggesting a positive diversity-productivity relationship.     

Characterization of Bacterial Community Structure on a Weathered Pegmatitic Granite

This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.     

秸秆覆盖免耕对土壤细菌群落区系的影响

多年连续秸秆覆盖免耕对土壤细菌群落影响很大,免耕可提高０－１０ｃｍ土层土壤细菌总数、放线菌数、棒状细菌数和贫营养细菌数量,特别是免耕土壤能使芽孢杆菌数量增多几倍。     

Bacterial Community Composition in the Rivers of the Novaya Sibir Island

Microbiology - The results of molecular genetic studies of prokaryotic communities of river ecosystems of the central and southeastern part of the Novaya Sibir Island are presented. Five phyla...     

Composition and Structure of the Chironomidae (Insecta: Diptera) Community Associated with Bryophytes in a First-Order Stream in the Atlantic Forest, Brazil

This study describes the structure of the Chironomidae community associated with bryophytes in a first-order stream located in a biological reserve of the Atlantic Forest, during two seasons. Samples of bryophytes adhered to rocks along a 100-m stretch of the stream were removed with a metal blade, and 200-mL pots were filled with the samples. The numerical density (individuals per gram of dry weight), Shannon’s diversity index, Pielou’s evenness index, the dominance index (DI), and estimated richness were calculated for each collection period (dry and rainy). Linear regression analysis was employed to test the existence of a correlation between rainfall and the individual’s density and richness. The high numerical density and richness of Chironomidae taxa observed are probably related to the peculiar conditions of the bryophyte habitat. The retention of larvae during periods of higher rainfall contributed to the high density and richness of Chironomidae larvae. The rarefaction analysis showed higher richness in the rainy season related to the greater retention of food particles. The data from this study show that bryophytes provide stable habitats for the colonization by and refuge of Chironomidae larvae, mainly under conductions of faster water flow and higher precipitation.     

Diatom-Derived Carbohydrates as Factors Affecting Bacterial Community Composition in Estuarine Sediments

Microphytobenthic biofilms in estuaries, dominated by epipelic diatoms, are sites of high primary productivity. These diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides and glycoproteins, providing a substantial pool of organic carbon available to heterotrophs within the sediment. In this study, sediment slurry microcosms were enriched with either colloidal carbohydrates or colloidal EPS (cEPS) or left unamended. Over 10 days, the fate of these carbohydrates and changes in β-glucosidase activity were monitored. Terminal restriction fragment length polymorphism (T-RFLP), DNA sequencing, and quantitative PCR (Q-PCR) analysis of 16S rRNA sequences were used to determine whether sediment bacterial communities exhibited compositional shifts in response to the different available carbon sources. Initial heterotrophic activity led to reductions in carbohydrate concentrations in all three microcosms from day 0 to day 2, with some increases in β-glucosidase activity. During this period, treatment-specific shifts in bacterial community composition were not observed. However, by days 4 and 10, the bacterial community in the cEPS-enriched sediment diverged from those in colloid-enriched and unamended sediments, with Q-PCR analysis showing elevated bacterial numbers in the cEPS-enriched sediment at day 4. Community shifts were attributed to changes in cEPS concentrations and increased β-glucosidase activity. T-RFLP and sequencing analyses suggested that this shift was not due to a total community response but rather to large increases in the relative abundance of members of the γ-proteobacteria, particularly Acinetobacter-related bacteria. These experiments suggest that taxon- and substrate-specific responses within the bacterial community are involved in the degradation of diatom-derived extracellular carbohydrates.     

Antarctic Stream Ecosystems: Variability in Environmental Properties and Algal Community Structure

The variability in physical, chemical and biological properties was examined for a number of glacier melt streams in south Victoria Land, Antarctica. Streams flowed for between one and two months. Stream water temperatures (range = 0–11°C) varied over short (hr) time scales whilst discharges varied considerably between streams (range 0.001–15 m³s⁻¹) and over diel cycles. Solar radiation and air temperature were major determinants of stream discharge. Variability in discharge was reflected in variability in nutrient chemistry and sediment load. Nitrogen and phosphorus varied considerably between streams; the meltwaters early in summer contained 10–20 times higher levels of dissolved N and P than later in the season. Within stream nutrient levels were modified by dense algal growths and penguin rookeries. Epilithic algal communities were made up predominantly of cyanophyceae which formed mats and crusts. Longitudinal and horizontal variability of species in the communities in selected streams is described. Analyses of algal cover and biomass (chlorophyll a) show that substrate type and flow rates are of greater importance than nutrients in influencing algal abundance and biomass. In some streams biomass values of over 20 μg Ch. a cm⁻² were recorded, much of which remains viable but inactive over the antarctic winter.