Determination of abundance and biovolume of bacteria in sediments by dual staining with 4',6-diamidino-2-phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics

The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments

Sandy sediments cover 50-60% of the continental shelves and are highly efficient bioreactors in which organic carbon is remineralized and inorganic nitrogen is reduced to N2. As such they seem to play an important role, buffering the open ocean from anthropogenic nitrogen inputs and likely remineralizing the vast amounts of organic matter formed in the highly productive surface waters. To date however, little is known about the interrelation between porewater transport, grain properties and microbial colonization and the consequences for remineralization rates in sandy sediments. To constrain the effect of theses factors on remineralization in silicate sands, we incubated North Sea sediments in flow-through reactors after separating into five different grain size fractions. Bulk sediment and sediment grain properties were measured along with microbial colonization and cell abundances, oxygen consumption and denitrification rates. Volumetric oxygen consumption ranged from 14 to 77 µmol O2 l-1 h-1 while nitrogen-loss via denitrification was between 3.7 and 8.4 µmol N l-1 h-1. Oxygen consumption and denitrification rates were linearly correlated to the microbial cell abundances, which ranged from 2.9 to 5.4·108 cells cm-3. We found, that cell abundance and consumption rates in sandy sediments are influenced (i) by the surface area available for microbial colonization and (ii) by the exposure of these surfaces to the solute-supplying porewater flow. While protective structures such as cracks and depressions promote microbial colonization, the oxygen demand is only met by good ventilation of these structures, which is supported by a high sphericity of the grains. Based on our results, spherical sand grains with small depressions, i.e. golf ball like structures, provide the optimal supporting mineral structure for microorganisms on continental shelves.

Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake

Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day⁻¹. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.

Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy)

The aims of this study were: (i) the characterization of the structure of the indigenous microbial community associated with the sediments under study; (ii) the isolation and characterization of microbial consortia able to degrade the aged hydrocarbons contaminating the sediments, and (iii) the assessment of related biodegradation capability of selected consortia. Samples of surface sediments were collected in Priolo Gargallo harbour (Sicily, Italy). The samples were analysed for physical, chemical (GC-FID analysis) and microbiological characteristics (qualitative (16S rDNA clone library) and quantitative (DAPI, CFU and MPN count) analysis). The sediment samples were used for the selection of two microbial consortia (indicated as PSO and PSM) with high biodegradation capacity for crude oil (∼95%) and PAHs (∼63%) respectively. Genetic analysis showed that Alcanivorax and Cycloclasticus were the dominant genera in both the PSO and PSM consortia. Oil-polluted environments naturally develop an elevated biorecovery potential. The presence of a highly specialized microbial flora (adapted to support the contamination) and their stimulation through favourable induced conditions provides a promising recovery strategy. The chance to identify and select indigenous bacteria and/or consortia with a high biodegradation capacity is fundamental for the development and optimization of bioaugmentation strategies especially for those concerning in situ applications.

Factors affecting the spatial and temporal distribution of E. coli in intertidal estuarine sediments

Microbiological water quality monitoring of bathing waters does not account for faecal indicator organisms in sediments. Intertidal deposits are a significant reservoir of FIOs and this indicates there is a substantial risk to bathers through direct contact with the sediment, or through the resuspension of bacteria to the water column. Recent modelling efforts include sediment as a secondary source of contamination, however, little is known about the driving factors behind spatial and temporal variation in FIO abundance. E. coli abundance, in conjunction with a wide range of measured variables, was used to construct models to explain E. coli abundance in intertidal sediments in two Scottish estuaries. E. coli concentrations up to 6 log₁₀ CFU 100 g dry wt^-1 were observed, with optimal models accounting for E. coli variation up to an adjusted R² of 0.66. Introducing more complex models resulted in overfitting of models, detrimentally affected the transferability of models between datasets. Salinity was the most important single variable, with season, pH, colloidal carbohydrates, organic content, bulk density and maximum air temperature also featuring in optimal models. Transfer of models, using only lower cost variables, between systems explained an average deviance of 42%. This study demonstrates the potential for cost-effective sediment characteristic monitoring to contribute to FIO fate and transport modelling and consequently the risk assessment of bathing water safety.

Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment

Transmission of bacteria vertically through host tissues ensures offspring acquire symbionts; however, horizontal transmission is an effective strategy for many associations and plays a role in some vertically transmitted symbioses. The bivalve Solemya velum and its gammaproteobacterial chemosynthetic symbionts exhibit evolutionary evidence of both transmission modes, but the dominant strategy on an ecological time scale is unknown. To address this, a specific primer set was developed and validated for the S. velum symbiont using a novel workflow called specific marker design (SMD). Symbionts were quantified in spawned eggs and sediment and seawater samples from S. velum habitats with qPCR. Each egg was estimated to contain 50-100 symbiont genomes. By contrast, symbiont DNA was found at low abundance/occurrence in sediment and seawater, often co-occurring with host mitochondrial DNA, obscuring its origin. To ascertain when eggs become infected, histological sections of S. velum tissues were labelled for symbiont 16S rRNA via in situ hybridization. This revealed symbionts in the ovary walls and mature oocytes, suggesting association in late oogenesis. These data support the hypothesis that S. velum symbionts are vertically transmitted every host generation, thus genetic signatures of horizontal transmission are driven by ecologically infrequent events. This knowledge furthers our understanding of vertical and horizontal mode integration and provides insights across animal-bacterial chemosynthetic symbioses.

Flow-cytometric quantification of microbial cells on sand from water biofilters

Rapid quantification of absolute microbial cell abundances is important for a comprehensive interpretation of microbiome surveys and crucial to support theoretical modelling and the design of engineered systems. In this paper, we propose a protocol specifically optimised for the quantification of microbial abundances in water biofilters using flow cytometry (FCM). We optimised cell detachment from sand biofilter particles for FCM quantification through the evaluation of five chemical dispersants (NaCl, Triton-X100, CaCl₂, sodium pyrophosphate (PP), Tween 80 combined with PP), different mechanical pre-treatments (low and high energy sonication and shaking) and two fixation methods (glutaraldehyde and ethanol). The developed protocol was cross-compared using other established and commonly employed methods for biomass quantification in water filter samples (adenosine triphosphate (ATP) quantification, real-time quantitative PCR (qPCR) and volatile solids (VS)). The highest microbial count was obtained by detaching the biofilm from biofilter grains and dispersing clusters into singles cells using Tween 80 and sodium pyrophosphate combined with four steps of high energy sonication (27W, for 80 s each step); glutaraldehyde was shown to be the best fixative solution. The developed protocol was reliable and highly reproducible and produced results that are comparable to data from alternative quantification methods. Indeed, high correlations were found with trends obtained through ATP and qPCR (ρ = 0.98 and ρ = 0.91) measurements. The VS content was confirmed as an inaccurate method to express biomass in sand samples since it correlated poorly with all the other three methods (ρ = 0.005 with FCM, 0.002 with ATP and 0.177 with qPCR). FCM and ATP showed the strongest agreement between absolute counts with a slope of the correlation equal to 0.7, while qPCR seemed to overestimate cell counts by a factor of ten. The rapidity and reproducibility of the method developed make its application ideal for routine quantification of microbial cell abundances on sand from water biofilters and thus useful in revealing the ecological patterns and quantifying the metabolic kinetics involved in such systems.

Benthic ciliate diversity and community composition along water depth gradients: a comparison between the intertidal and offshore areas

The diversity of marine benthic ciliates is largely known from the intertidal zone. No comparative data are available for the change of ciliate communities from the intertidal to offshore sediments in the Yellow Sea. We investigated the community composition and diversity of benthic ciliates at two intertidal (sandy and silty-sand) stations and eight offshore stations along a latitudinal transect in the Yellow Sea. The ciliate abundance and biomass decreased almost linearly with increasing water depth and distance from the intertidal zone. Diversity indices showed a similar trend. By contrast, the total species richness and taxonomic diversity were much higher in the offshore sediments than in the intertidal area. Among the total of 94 species identified, only 20 species were shared by the two habitats, which were characterized by different dominant ciliate assemblages. Carnivorous ciliates always constituted the primary feeding type in terms of biomass at all offshore stations and the intertidal sandy station, whereas at the intertidal silty-sand station the primary feeding group varied throughout the period of sampling. Multivariate analyses indicates the ciliate communities were significantly different between the two habitats. Bottom water temperature and sediment grain size were the key factors that explained the ciliate community structure.

Trophic ecology of glass sponge reefs in the Strait of Georgia, British Columbia

Sponges link the microbial loop with benthic communities by feeding on bacteria. Glass sponge reefs on the continental shelf of western Canada have extremely high grazing rates, consuming seven times more particulate carbon than can be supplied by vertical flux alone. Unlike many sponges, the reef building species Aphrocallistes vastus has no microbial symbionts and removes little dissolved organic carbon. To determine how reef sponges therefore get enough food to sustain such substantial grazing we measured stable carbon and nitrogen isotope signatures of water, sediment and sponge tissues. To ensure samples were temporally associated, we also studied the duration particles were retained in tissues in controlled feeding studies using microscopic beads and ¹³C-labeled bacteria. Although fecal pellets were expelled from sponges within 24 hours of feeding, intact bacteria were still found in tissues and sponge tissues retained elevated ¹³C levels for at least 14 days. These independent lines of evidence suggest that carbon in reef sponge tissues may reflect food consumed from days to weeks earlier. Stable isotope analysis suggests that heterotrophic bacteria ingested by the sponges comes from a confluence of trophic subsidies: from terrestrial and oceanic sources, and also potentially on sediment-borne bacteria resuspended by tidal currents.

Feasibility of treating emulsified oily and salty wastewaters through coagulation and bio-regenerated GAC filtration

In the present study, chemical oxygen demand (COD) removal by coagulation and packed-columns of both fresh and bioregenerated granular activated carbon (GAC) is reported as a feasible treatment for saline and oily wastewaters (slops) generated from marine oil tankers cleaning. The use of Ferric chloride (FeCl₃), Aluminium sulphate (Al₂(SO₄)₃) and Polyaluminum chloride (Al₂(OH₃)Cl₃) was evaluated in the pre-treatment by coagulation of a real slop, after a de-oiling phase in a tank skimmer Comparison of coagulation process indicated that Polyaluminum chloride and Aluminium sulphate operate equally well (20-30% of COD removal) when applied at their optimal dose (40 and 90 mg/l respectively) but the latter should be preferred in order to significantly control the sludge production. The results from the column filtration tests indicated the feasibility of using the selected GAC (Filtrasorb 400 -Calgon Carbon Corporation) to achieve the respect of the discharge limits in the slops treatment with a carbon usage rate in the range 0.1-0.3 kg/m³ of treated effluent. Moreover, biological regeneration through Alcalinovorax borkumensis SK2 was proved to be a cost-effective procedure since the reuse of spent GAC through such regeneration process for further treatment could still achieve approximately 90% of the initial sorption capacity, reducing then costs for the use of new sorbents and also the need for waste disposal.

Utilization of carbon substrates by heterotrophic bacteria through vertical sediment profiles in coastal and estuarine seagrass meadows

Coastal vegetated ecosystems play an important role in carbon cycling and bacterial communities inhabiting coastal sediments are responsible for the remineralization and processing of organic carbon (OC). We collected 1 m-long sediment cores in Posidonia seagrass meadows from coastal and estuarine sites in Australia that differed in their sedimentary organic and inorganic carbon, nitrogen and mud contents. The metabolic diversity of sediment heterotrophic bacterial communities was characterized at different sediment depths, based on the utilization pattern of 31 individual carbon substrates using Biolog EcoPlates^TM . High metabolic diversity was recorded at both sites, but the carbon substrate utilization rates and the use of carbohydrates were higher at the coastal site compared to the estuarine site. The heterotrophic bacterial community in the coastal sediment appeared to metabolize a more diverse OC pool compared to the estuarine site, which might partly explain the differences in OC storage among the seagrass habitats studied. The Biolog EcoPlates^TM provided a useful tool for characterising the sediment heterotrophic bacterial communities in the meadows and sediment characteristics and biochemical composition of the organic matter played an important role in shaping heterotrophic bacterial communities and their carbon utilization rates, potentially affecting carbon accumulation and preservation within seagrass sediments.

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic

Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7)  cells ml(-1) (mean 3.12 × 10(6)  cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.

Intrinsic bioremediation potential of a chronically polluted marine coastal area

A microbiological survey of the Priolo Bay (eastern coast of Sicily, Ionian Sea), a chronically polluted marine coastal area, was carried out in order to discern its intrinsic bioremediation potential. Microbiological analysis, 16S rDNA-based DGGE fingerprinting and PLFAs analysis were performed on seawater and sediment samples from six stations on two transects. Higher diversity and variability among stations was detected by DGGE in sediment than in water samples although seawater revealed higher diversity of culturable hydrocarbon-degrading bacteria. The most polluted sediment hosted higher total bacterial diversity and higher abundance and diversity of culturable HC degraders. Alkane- and PAH-degrading bacteria were isolated from all stations and assigned to Alcanivorax, Marinobacter, Thalassospira, Alteromonas and Oleibacter (first isolation from the Mediterranean area). High total microbial diversity associated to a large selection of HC degraders is believed to contribute to natural attenuation of the area, provided that new contaminant contributions are avoided.

Metabolic activity and functional diversity changes in sediment prokaryotic communities organically enriched with mussel biodeposits

This experimental microcosm study reports the influence of organic enrichments by mussel biodeposits on the metabolic activity and functional diversity of benthic prokaryotic communities. The different biodeposit enrichment regimes created, which mimicked the quantity of faeces and pseudo-faeces potentially deposited below mussel farms, show a clear stimulatory effect of this organic enrichment on prokaryotic metabolic activity. This effect was detected once a certain level of biodeposition was attained with a tipping point estimated between 3.25 and 10 g day^-1 m^-2. Prokaryotic communities recovered their initial metabolic activity by 11 days after the cessation of biodeposit additions. However, their functional diversity remained greater than prior to the disturbance suggesting that mussel biodeposit enrichment may disturb the functioning and perhaps the role of prokaryotic communities in benthic ecosystems. This manipulative approach provided new information on the influence of mussel biodeposition on benthic prokaryotic communities and dose-response relationships and may support the development of carrying capacity models for bivalve culture.

Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities

Cell biovolume is a commonly used metric of microbial abundance analyzed by computer-assisted microscopy, but the accuracies of most biovolume formulas have not been validated by ground truth data. We examined the accuracy of 17 biovolume formulas by comparing the computed volumes of 3D models representing 11 microbial morphotypes (cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, prosthecates, rudimentary branched rods, and branched filaments) to the volume displacement of the same objects as ground truth. As anticipated, formula accuracy was significantly influenced by the morphotype examined. A few formulas performed very accurately (> 95 %), especially those that adapted to the cell's shape, whereas others were consistently inaccurate or only accurate for one or two morphotypes. As an example of application, indices of morphological diversity in a freshwater biofilm assemblage were shown to be significantly different when microbial abundance among morphotype classes was measured as biovolume body mass rather than cell counts. Spatial analysis of biovolume body mass can also provide insights on the in situ ecophysiological attributes among individuals in microbial populations and communities, including their spatially autocorrelated allometric scaling interrelationships between body size, metabolic activity, resource apportionment and use, food web dynamics, and various cell-cell interactions affecting their growth and colonization behavior within spatially structured biofilm landscapes. This improved computing technology of biovolume algorithms with proven accuracy identifies which formula(s) should be used to compute microbial biovolumes in 2D images of morphologically diverse communities acquired by conventional phase-contrast light microscopy at single-cell resolution.

An efficient and rapid method for the enumeration of heterotrophic prokaryotes in coastal sediments by flow cytometry

Flow cytometry offers an easy and powerful way to assess multi-parametric data in different domains, notably in the environmental sciences. Because evaluating heterotrophic prokaryotic abundance is crucial to understand an ecosystem's functioning, we propose a quick and efficient protocol for (1) cell's detachment in muddy coastal sediments followed by (2) enumeration of prokaryotes by flow cytometry compared to epifluorescence microscopy and (3) a type of storage adapted for benthic samples. First, sample preparation by incubation in a detergent mix containing sodium pyrophosphate (0.01M final concentration) and Tween 80 (0.1% final concentration) drastically increased cell detachment from sediment particles (+130.40%) compared to extraction with sodium pyrophosphate only. Cell sorting allowed to control the efficiency of the extraction as few cells were found attached to sediment particles in epifluorescence microscopy after sorting. Flow cytometry gave consistent results with strong reliability by counting 1.81 times more cells compared to epifluorescence microscopy. Thirdly, results revealed that sediment samples fixed with formaldehyde and then liquid-N2 frozen and directly stored at -80°C can be analyzed within 3months. In routine, our method of extraction and counting allowed to evaluate 83.67% of the real abundance in a sediment sample. Finally, this optimized technique was applied on sandy and muddy coastal and freshwater sediments and allowed us to prove the high efficiency of this new method. Flow cytometry is a fast, replicable and low-cost method for counting heterotrophic prokaryotes, even for sediment samples. The two-step method that we developed enables high frequency analyses (30 samples in less than 4h).

Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation

The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs) in coastal sediments. Approximately 1000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6500 ppm). The rapid consumption of oxygen by aerobic heterotrophs created highly reduced conditions in the sediments with subsequent recession of biodegradation rates. As follows, after 3 months of ageing, the anaerobic sediments did not exhibit any significant levels of biodegradation and more than 80% of added Bunker C fuel oil remained buried. Anaerobic microbial community exhibited a strong enrichment in sulfate-reducing PHs-degrading and PHs-associated Deltaproteobacteria. As an effective bioremediation strategy to clean up these contaminated sediments, we applied a Modular Slurry System (MSS) allowing the containment of sediments and their physical-chemical treatment, e.g., aeration. Aeration for 3 months has increased the removal of main PHs contaminants up to 98%. As revealed by CARD-FISH, qPCR, and 16S rRNA gene clone library analyses, addition of Bunker C fuel oil initially affected the activity of autochthonous aerobic obligate marine hydrocarbonoclastic bacteria (OMHCB), and after 1 month more than the third of microbial population was represented by Alcanivorax-, Cycloclasticus-, and Marinobacter-related organisms. In the end of the experiment, the microbial community composition has returned to a status typically observed in pristine marine ecosystems with no detectable OMHCB present. Eco-toxicological bioassay revealed that the toxicity of sediments after treatment was substantially decreased. Thus, our studies demonstrated that petroleum-contaminated anaerobic marine sediments could efficiently be cleaned through an in situ oxygenation which stimulates their self-cleaning potential due to reawakening of allochtonous aerobic OMHCB.

Diversity, cold active enzymes and adaptation strategies of bacteria inhabiting glacier cryoconite holes of High Arctic

Cryoconite holes have biogeochemical, ecological and biotechnological importance. This communication presents results on culturable psychrophilic bacterial diversity from cryoconite holes at Midre Lovénbreen (ML), Austre Brøggerbreen (AB), and Vestre Brøggerbreen (VB) glaciers. The culturable bacterial count ranged from 2.7 × 10(3) to 8.8 × 10(4) CFUs/g while the total bacterial numbers ranged from 5.07 × 10(5) to 1.50 × 10(6) cells at the three glaciers. A total of 35 morphologically distinct bacterial isolates were isolated. Based on 16S rRNA gene sequence data, the identified species belonged to eight genera namely Pseudomonas, Polaromonas, Micrococcus, Subtercola, Agreia, Leifsonia, Cryobacterium and Flavobacterium. The isolates varied in their growth temperature, NaCl tolerance, growth pH, enzyme activities, carbon utilization and antibiotic sensitivity tests. Fatty acid profiles indicate the predominance of branched fatty acids in the isolates. To the best of our knowledge, this is the first record of culturable bacterial communities and their characterization from glacier cryoconites from High Arctic. High amylase and protease activities expressed by Micrococcus sp. MLB-41 and amylase, protease and lipase activities expressed by Cryobacterium sp. MLB-32 provide a clue to the potential applications of these organisms. These cold-adapted enzymes may provide an opportunity for the prospect of biotechnology in Arctic.

Effects of a chronic lower range of triclosan exposure on a stream mesocosm community

Triclosan (5-chloro-2-(2,4-dichlorophenoxy)phenol) is an antimicrobial found in consumer soaps and toothpaste. It is in treated wastewater effluents at low parts-per-billion concentrations, representing a potentially chronic exposure condition for biota inhabiting receiving streams. For the present study, a naturally colonized benthos was created using flow-through indoor mesocosms; then, the benthic communities were dosed to achieve different in-stream triclosan concentrations (control, 0.1 μg/L, 0.5 μg/L, 1.0 μg/L, 5.0 μg/L, and 10 μg/L) for 56 d. Water quality parameters and endpoints from bacteria to macroinvertebrates, as well as interacting abiotic components, were measured. Effects of triclosan on specific microbial endpoints were observed at all doses, including an effect on litter decomposition dynamics at doses of 1.0 μg/L and higher. Resistance of periphytic bacteria to triclosan significantly increased at doses of 0.5 μg/L and above. By the end of dosing, the antimicrobial appeared to stimulate the stream periphyton at the 3 lowest doses, while the 2 highest doses exhibited decreased stocks of periphyton, including significantly lower bacteria cell densities and cyanobacteria abundance compared with the control. Other than an effect on benthic ostracods, the changes that occurred in the periphyton did not translate to significant change in the colonizing nematodes, the macroinvertebrate community as a whole, or other measurements of stream function. The results shed light on the role a low, chronic exposure to triclosan may play in effluent-dominated streams.

[Comparison of techniques for coliform bacteria extraction from sediment of Xochimilco Lake, Mexico]

The need to separate bacteria from sediment in order to appropriately count them has led to test the efficacy of different techniques. In this research, traditional techniques such as manual shaking, homogenization, ultrasonication, and surfactant are compared. Moreover, the possibility of using a set of enzymes (pancreatine) and an antibiotic (ampicillin) for sediment coliform extraction is proposed. Samples were obtained from Xochimilco Lake in Mexico City. The most probable number of coliform bacteria was determined after applying the appropriate separation procedure. Most of the techniques tested led to numbers similar to those of the control (manual shaking). Only with the use of ampicillin, a greater total coliform concentration was observed (Mann-Whitney, z = 2.09; p = 0.03). It is possible to propose the use of ampicillin as a technique for total coliform extraction; however, it is necessary to consider sensitivity of bacteria to the antibiotic.

Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

Impact of copper on the abundance and diversity of sulfate-reducing prokaryotes in two chilean marine sediments

We studied the abundance and diversity of the sulfate-reducing prokaryotes (SRPs) in two 30-cm marine chilean sediment cores, one with a long-term exposure to copper-mining residues, the other being a non-exposed reference sediment. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and showed that SRPs are sensitive to high copper concentrations, as the mean number of SRPs all along the contaminated sediment was two orders of magnitude lower than in the reference sediment. SRP diversity was analyzed by using the dsrB-sequences-based PCR-DGGE method and constructing gene libraries for dsrB-sequences. Surprisingly, the diversity was comparable in both sediments, with dsrB sequences belonging to Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae, SRP families previously described in marine sediments, and to a deep branching dsrAB lineage. The hypothesis of the presence of horizontal transfer of copper resistance genes in the microbial population of the polluted sediment is discussed.

Benthic diatom communities from two salt marshes of the St. Lawrence Estuary (Canada)

Microphytobenthic diatom communities were investigated in the high and low sections of two salt marshes of the Lower St. Lawrence Estuary (eastern Canada): one featuring a sandy low marsh zone (Pointe-aux-Épinettes; PE) and one with a muddy low marsh area (Pointe-au-Père; PP). Based on diatom composition and diversity, bacterial abundance, chlorophyll-a, phaeopigments and geochemical analyses (Corg, Ntot, granulometry, extracellular polymeric substances), the PP high marsh area appeared to be singular compared to the other sampling sites. Estimated surface biomass ranged from 11 to 71 g C•m-2in the PE marsh and from 24 to 486 g C•m-2in the PP marsh. A higher diversity of diatom species was observed in the PP high marsh area with a dominance of epipelic forms, in opposition to the dominant epipsammic forms at the other sites. Statistical analyses showed that diatom density was mainly affected by nutrient availability while the relative abundance of epipelic and epipsammic species was related to sediment grain size. This study provides original data on the composition of benthic diatoms in surface sediments in St. Lawrence saltmarshes during summer time that represent the first step to the determination of the DBI (Diatom biological index) of these northern environments.

Complexation between Hg(II) and biofilm extracellular polymeric substances: an application of fluorescence spectroscopy

The three-dimensional excitation emission matrix (EEM) fluorescence spectroscopy was employed to investigate the interaction of extracellular polymeric substances (EPS) from natural biofilm with Hg(II). The EEM spectra demonstrated that EPS with molecular weight over 14 kDa had two protein-like fluorescence peaks. The fluorescence intensity at both peaks was strongly dependent on the solution pH in the absence and presence of Hg(II), with the maximal fluorescence intensity at neutral pH. Fluorescence of both protein-like peaks was significantly quenched by Hg(II). The values of conditional stability constants (log K(a)=3.28-4.48) derived from modified Stern-Volmer equation are approximate to those for humic substances and dissolved organic matter (DOM), indicating that fluorescent components in EPS have strong binding capacity for Hg(II). Our findings suggest that EPS from biofilm is a class of important organic ligands for complexation with Hg(II) and may significantly affect the chemical forms, mobility, bioavailability and ecotoxicity of heavy metals in the aquatic environment.

Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandrium catenella

Dinoflagellates of the genus Alexandrium are photosynthetic microalgae that have an extreme importance due to the impact of some toxic species on shellfish aquaculture industry. Alexandrium catenella is the species responsible for the production of paralytic shellfish poisoning in Chile and other geographical areas. We have constructed a cDNA library from midexponential cells of A. catenella grown in culture free of associated bacteria and sequenced 10,850 expressed sequence tags (ESTs) that were assembled into 1,021 contigs and 5,475 singletons for a total of 6,496 unigenes. Approximately 41.6% of the unigenes showed similarity to genes with predicted function. A significant number of unigenes showed similarity with genes from other dinoflagellates, plants, and other protists. Among the identified genes, the most expressed correspond to those coding for proteins of luminescence, carbohydrate metabolism, and photosynthesis. The sequences of 9,847 ESTs have been deposited in Gene Bank (accession numbers EX 454357-464203).

Fluorescence microscopy as a tool for in situ life detection

The identification of extant and, in some cases, extinct bacterial life is most convincingly and efficiently performed with modern high-resolution microscopy. Epifluorescence microscopy of microbial autofluorescence or in conjunction with fluorescent dyes is among the most useful of these techniques. We explored fluorescent labeling and imaging of bacteria in rock and soil in the context of in situ life detection for planetary exploration. The goals were two-fold: to target non-Earth-centric biosignatures with the greatest possible sensitivity and to develop labeling procedures amenable to robotic implementation with technologies that are currently space qualified. A wide panel of commercially available dyes that target specific biosignature molecules was screened, and those with desirable properties (i.e., minimal binding to minerals, strong autofluorescence contrast, no need for wash steps) were identified. We also explored the potential of semiconductor quantum dots (QDs) as bacterial and space probes. A specific instrument for space implementation is suggested and discussed.

Recovery and quantification of bacterial cells associated with streambed sediments

Efficient detachment and purification of bacterial cells associated with streambed sediments are required in order to quantify cell abundance and to assess community composition through the application of epifluorescence microscopy techniques. We applied chemical (i.e., sodium pyrophosphate and polysorbate) and physical treatments (i.e., shaking and sonication), followed by Nycodenz density gradient centrifugation to efficiently recover benthic bacteria. This procedure resulted in a highly purified cell suspension allowing for a precise cell quantification through the application of fluorescent dyes. About 93% of total cells were recovered from the original sediment, with higher recovery from the finer grain-size class (90%) in comparison to the coarse fraction (69%). The potential damaging effects of the applied procedures on cell integrity were assessed on planktonic bacteria in a pre-filtered water control. As a consequence of the high purity of the extracted bacteria, flow cytometry was successfully applied as counting method for sediment cell suspension. However, a significant decrease of protein synthesis in purified samples was measured by estimating the (3)H-Leucine incorporation rates, rising uncertainties on the possibility to apply potential metabolic assays after Nycodenz purification.

Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession

Bacterial community succession corresponds to changes in the phylogenetic identity, growth-response time and rRNA operon (rrn) copy number of culturable populations. To test this hypothesis, we compared the bacterial fractions culturable from the oxic zone of flooded, unplanted paddy soil microcosms after 1-day (early succession) and 70-day (late succession) incubation periods. The proportion of bacteria that was cultivable on solid media corresponded for early and late succession to 37-40% and 31-35% of total DAPI cell counts, which were 7.40 (+/-0.36) x 10(8) and 5.54 (+/-0.28) x 10(8) cells per gram of dry soil, respectively. In colony-forming curve analysis, late successional bacteria showed a significant delay in their growth response compared with those from early succession. A total of 59 early successional isolates grouped into 16 species-level clusters (SLC) plus three Bacilli-like SLC, while 66 late successional isolates formed 25 SLC plus five Bacilli-like SLC. Except Bacilli-like spp., isolates from early succession always belonged to different SLC than those from late succession. Betaproteobacteria and Gammaproteobacteria were typical of the early stage, while Alphaproteobacteria and Actinobacteria prevailed in late succession. Considering all SLC except those assigned to Bacilli, growth-response time and rrn copy number were significantly correlated with successional stage. Isolates of most early successional SLC (14 of 16) formed visible colonies within 1 (11 SLC) or 2 days (three SLC) and contained >or= 4 rrn copies. In contrast, isolates of late successional SLC (23 of 25) formed visible colonies within 2 days (four SLC) or, in most cases, only within 3-15 days (19 SLC) and contained <or= 2 rrn copies. Regardless of whether isolated from early or late succession, Bacilli-like isolates always showed a colony-forming time of 2 days and had 9-11 rrn copies.

A new method based on image analysis for determining cyanobacterial biomass by CLSM in stratified benthic sediments

Cyanobacteria are the dominant primary producers in microbial mats, which are stratified benthic microbial ecosystems found in coastal environments. Some cyanobacteria form long filaments, which make difficult to apply classical methods to estimate their biomass because they establish strong interactions with detritic particles. In a previous study, we described a method for determining cyanobacterial biomass by means of confocal laser scanning microscopy (CLSM). However, the manual method used, based on summa projection images, was difficult to apply when analyzing a large number of samples. In this paper, we described a new automated method, based on stacks and applying the plugin voxel counter in the ImageJ analysis system, more adequate for obtaining biomass data quickly from a large number of CLSM images.

Enumeration of soil bacteria with the green fluorescent nucleic acid dye Sytox green in the presence of soil particles

Total counts in soils are usually determined using fluorescent dyes, such as DAPI or Sybr green, due to fluorescence enhancement if they are bound to nucleic acids. Unfortunately, these commonly used dyes stain soil particles as well. Therefore, besides fluorescence enhancement, sufficient spectral differentiation is also required. We present a new procedure that overcomes the problems of visualising bacteria on surfaces in soil and avoids the separation of soil particles to a large extent. Spectral differentiation between bacteria and soil matrix is achieved by using Sytox green and a suboptimal excitation wavelength. Bacteria exhibit a bright green fluorescence, while soil particles fluoresce blue or red. Slight homogenisation and sedimentation of the sand and coarse silt that were too big for microscopic investigations were the only separation steps required. We compared the proposed Sytox green staining with Sybr green staining. The recovery of Sybr green-stained cells amounted to 38%, whereas in samples stained by Sytox green 81% of the spiked cells were counted. Sytox green can also be combined with fluorescence in situ hybridisation (FISH) using deep red dyes such as Cy5.

A disintegration method for direct counting of bacteria in clay-dominated sediments: dissolving silicates and subsequent fluorescent staining of bacteria

The masking of bacteria by abundant microparticles of the clay and silt fraction and cell losses due to sonication hampered direct enumeration of bacteria in sediments dominated by fine sediments. These problems can be circumvented by dissolving silicate fine particles using hydrofluoric acid and subsequent staining of bacteria by DTAF. The developed disintegration method partly replaces mechanical separation of bacteria from sediment particles by chemical disintegration of the silicates. Recovery efficiency ranged from 90% to 111% for different clays and clay-dominated sediments. Especially for the analysis of fine sediments and clays, this method circumvents both strong dilution of the sediment sample and harsh sonication. The method can also therefore be used in sediments where particle abundance is several orders of magnitude higher than bacterial abundance and simple dilution would not suffice in reliably counting bacteria.

Quantitative importance, composition, and seasonal dynamics of protozoan communities in polyhaline versus freshwater intertidal sediments

The quantitative importance and composition of protozoan communities was investigated in sandy and silty intertidal sediments of a polyhaline and a freshwater site in the Schelde estuary. Total biomass of the protozoans studied, integrated over the upper 4 cm of the sediment, ranged from 41 to 597 mg C m(-2) and was in the same order of magnitude at the polyhaline and the freshwater intertidal site. Nanoheterotrophs were the dominant protozoans, in terms of both abundance and biomass. Ciliate abundances appeared to be largely determined by physical constraints, namely, the amount of interstitial space and hydrodynamic disturbances. It remains unclear which factors control nanoheterotrophic abundances and biomasses, which showed comparatively little seasonal and between-site fluctuations. Salinity differences were clearly reflected in the protozoan community composition. The dominant role of sessile ciliates is a unique feature of sediments in the freshwater tidal reaches, which can be attributed to the dynamic nature of sedimentation and resuspension processes associated with the maximum turbidity zone. Based on biomass ratios and estimated weight-specific metabolic rates, protozoa possibly accounted for approximately 29 to 96% of the estimated combined metabolic rate of protozoan and metazoan consumers at our sampling stations in late spring/early autumn. The contribution of protozoa to this combined metabolic rate was higher at the sandy than at the silty stations and was mainly accounted for by the nanoheterotrophs. These data emphasize the potential importance of small protozoa in sediments and suggest that protozoa are important components of benthic food webs.

Development of multicolour digital image analysis system to enumerate actively respiring bacteria in natural river water

AIMS

To develop a rapid and simple method for the assessment of metabolic activity of bacteria in natural environment.

METHODS AND RESULTS

A rapid and simple multicolour digital image analysis system for enumerating viable bacteria based on active fluorescent staining has been developed. This system can accurately differentiate actively respiring bacteria and non-respiring bacteria by distinctive colour information in the digital image captured by an epifluorescence microscope equipped with low magnification objective lens. An algorithm to distinguish bacteria from considerable detritus, which produced bright fluorescence in different colours, by colour segmentation has also been developed. This system was applied to river water samples, and the total and respiratory active bacterial counts by digital image analysis were highly related to those by epifluorescence microscopy (r2 = 0.96 and 0.93, respectively).

CONCLUSION

This system allowed the rapid and simple differentiation of bacteria from detritus and concurrent assessment of their metabolic activity, with results being available within 1 h.

SIGNIFICANCE AND IMPACT OF THE STUDY

The low magnification image analysis allows more rapid and simple quantification of bacteria and could considerably decrease image data amount and acquisition time. This system could be easily applied to the rapid analysis of microbes in various environments.

Flow cytometry and conventional enumeration of microorganisms in ships' ballast water and marine samples

Conventional methods for bacteriological testing of water quality take long periods of time to complete. This makes them inappropriate for a shipping industry that is attempting to comply with the International Maritime Organization's anticipated regulations for ballast water discharge. Flow cytometry for the analysis of marine and ship's ballast water is a comparatively fast and accurate method. Compared to a 5% standard error for flow cytometry analysis the standard methods of culturing and epifluorescence analysis have errors of 2-58% and 10-30%, respectively. Also, unlike culturing methods, flow cytometry is capable of detecting both non-viable and viable but non-culturable microorganisms which can still pose health risks. The great variability in both cell concentrations and microbial content for the samples tested is an indication of the difficulties facing microbial monitoring programmes. The concentration of microorganisms in the ballast tank was generally lower than in local seawater. The proportion of aerobic, microaerophilic, and facultative anaerobic microorganisms present appeared to be influenced by conditions in the ballast tank. The gradual creation of anaerobic conditions in a ballast tank could lead to the accumulation of facultative anaerobic microorganisms, which might represent a potential source of pathogenic species.

Effect of associated bacteria on the growth and toxicity of Alexandrium catenella

Saprophytic bacteria in cultures of the marine dinoflagellate Alexandrium catenella were removed to assess their effect on growth and paralytic shellfish poisoning toxin production of this dinoflagellate. The actual axenic status was demonstrated by the lack of observable bacteria both immediately after treatment and following extended incubation in the absence of antibiotics. Bacteria were measured by counting CFU and also by epifluorescence microscopy and PCR amplification of bacterial 16S-23S spacer ribosomal DNA to detect noncultivable bacteria. Removal of bacteria did not have any effect on the growth of the dinoflagellate except for the inhibition of A. catenella disintegration after reaching the stationary phase. Toxicity was determined in dinoflagellate cell extracts by different methods: high-performance liquid chromatography (HPLC); an electrophysiological test called the Electrotest, which measures the inhibition of saxitoxin-sensitive Na(+) channels expressed in a cell line; and a mouse bioassay, which measures the toxic effect on the whole mammal neuromuscular system. A lower toxicity of the dinoflagellates in axenic culture was observed by these three methods, though the difference was significant only by the mouse bioassay and HPLC methods. Altogether the results indicate that axenic cultures of A. catenella are able to produce toxin, though the total toxicity is probably diminished to about one-fifth of that in nonaxenic cultures.

Ultrasound increases the rate of bacterial cell growth

Ultrasound was employed to increase the growth rate of bacterial cells attached to surfaces. Staphylococcus epidermidis, Pseudomonas aeruginosa, and Escherichia coli cells adhered to and grew on a polyethylene surface in the presence of ultrasound. It was found that low-frequency ultrasound (70 kHz) of low acoustic intensity (<2 W/cm(2)) increased the growth rate of the cells compared to growth without ultrasound. However, at high intensity levels, cells were partially removed from the surface. Ultrasound also enhanced planktonic growth of S. epidermidis and other planktonic bacteria. It is hypothesized that ultrasound increases the rate of transport of oxygen and nutrients to the cells and increases the rate of transport of waste products away from the cells, thus enhancing their growth.

Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys

The culturability of microorganisms in a 10 cm core of an Australian pasture soil was investigated using a minimal agar medium with xylan as the growth substrate. Culturability decreased with increasing depth, from a maximum of 19% of the total microscopically countable cells in the 0-2 cm section to 2.4% in the 8-10 cm section. Seventy-one isolates from the core were identified by comparative 16S rRNA gene sequence analysis. Many of these isolates belong to groups of globally distributed soil bacteria, including well-characterized families of the classes Alphaproteobacteria and Betaproteobacteria, and of the subclass Actinobacteridae. Other isolates belong to groups with few or no cultivated representatives: 10 isolates in two subdivisions of the phylum Acidobacteria, five isolates in a new order and nine isolates in a new family of the class Alphaproteobacteria, two isolates in a new order of the class Gammaproteobacteria, three isolates in two new families of the subclass Actinobacteridae, and two isolates in the subclass Rubrobacteridae. These new isolates represent the first laboratory cultures able to be assigned to some of these groups and greatly increase the number of cultivated strains known for others. This demonstrates that a minimal change in cultivation strategy (using a polymeric growth substrate and longer incubation times) can result in the isolation of globally distributed but previously uncultured phylogenetically novel soil bacteria.