Contribution of particle-bound bacteria to total microheterotrophic activity in five ponds and two marshes

Sequential Reductive Dechlorination of Triclosan by Sediment Microbiota Harboring Organohalide-Respiring Dehalococcoidia

Aquatic ecosystems represent a prominent reservoir of xenobiotic compounds, including triclosan (TCS), a broad-spectrum biocide extensively used in pharmaceuticals and personal care products. As a biogeochemical hotspot, the potential of aquatic sediments for the degradation of TCS remains largely unexplored. Here, we demonstrated anaerobic biotransformation of TCS in a batch microcosm established with freshwater sediment. The initial 43.4 ± 2.2 μM TCS was completely dechlorinated to diclosan, followed by subsequent conversion to 5-chloro-2-phenoxyphenol, a monochlorinated TCS (MCS) congener. Analyses of community profile and population dynamics revealed substrate-specific, temporal-growth of Dehalococcoides and Dehalogenimonas, which are organohalide-respiring bacteria (OHRB) affiliated with class Dehalococcoidia. Dehalococcoides growth was linked to the formation of diclosan but not MCS, yielding 3.6 ± 0.4 × 107 cells per μmol chloride released. A significant increase in Dehalogenimonas cells, from 1.5 ± 0.4 × 104 to 1.5 ± 0.3 × 106 mL-1, only occurred during the reductive dechlorination of diclosan to MCS. Dehalococcoidia OHRB gradually disappeared following consecutive transfers, likely due to the removal of sediment materials with strong adsorption capacity that could alleviate TCS's antimicrobial toxicity. Consequently, a solid-free, functionally stable TCS-dechlorinating consortium was not obtained. Our results provide insights into the microbial determinants controlling the environmental fate of TCS.

Regional factors as major drivers for microbial community turnover in tropical cascading reservoirs

The turnover of microbial communities across space is dictated by local and regional factors. Locally, selection shapes community assembly through biological interactions between organisms and the environment, while regional factors influence microbial dispersion patterns. Methods used to disentangle the effects of local and regional factors typically do not aim to identify ecological processes underlying the turnover. In this paper, we identified and quantified these processes for three operational microbial subcommunities (cyanobacteria, particle-attached, and free-living bacteria) from a tropical cascade of freshwater reservoirs with decreasing productivity, over two markedly different dry and rainy seasons. We hypothesized that during the dry season communities would mainly be controlled by selection shaped by the higher environmental heterogeneity that results from low hydrological flow and connectivity between reservoirs. We expected highly similar communities shaped by dispersal and a more homogenized environment during the rainy season, enhanced by increased flow rates. Even if metacommunities were largely controlled by regional events in both periods, the selection had more influence on free-living communities during the dry period, possibly related to elevated dissolved organic carbon concentration, while drift as a purely stochastic factor, had more influence on cyanobacterial communities. Each subcommunity had distinct patterns of turnover along the cascade related to diversity (Cyanobacteria), lifestyle and size (Free-living), and spatial dynamics (particle-attached).

Seasonal Variation of Bacterial Diversity Along the Marine Particulate Matter Continuum

Seasonal dynamics of ocean prokaryotic communities in the free-living fraction have been widely described, but less is known about the seasonality of prokaryotes inhabiting marine particles. We describe the seasonality of bacterial communities in the particulate matter continuum by sampling monthly over two years in a temperate oligotrophic coastal ecosystem and using a serial filtration (including six size-fractions spanning from 0.2 to 200 μm). We observed that bacterial communities in the particulate matter continuum had annual changes following harmonic seasonal oscillations, where alpha, beta, and gamma diversity increased during the warm period and decreased during the cold period. Communities in each size-fraction changed gradually over time, being the communities in larger size-fractions the ones with stronger annual changes. Annual community changes were driven mainly by day length and sea surface temperature, and each size-fraction was additionally affected by other variables (e.g., smaller size-fractions by dissolved PO₄ and larger size-fractions by turbidity). While some taxonomic groups mantained their preference for a given size fraction during most of the year, others varied their distribution into different size fractions over time, as e.g., SAR11, which increased its presence in particles during the cold period. Our results indicate that the size-fractionation scheme provides novel seasonal patterns that are not possible to unveil by analyzing only free-living bacteria, and that help to better understand the temporal dynamics of prokaryotes.

Vertical shifts of particle-attached and free-living prokaryotes in the water column above the cold seeps of the South China Sea

Marine particle-attached (PA) and free-living (FL) microbes play important roles in the biogeochemical cycling of organic matter along the water column. Deep-sea cold seeps are highly productive and chemosynthetic ecosystems, their continuous emission of CH₄, CO₂, and H₂S can reach up to 100 m in the above water, therefore would influence the distribution and potential metabolic functions of deep-sea prokaryotes. In this study, the vertical distribution profiles of both PA and FL microbes in the water column above two cold seeps of the South China Sea were investigated using Illumina sequencing and quantitative PCR (qPCR) based on 16S rRNA gene. Photosynthetic and heterotrophic prokaryotes were predominant in respective surface and deep layers below the photic zone. The typical cold seep chemosynthetic microbes, such as methanotrophs and sulfate-reducing bacteria were observed with low proportions in the two cold seeps as well. Distinct PA and FL microbial fractions were found in terms of abundance and diversity. FL fraction exposed to the bulk water was significantly affected by temperature and inorganic nutrients, whereas PA fraction relied more on the organic matter of the particles and less susceptible to the environmental variability. Our study highlights the importance of vertical geochemical gradients on the distribution and potential metabolic choice of marine microbes and extends our current knowledge of depth-associated microbial distribution patterns.

Atmospheric respiratory CO2 efflux by aquatic suspended particle-bound microbial communities: A laboratory experimental study

Natural sources of atmospheric CO₂ are of increasing interest as possible contributors to global climate warming. This study documents the amount of respiratory CO₂ contributed by microbial communities associated with suspended particulates in aquatic water columns. Microcosms containing three different sources of water (pond freshwater, NY East River estuary and Hudson River estuary) were used to experimentally determine the atmospheric respiratory CO₂ released from particle-associated microbes. Two different approaches were used. In the first, finely powdered dried cereal leaves (alfalfa) were added to each of the three microcosms as a consistent source of particulate organic matter (POM). In the second, only Hudson River estuary water samples were used with natural densities of POM. Respiration rates associated with two sizes of particles were assessed: 1) ≥ 200 μm and 2) ≥ 50 μm but less than 200 μm. The total respiration rate for the three microcosms with cereal leaf POM ranged from 5.09 to 14.87 μmol CO₂ min⁻¹ L⁻¹. Of this, the amount contributed by larger particulates was in the range of 55–63%; and for smaller particulates ranged from 18 to 32 %. Data for microcosms containing water from the Hudson River estuary, with natural particulates, was as follows: total respiration ranged from ∼3 μmol CO₂ min⁻¹ L⁻¹ to ∼3.73 μmol CO₂ min⁻¹ L⁻¹. Larger particulates contributed approximately 40% of total respiration, and that of smaller particulates was substantially less (4–5% of total). Overall, these results indicate that microbial communities associated with particulates in the water column (especially larger particulates) may contribute substantial amounts of CO₂ to the atmosphere.

Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities

Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.

Living on the edge: biofilms developing in oscillating environmental conditions

For the first time, the densities and diversity of microorganisms developed on ocean gliders were investigated using flow cytometry and Illumina MiSeq sequencing of 16S and 18S rRNA genes. Ocean gliders are autonomous buoyancy-driven underwater vehicles, equipped with sensors continuously recording physical, chemical, and biological parameters. Microbial biofilms were investigated on unprotected parts of the glider and surfaces coated with base, biocidal and chitosan paints. Biofilms on the glider were exposed to periodical oscillations of salinity, oxygen, temperature, pressure, depth and light, due to periodic ascending and descending of the vehicle. Among the unprotected surfaces, the highest microbial abundance was observed on the bottom of the glider's body, while the lowest density was recorded on the glider's nose. Antifouling paints had the lowest densities of microorganisms. Multidimensional analysis showed that the microbial communities formed on unprotected parts of the glider were significantly different from those on biocidal paint and in seawater.

Relative contributions of norspermidine synthesis and signaling pathways to the regulation of Vibrio cholerae biofilm formation

The polyamine norspermidine is one of the major polyamines synthesized by Vibrionales and has also been found in various aquatic organisms. Norspermidine is among the environmental signals that positively regulate Vibrio cholerae biofilm formation. The NspS/MbaA signaling complex detects extracellular norspermidine and mediates the response to this polyamine. Norspermidine binding to the NspS periplasmic binding protein is thought to inhibit the phosphodiesterase activity of MbaA, increasing levels of the biofilm-promoting second messenger cyclic diguanylate monophosphate, thus enhancing biofilm formation. V. cholerae can also synthesize norspermidine using the enzyme NspC as well as import it from the environment. Deletion of the nspC gene was shown to reduce accumulation of bacteria in biofilms, leading to the conclusion that intracellular norspermidine is also a positive regulator of biofilm formation. Because V. cholerae uses norspermidine to synthesize the siderophore vibriobactin it is possible that intracellular norspermidine is required to obtain sufficient amounts of iron, which is also necessary for robust biofilm formation. The objective of this study was to assess the relative contributions of intracellular and extracellular norspermidine to the regulation of biofilm formation in V. cholerae. We show the biofilm defect of norspermidine synthesis mutants does not result from an inability to produce vibriobactin as vibriobactin synthesis mutants do not have diminished biofilm forming abilities. Furthermore, our work shows that extracellular, but not intracellular norspermidine, is mainly responsible for promoting biofilm formation. We establish that the NspS/MbaA signaling complex is the dominant mediator of biofilm formation in response to extracellular norspermidine, rather than norspermidine synthesized by NspC or imported into the cell.

Patterns of bacterial diversity in the marine planktonic particulate matter continuum

Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23-42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions.

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013. Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH₄, CO₂, H₂, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO₄^2-, O₂ and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments

Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.

Occurrence of Vibrio alginolyticus in Ligurian Coast Rock Pools (Tyrrhenian Sea, Italy) and Its Association with the Copepod Tigriopus fulvus (Fisher 1860)

A study of heterotrophic bacteria and vibrios adhering to the copepod Tigriopus fulvus, which lives in Ligurian coast rock pools (Tyrrhenian Sea), was carried out from November 1990 to October 1991. Heterotrophic bacteria, which were always found both free in the water and bound to the T. fulvus organisms, showed a correlation with water temperature and salinity. Vibrio alginolyticus was found free in the water and bound to T. fulvus surfaces during the warmest months. Temperature is the main factor influencing the presence of V. alginolyticus in the rock pool. Attachment of this microorganism to the copepod provides a mechanism for its extended geographic distribution.

Activity measurements of planktonic microbial and microfouling communities in a eutrophic estuary

[H]thymidine incorporation, the rate of reduction of iodonitrotetrazolium violet (INT) to INT formazan normalized to DNA, and the ratio of ATP to DNA were adapted to measure the activity of attached and unattached microbial assemblages of Bayboro Harbor, Fla. Activity measurements by [H]thymidine incorporation were made of cells attached to polystyrene culture dishes, in unfiltered water samples, and in the <1-mum-filtered fraction. In most cases, the activity of attached cells was greater than that of unattached cells either in unfiltered water samples or in the <1-mum fraction. The calculated thymidine incorporation rates for cells in the >1-mum fraction were higher than those for cells either in unfiltered water or in the <1-mum-filtered fraction. By the rate of reduction of INT to INT formazan normalized to DNA and by ATP-to-DNA ratios, attached cells were also more active than cells in unfiltered water samples. These results indicate that the microenvironment afforded by attachment is a more beneficial habitat for microbial growth. Reasons for greater activity by natural populations of attached bacteria are discussed.

Comparison of free-living and particle-associated bacterial communities in the chesapeake bay by stable low-molecular-weight RNA analysis

Free-living and particle-associated bacterial communities in the Chesapeake Bay estuary were analyzed and compared by using acridine orange direct counts and low-molecular-weight (LMW) RNA analysis. Samples were taken from top and bottom waters at upper- and mid-bay sites in December 1992. Free-living bacteria dominated the bacterial numbers at all sampling sites, although particle-associated bacteria increased in areas with greater particle loads. LMW RNAs (5S rRNA and tRNA) obtained directly from free-living, particle-associated, and total bacterioplankton communities were analyzed by high-resolution electrophoresis. There were distinct differences in the migration distances between LMW RNAs of free-living and particle-associated communities taken from the same site, indicating that the two communities differ in composition. In addition, LMW RNA profiles differed minimally with depth for all of the communities examined, presumably because of vertical mixing. 5S rRNAs of free-living communities from the upper- and mid-bay regions differed considerably. Particle-associated RNAs, on the other hand, were very similar, suggesting consistent environmental conditions on particles that select for similar community members. Lastly, several isolated bacteria had 5S rRNAs that were not detected in their respective extracted community 5S rRNAs, indicating that these isolated organisms were not representative of dominant members.

Bacterial production and growth rate estimation from [h]thymidine incorporation for attached and free-living bacteria in aquatic systems

Production and specific growth rates of attached and free-living bacteria were estimated in an oligotrophic marine system, La Salvaje Beach, Vizcaya, Spain, and in a freshwater system having a higher nutrient concentration, Butron River, Vizcaya, Spain. Production was calculated from [methyl-H]thymidine incorporation by estimating specific conversion factors (cells or micrograms of C produced per mole of thymidine incorporated) for attached and free-living bacteria, respectively, in each system. Conversion factors were not statistically different between attached and free-living bacteria: 6.812 x 10 and 8.678 x 10 mug of C mol for free-living and attached bacteria in the freshwater system, and 1.276 x 10 and 1.354 x 10 mug of C mol for free-living and attached bacteria in the marine system. Therefore, use of a unique conversion factor for the mixed bacterial population is well founded. However, conversion factors were higher in the freshwater system than in the marine system. This could be due to the different trophic conditions of the two systems. Free-living bacteria contributed the most to production in the two systems (85% in the marine system and 67% in the freshwater system) because of their greater contribution to total biomass. Specific growth rates calculated from production data and biomass data were similar for attached and free-living bacteria.

Improved Microfouling Assay Employing a DNA-Specific Fluorochrome and Polystyrene as Substratum

With a direct count assay, 10 fouling bacterial isolates have been characterized for their ability to adhere to glass cover slips and polystyrene dishes. Although most adhered in greater numbers to polystyrene, the preference was statistically significant for only seven isolates at the 95% confidence level, due in part to the greater variability in cell attachment to glass (coefficient of variation, 32.3% for glass compared with 10.0% for polystyrene). Employing polystyrene dishes, a novel microfouling assay was developed, based on the extraction and fluorometric determination of DNA. The assay was rapid, enabled the detection of as little as 0.15 mug of DNA per dish ( approximately 5,000 cells per mm), and showed good agreement with the direct count assay. The DNA method resulted in less variability among three replicates (average coefficient of variation, 7.06%) and allowed for estimation of bacterial density over a larger surface area per sample (1.89 x 10 mm) than was feasible with epifluorescence microscopy (0.06 to 0.1 mm).

Natural Microbial Community Compositions Compared by a Back-Propagating Neural Network and Cluster Analysis of 5S rRNA

The community compositions of free-living and particle-associated bacteria in the Chesapeake Bay estuary were analyzed by comparing banding patterns of stable low-molecular-weight RNA (SLMW RNA) which include 5S rRNA and tRNA molecules. By analyzing images of autoradiographs of SLMW RNAs on polyacrylamide gels, band intensities of 5S rRNA were converted to binary format for transmission to a back-propagating neural network (NN). The NN was trained to relate binary input to sample stations, collection times, positions in the water column, and sample types (e.g., particle-associated versus free-living communities). Dendrograms produced by using Euclidean distance and average and Ward's linkage methods on data of three independently trained NNs yielded the following results. (i) Community compositions of Chesapeake Bay water samples varied both seasonally and spatially. (ii) Although there was no difference in the compositions of free-living and particle-associated bacteria in the summer, these community types differed significantly in the winter. (iii) In the summer, most bay samples had a common 121-nucleotide 5S rRNA molecule. Although this band occurred in the top water of midbay samples, it did not occur in particle-associated communities of bottom-water samples. (iv) Regardless of the season, midbay samples had the greatest variety of 5S rRNA sizes. The utility of NNs for interpreting complex banding patterns in electrophoresis gels was demonstrated.

Initial phases of starvation and activity of bacteria at surfaces

The activity of the hydrophilic Vibrio sp. strain DW1 and the hydrophobic Pseudomonas sp. strain S9, which both undergo starvation-induced responses, was examined at nutrient-enriched and nutrient-deficient interfaces. The initial period of response to a starvation regime ("dwarfing" phase) is a sequence of two processes: fragmentation and continuous size reduction of the fragmented cells. This dwarfing phase is also one of intense metabolic activity as supported by O(2) uptake measurements of the endogenous metabolism and the use of inhibitors of the proton flow, the electron transport chain, and membrane-bound ATPase. Hydrophilic bacteria become even smaller at nutrient-deficient surfaces than in the liquid phase upon starvation, and this is reflected in a higher endogenous metabolism exhibited by surface-associated cells compared with those in the liquid phase. On the other hand, hydrophobic bacteria dwarfing at surfaces did not exhibit a greater size reduction and exhibited an endogenous metabolism that was only slightly higher than that of cells in the liquid phase. Bacterial scavenging of surface-localized nutrients is related to the degree of irreversible binding of dwarf and starved bacteria, which in turn may be related to the degree of cell surface hydrophobicity.

Bacterial biomass, metabolic state, and activity in stream sediments: relation to environmental variables and multiple assay comparisons

Bacterial biomass, metabolic condition, and activity were measured over a 16-month period in the surface sediments of the following four field sites with differing dissolved organic matter regimes: a woodlot spring seep, a meadow spring seep, a second-order stream, and a third-order stream. Total bacterial biomass was measured by lipid phosphate and epifluorescence microscopic counts (EMC), and viable biomass was measured by C most probable number, EMC with 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride reduction, and ATP. Bacterial metabolic condition was determined from the percentage of respiring cells, poly-beta-hydroxybutyrate concentrations, and adenylate energy charge. Activity measures included C-lipid synthesis, P-phospholipid synthesis, the rate of uptake of algal lysate dissolved organic carbon, and respiration, from which biosynthesis was calculated (dissolved organic carbon uptake corrected for respiration). Total bacterial biomass (from EMC) ranged from 0.012 to 0.354 mug of C/mg of dry sediment and was usually lowest in the third-order stream. The percentage of cells respiring was less than 25% at all sites, indicating that most bacteria were dormant or dead. Adenylate energy charge was measured only in the third-order stream and was uniformly low. Poly-beta-hydroxybutyrate concentrations were greater in the woodlot spring seep than in the second- and third-order streams. Uptake of algal lysate dissolved organic carbon ranged from undetectable levels to 166 mg of C . m . h. Little community respiration could be attributed to algal lysate metabolism. Phospholipid synthesis ranged from 0.006 to 0.354 pmol . mg of dry sediment . h. Phospholipid synthesis rates were used to estimate bacterial turnover at the study sites. An estimated 375 bacterial generations per year were produced in the woodlot spring seep, and 67 per year were produced in the third-order stream.

Measurement of Glucose Utilization by Pseudomonas fluorescens That Are Free-Living and That Are Attached to Surfaces

The assimilation and respiration of glucose by attached and free-living Pseudomonas fluorescens were compared. The attachment surfaces were polyvinylidene fluoride, polyethylene, and glass. Specific uptake of [C]glucose was determined after bacterial biomass was measured by (i) microscopic counts or (ii) prelabeling of cells by providing [H]leucine as substrate, followed by dual-labeling scintillation counting. The glucose concentration was 1.4, 3.5, 5.5, 7.6, or 9.7 muM. Glucose assimilation by cells which became detached from the surfaces during incubation with glucose was also measured after the detached cells were collected by filtration. The composition of the substratum had no effect on the amount of glucose assimilated by attached cells. Glucose assimilation by attached cells exceeded that by free-living cells by a factor of between 2 and 5 or more, and respiration of glucose by surface-associated cells was greater than that by free-living bacteria. Glucose assimilation by detached cells was greater than that by attached bacteria. Measurements of biomass by microscopic counts gave more consistent results that those obtained with dual-labeling, but in general, results obtained by both methods were corroborative.

Production and consumption of hydrogen in a eutrophic lake

The vertical distribution of hydrogen was measured in the Loclat, a eutrophic and holomictic lake near Neuchâtel, Switzerland, before and during summer stratification. H(2) concentrations decreased with depth in the anaerobic hypolimnion and were often below the detection limit (2.5 nl of H(2) liter) in the water adjacent to the lake sediment. H(2) was apparently not released from the lake sediment. The highest H(2) concentrations (>4 mul of H(2) liter) were observed in the aerobic water of the epilimnion and metalimnion. There, the H(2) concentrations changed with time, indicating a turnover of H(2). The H(2) production processes could not be studied in the laboratory since incubation of water samples in light or darkness did not result in H(2) production but rather always in H(2) consumption. The possible role of cyanobacteria and algae for H(2) production is discussed. Aerobic or anaerobic H(2) consumption activities were observed at all depths of the water column, with highest activities in the hypolimnion. Aerobic H(2) consumption activity was insensitive to azide inhibition, but sensitive to heat, mercuric chloride, or cyanide. It was restricted to a particle fraction of 0.2 to 3.0 mum in size, so that it must be due to single bacterial cells. Aerobic hydrogen bacteria, on the other hand, occurred in clusters of >3.0 mum. Therefore, the hydrogen bacteria could not have caused the H(2) consumption in lake water. The aerobic H(2) consumption activity followed Michaelis-Menten kinetics, with a K(m) of 67 nM H(2). This is an exceptionally low value compared with K(m) values of hydrogenases in hydrogen bacteria and other species, but is similar to that for H(2)-decomposing abiontic soil hydrogenases.

Seasonal variation in population density and heterotrophic activity of attached and free-living bacteria in coastal waters

The abundance and heterotrophic activity of attached and free-living bacteria were examined seasonally in coastal water. Heterotrophic activity was determined by the uptake of [C]glucose. The density of attached bacteria was always minor, not showing a seasonal variation, whereas the free-living bacteria were more numerous and showed a marked seasonal variation, their density being higher under warmer conditions. The contribution of the attached bacteria to the total assimilation of [C]glucose (from 10 to 38%) was lower than that of the free-living bacteria, neither of them showing a seasonal variation. On a cellular basis, attached bacteria were more active, since they assimilated more [C]glucose and showed, under warmer conditions, a higher cellular volume (0.102 versus 0.047 mum). We consider that the factors responsible for these observations were the amount and quality of the particulate material, the different availability of organic matter for the two types of bacteria, and in a fundamental way, the variation in water temperature.

Methodology for estimating numbers of free-living and attached bacteria in estuarine water

A fundamental problem in estuarine microbiology studies is the accurate determination of the density in the water column of both free-living bacteria and those attached to suspended particulate matter. When a water sample is filtered and the filter is viewed by epifluorescence microscopy, counts can be made of the numbers of bacteria which are seen on the filter background (free-living) and those which appear to lie on sediment particles (both free-living and attached). With only the additional knowledge of the proportion of the filter area covered by particles (a quantity that is straightforwardly determined by stereological point counting), results from geometric probability were used to determine the expected number of bacteria which are hidden by particles and hence to provide an estimation scheme for the true densities of free-living and attached bacteria. Variance equations based on a Taylor series are given, and a partial check of the method is attempted with controlled mixtures of bacteria and sediment. An alternative procedure is also proposed, in which the natural attached/free-living ratio is altered by an intervention experiment, allowing an estimation which is less model dependent but more labor intensive. Both methods are applied to a series of samples from the Tamar estuary, United Kingdom, taken in April 1985. A notable conclusion is that there are always more free-living than attached bacteria in the water column throughout the estuary.

Electrolyte effects on attachment of an estuarine bacterium

The effect of electrolyte concentration on attachment of Vibrio alginolyticus to hydroxyapatite was determined. Bacterial affinity for attachment to the surface and surface capacity were derived from linearization of bacterial adsorption isotherms. At low concentrations (<0.1 M) the affinity of the bacteria for the surface increased with increasing ionic strength, in agreement with the D.L.V.O. theory of colloid interaction. At higher concentrations, bacterial affinity for the surface decreased with increasing concentration of cations and was not related to ionic strength changes in the medium. These results demonstrate a change in the mechanism by which salts affect bacterial attachment at salt concentrations above 0.1 M. The results are consistent with the relationship between the proportion of attached bacteria and salinity observed in previously published field studies. The results may also resolve differences between various attachment studies carried out in different ionic strength media, utilizing different bacteria, surfaces, and experimental methods.

Thymidine incorporation by free-living and particle-bound bacteria in a eutrophic dimictic lake

The percentage of [methyl-H]thymidine incorporated into samples from a dimictic eutrophic lake and retained on polycarbonate membranes of 3.0-, 1.0-, and 0.2-mum pore size was studied in a lake with filamentous cyanobacteria as the dominant phytoplankton type throughout the period of thermal stratification. Water samples were also examined by epifluorescence microscopy for evidence of algal senescence and bacterial colonization of intact and damaged cyanobacterial filaments. A small percentage (2 to 20%) of bacterial activity was retained by filters with pore sizes >/= 1 mum in epilimnetic samples. Epilimnetic samples also had a small percentage of cyanobacterial filaments, either intact or damaged, which were visibly colonized by bacteria in summer and fall samples. A significant proportion (20 to 35%) of bacterial activity was retained by filters with pore sizes >/= 1 mum in samples collected from the metalimnion and hypolimnion during late summer and fall. The proportion of damaged cyanobacterial filaments was higher in these samples than in those from the epilimnion or from those obtained early in the summer. Furthermore, the filaments in these samples were more heavily colonized by bacteria. Overall, particle-bound production accounted for only 2 to 19% of total bacterial production from April to August in all water layers. It appears that the supply of colonizable particles (damaged cyanobacterial filaments) is an important factor affecting the level of particle-bound bacterial activity in this lake.

Modification of the gelatin-matrix method for enumeration of respiring bacterial cells for use with salt-marsh water samples

In this report I describe a modification of the gelatin-matrix method for determining the percentages of bacterial cells having active electron transport systems. This modification is one-step fluorochroming followed by use of an antioxidant solution instead of the secondary gelatin layer. The modified technique is more successfully applicable to water samples containing high densities of flocculant particulate matter, owing to the brighter green fluorescence of the cells, which contrasts with the red-orange fluorescence of the floc.

Improved method of enumeration of attached bacteria for study of fluctuation in the abundance of attached and free-living bacteria in response to diel variation in seawater turbidity

Sample preparation for enumerating attached bacteria in turbid seawater by epifluorescence microscopy was improved by treating samples with a surfactant (Tween 80) followed by sonication. With optimal treatment with Tween 80 (final concentration, 10 ppm [10 mug/ml]) and sonication, as many as 10 times more attached bacteria were enumerated from turbid seawater relative to the number enumerated from an untreated control. Dispersion of bacteria by sonication alone resulted in the enumeration of only 42 to 72% of the attached bacteria. By this technique, fluctuations in the number of attached and free-living bacteria were determined in water from Aransas Pass, Tex., where surface sediments are resuspended on a regular basis by tidal currents. The abundance of attached bacteria increased in proportion to the seawater turbidity that resulted from sediment resuspension. The variation in abundance of free-living bacteria was not directly related to seawater turbidity. However, the magnitude of fluctuation in the abundance of free-living bacteria was related to the extent of turbidity variation during diurnal tides.

Comparison of substrate utilization and growth kinetics between immobilized and suspended Pseudomonas cells

A methodology is described for measurement if immobilized and suspended cell growth and substrate utilization kinetics parameters. Substrate utilization and growth kinetics were compared between immobilized and suspended cells for toluene degrading Pseudomonas strains K3-2 and 2,4-dichlorophenoxyacetic acid (2,4-D) degrading strain DBO131(pR0101), respectively. Kinetic parameters were estimated using nonlinear parameter estimation methods and compared between the immobilized and suspended Pseudomonas cells to determine the effect of immobilization on cellular growth and substrate utilization. Factors influencing the experimental design included calculated oxygen flux rates, primary carbon substrate flux rates, and shear stresses on the immobilize cell. Statistical interpretation of the cellular reaction rate parameters indicates that only the growth kinetics of the toluene system were significantly altered upon immobilization. Substrate utilization kinetics remained unchanged upon immobilization. The substrate growth associated half-saturation constant (K(g)) for the toluene system increased by 30-fold and the maximum specific growth rate (micro(max)) decreased by 2-fold upon immobilization. Implication of these results for experimental determination of cellular kinetic parameters and for immobilization cell bioreactors design are discussed.

Viruses, bacteria and suspended particles in a backwater and main channel site of the Danube (Austria)

A short overview of currently available studies on the ecology of viruses in running waters is provided. Additionally, a survey was conducted on the dynamics of both viruses and bacteria in an isolated floodplain segment of the Danube River and in the main channel near Vienna (Austria) during the hydrologically most dynamic phase (spring - summer). The study evaluates the differences between the main channel and the floodplain segment for suspended particle abundance and quality in relation to bacterial and viral parameters; both free-living forms and those attached to particles are examined. The hydrological disconnection of these two contrasting sampling sites influenced particle abundance and quality as well as the distribution of free-living vs. attached bacteria and viruses. The per-cell activity of bacteria attached to particles was significantly higher than that of the free-living fraction, particularly in the isolated water body. The abundance of bacteria and viruses on particles depended on particle quality (size). In the main channel, bacteria were significantly more abundant on surfaces (per mm(2)) of suspended matter > 5 μm (aggregates with organic constituents) compared to particles < 5 μm (mostly mineral grains). In the isolated water body, both bacteria and viruses were more abundant on the larger particles/aggregates. Data from both locations revealed a positive correlation between abundance of particles > 5μm and attached viruses; free-living viruses were less abundant at high > 5μm particle loads. Only in the isolated floodplain section was viral abundance positively influenced by elevated per-cell productivity of potential host bacteria. The results demonstrate that system variability on a relatively small topographical scale (within a river-floodplain system) has consequences for microbial life, including viruses.

Mercury methylation by planktonic and biofilm cultures of Desulfovibrio desulfuricans

While biofilms are now known to be the predominant form of microbial growth in nature, very little is yet known about their role in environmental mercury (Hg) methylation. Findings of Hg methylation in periphyton communities have indicated the importance of investigating how environmental biofilms affect Hg methylation, as periphyton can be the base of the food webs in aquatic ecosystems. Chemical speciation influences the microbial uptake and methylation of inorganic Hg by planktonic cultures of sulfate-reducing bacteria; however, the effect of speciation on Hg methylation by biofilm cultures of these organisms has previously not been studied. In the present study, Hg methylation rates in biofilm and planktonic cultures of two isolates of Desulfovibrio desulfuricans from a coastal wetland were compared. Notably, the specific Hg methylation rate found was approximately an order of magnitude higher (0.0018 vs. 0.0002 attomol cell(-1) day(-1)) in biofilm cells than in planktonic cells, suggesting an important role for environmental biofilms in Hg methylation. To investigate the role of chemical speciation of Hg, experiments were conducted at two levels of sulfide. Both biofilm and planktonic cultures produced methylmercury at roughly twice the rate at low sulfide, when HgS(0)(aq), rather than HgHS2-, was the dominant Hg species. This indicates that the presence of a biofilm does not alter the relative availability of the dominant Hg species in sulfidic medium, in accordance with our previous studies of Hg uptake by Escherichia coli along a chloride gradient.

Aerobic anoxygenic phototrophic bacteria attached to particles in turbid waters of the Delaware and Chesapeake estuaries

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that, if abundant, may be biogeochemically important in the oceans. We used epifluorescence microscopy and quantitative PCR (qPCR) to examine the abundance of these bacteria by enumerating cells with bacteriochlorophyll a (bChl a) and the light-reaction center gene pufM, respectively. In the surface waters of the Delaware estuary, AAP bacteria were abundant, comprising up to 34% of prokaryotes, although the percentage varied greatly with location and season. On average, AAP bacteria made up 12% of the community as measured by microscopy and 17% by qPCR. In the surface waters of the Chesapeake, AAP bacteria were less abundant, averaging 6% of prokaryotes. AAP bacterial abundance was significantly correlated with light attenuation (r=0.50) and ammonium (r=0.42) and nitrate (r=0.71) concentrations. Often, bChl a-containing bacteria were mostly attached to particles (31 to 94% of total AAP bacteria), while usually 20% or less of total prokaryotes were associated with particles. Of the cells containing pufM, up to 87% were associated with particles, but the overall average of particle-attached cells was 15%. These data suggest that AAP bacteria are particularly competitive in these two estuaries, in part due to attachment to particles.

Mercury methylation and bacterial activity associated to tropical phytoplankton

The methylated form of mercury (Hg), methylmercury (MeHg), is one of the most toxic pollutants. Biotic and/or abiotic methylation, often associated to sulfate-reducing bacteria metabolism, occurs in aquatic environments and in many tropical areas, mostly in the periphyton associated to floating macrophyte roots. Data about mercury methylation by phytoplankton are scarce and the aim of this study was to verify the biotic influence in the methylation process in Microcystis aeruginosa and Sineccocystis sp. laboratory strains and in natural populations of phytoplankton from two different aquatic systems, the mesotrophic Ribeirão das Lajes reservoir and hypereutrophic oligohaline Jacarepaguá lagoon, Rio de Janeiro state, Brazil. Adapted radiochemical techniques were used to measure sulfate-reduction, mercury methylation and bacterial activity in phytoplankton samples. Methyl-(203)Hg formation from added inorganic (203)Hg and (3)H-Leucine uptake were measured by liquid scintillation as well as sulfate-reduction, estimated as H(2)(35)S produced from added Na(2)(35)SO(4). There was no significant difference in low methylation potentials (0.37%) among the two cyanobacterium species studied in laboratory conditions. At Ribeirão das Lajes reservoir, there was no significant difference in methylation, bacterial activity and sulfate-reduction of surface sediment between the sampling points. Methylation in sediments (3-4%) was higher than in phytoplankton (1.5%), the opposite being true for bacterial activity (sediment mean 6.6 against 150.3 nmol gdw(-1) h(-1) for phytoplankton samples). At Jacarepaguá lagoon, an expressive bacterial activity (477.1 x 10(3) nmol gdw(-1) h(-1) at a concentration of 1000 nM leucine) and sulfate-reduction ( approximately 21% H(2)(35)S trapped) associated to phytoplankton (mostly cyanobacteria M. aeruginosa) was observed, but mercury methylation was not detected.

Biofouling and biocorrosion in industrial water systems

Corrosion associated with microorganisms has been recognized for over 50 years and yet the study of microbiologically influenced corrosion (MIC) is relatively new. MIC can occur in diverse environments and is not limited to aqueous corrosion under submerged conditions, but also takes place in humid atmospheres. Biofouling of industrial water systems is the phenomenon whereby surfaces in contact with water are colonized by microorganisms, which are ubiquitous in our environment. However, the economic implications of biofouling in industrial water systems are much greater than many people realize. In a survey conducted by the National Association of Corrosion Engineers of the United States ten years ago, it was found that many corrosion engineer did not accept the role of bacteria in corrosion, and many of then that did, could not recognize and mitigate the problem. Biofouling can be described in terms of its effects on processes and products such as material degradation (bio-corossion), product contamination, mechanical blockages, and impedance of heat transfer. Microorganisms distinguish themselves from other industrial water contaminants by their ability to utilize available nutrient sources, reproduce, and generate intra- and extracellular organic and inorganic substances in water. A sound understanding of the molecular and physiological activities of the microorganisms involved is necessary before strategies for the long term control of biofouling can be format. Traditional water treatment strategies however, have largely failed to address those factors that promote biofouling activities and lead to biocorrosion. Some of the major developments in recent years have been a redefinition of biofilm architecture and the realization that MIC of metals can be best understood as biomineralization.

Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark

A number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30(T), belonged to the Flavobacteriaceae within the Cytophaga-Flavobacterium-Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA-DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within TENACIBACULUM: Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30(T) (=ATCC BAA-458(T)=DSM 14836(T)) as the type strain.

A simple method for differential isolation of freely dispersed and particle-associated peat microorganisms

Differential isolation of physiologically and ecologically diverse microbial groups facilitates evaluation of their activities in the environment. Here we describe a new method for differential isolation of freely dispersed and particle-associated peat microorganisms. The method is based on sequential elution of peat. Two types of natural peat, "young" sphagnum peat and "old" reed-based peat that have significantly different molecular composition as revealed by solid-state 13C NMR, were used for the method development. Various combinations of elution parameters (pH values, surfactant concentration, and sonication) were tested. Protein yield, CFU counts, 16S rDNA gene sequence, and T-RFLP analyses were used as criteria for evaluating the effectiveness of the elution protocols. The optimal method consisted of sequential elutions with (i) pH 6.2, 0.1 M potassium phosphate buffer, (ii) the same buffer amended with 0.01% of Tween 80, and (iii) treatment (ii) amended with sonication for 2 min. This method allowed differential isolation of freely dispersed and particle-associated microorganisms with (i) highest yield, (ii) highest diversity within the each microbial fraction, and (iii) best discrimination between the freely dispersed and particle-associated microbial communities. The method was applied for characterization of peat microbial communities and revealed different taxonomic composition and similar spatial organization of sphagnum and reed-sage peat microorganisms.

Bacteria of the gamma-subclass Proteobacteria associated with zooplankton in Chesapeake Bay

The seasonal abundance of gamma-subclass Proteobacteria, Vibrio-Photobacterium, Vibrio cholerae-Vibrio mimicus, Vibrio cincinnatiensis, and Vibrio vulnificus in the Choptank River of Chesapeake Bay associated with zooplankton was monitored from April to December 1996. Large (>202- microm) and small (64- to 202- microm) size classes of zooplankton were collected, and the bacteria associated with each of the zooplankton size classes were enumerated by fluorescent oligonucleotide direct count. Large populations of bacteria were found to be associated with both the large and small size classes of zooplankton. Also, the species of bacteria associated with the zooplankton showed seasonal abundance, with the largest numbers occurring in the early spring and again in the summer, when zooplankton total numbers were correspondingly large. Approximately 0.01 to 40.0% of the total water column bacteria were associated with zooplankton, with the percentage of the total water column bacteria population associated with zooplankton varying by season. A taxonomically diverse group of bacteria was associated with zooplankton, and a larger proportion was found in and on zooplankton during the cooler months of the year, with selected taxa comprising a larger percent of the Bacteria in the summer. V. cholerae-V. mimicus and V. vulnificus comprised the bulk of the large and small zooplankton-associated Vibrio-Photobacterium species. In contrast, V. cincinnatiensis accounted for less than 0.1 to 3%. It is concluded that water column and zooplankton bacterial populations vary independently with respect to species composition since no correlation was observed between taxa occurring with highest frequency in the water column and those in association with zooplankton.

Salmonella typhimurium survival and viability is unaltered by suspended particles in freshwater

Rolling microcosm experiments were conducted to determine whether suspended particles affect the survival and viability of a model pathogen, Salmonella choleraesuis, serotype typhimurium (American Type Culture Collection no. 23567), in a freshwater microbial community. Water from the Duluth, MN harbor of Lake Superior (including native microorganisms) was inoculated with clay, silt, or flocculent organic particles in a range of concentrations and a streptomycin-resistant strain of S. typhimurium. Microcosms (incubated at 20 degrees C) were rolled horizontally (3 rpm) and sampled periodically for total bacteria and total, viable, and culturable S. typhimurium. Total S. typhimurium abundance decreased rapidly in all experiments (8.5-73.1% d-1). Total bacteria did not decrease as rapidly as the S. typhimurium population in any experiment, suggesting that a microcosm effect was not responsible for the decline in S. typhimurium populations. Loss rates of attached and free cells were similar, indicating that attachment to particles did not enhance the persistence of Salmonella cells beyond our minimum detectable differences. After eight days, only 0.1 to 11.9% of the initial S. typhimurium inocula were detected by direct counts. Suspended particles had a minimal effect on the survival and viability of S. typhimurium; the losses of total, viable, or culturable Salmonella were generally the same across particle treatments and concentrations. Silt and flocculent particles affected loss rates of total and viable S. typhimurium similarly to inorganic particles (clay). It appears unlikely that suspended particles would provide a means for S. typhimurium to persist at hazardous levels in freshwater.

The protective effects of high amylose maize (amylomaize) starch granules on the survival of Bifidobacterium spp. in the mouse intestinal tract

The possibility of using high amylose maize starch granules as a delivery system for probiotic bacteria has been investigated using Bifidobacterium spp. LaftiTM 8B and LaftiTM 13B which were isolated from a healthy human. The Bifidobacterium cells were able to adhere to the amylomaize starch granules and were also able to hydrolyse the starch during growth. Initially, in vitro studies were carried out by studying the survival of strains Bifidobacterium LaftiTM 8B and LaftiTM 13B when exposed to pH 2.3, 3.5 and 6.5 as well as 0.03 and 0.05% w/v bile acids. Both strains were grown either in the absence or presence of high amylose maize starch granules, then mixed with the high amylose maize starch granules and exposed to acidic buffers or bile acid solutions. It was shown that growth in and the presence of high amylose maize starch granules led to enhanced survival of strains LaftiTM 8B and LaftiTM 13B. Subsequently, survival in vivo was monitored by measuring the faecal level of Bifidobacterium LaftiTM 8B after oral administration of the strain to mice. A sixfold better recovery of strain LaftiTM 8B from mice faeces after oral dosage was noted for cells grown in amylose-containing medium compared with controls. It was concluded that high amylose maize starch granules contributed to enhanced survival of Bifidobacterium sp. LaftiTM 8B and LaftiTM 13B.

Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Northwestern Mediterranean Sea

The aim of this study was to determine if there were differences between the types of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria associated with particulate material and planktonic samples obtained from the northwestern Mediterranean Sea. A nested PCR procedure performed with ammonia oxidizer-selective primers was used to amplify 16S rRNA genes from extracted DNA. The results of partial and full-length sequence analyses of 16S rRNA genes suggested that different groups of ammonia-oxidizing bacteria were associated with the two sample types. The particle-associated sequences were predominantly related to Nitrosomonas eutropha, while the sequences obtained from the planktonic samples were related to a novel marine Nitrosospira group (cluster 1) for which there is no cultured representative yet. A number of oligonucleotide probes specific for different groups of ammonia oxidizers were used to estimate the relative abundance of sequence types in samples of clone libraries. The planktonic libraries contained lower proportions of ammonia oxidizer clones (0 to 26%) than the particulate material libraries (9 to 83%). Samples of the planktonic and particle-associated libraries showed that there were depth-related differences in the ammonia oxidizer populations, with the highest number of positive clones in the particle-associated sample occurring at a depth of 700 m. The greatest difference between planktonic and particle-associated populations occurred at a depth of 400 m, where only 4% of the clones in the planktonic library were identified as Nitrosomonas clones, while 96% of these clones were identified as clones that were related to the marine Nitrosospira species. Conversely, all ammonia oxidizer-positive clones obtained from the particle-associated library were members of the Nitrosomonas group. This is the first indication that Nitrosomonas species and Nitrosospira species may occupy at least two distinct environmental niches in marine environments. The occurrence of these groups in different niches may result from differences in physiological properties and, coupled with the different environmental conditions associated with these niches, may lead to significant differences in the nature and rates of nitrogen cycling in these environments.

Interactions and biodegradation of the herbicide metolachlor with different surfaces

Degradation of the herbicide metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylethyl) acetamide] was used as a model compound to study degradation in aqueous media with different biofilm carriers. Biofilm carriers used were naturally occurring minerals (NOMI), activated carbons (AC), and synthetic minerals combined with activated carbon (MIAC). No transformation was found without biofilm carriers or with NOMI as carriers. Degradation with AC was accompanied by consumption of oxygen but not by release of chloride. On MIAC carriers, release of chloride was observed. Results indicate that abiotic mechanisms play a major role in this type of degradation, which can be the basis for the development of a microbial community with the ability to degrade metolachlor.