A microautoradiographic study of the activity of attached and free-living bacteria

Microautoradiography, combined with epifluorescent microscopy, was used to evaluate the uptake of tritiated amino acids by a marine Pseudomonas sp. A comparison was made between the activity of bacteria free-living in the medium and bacteria which were attached to glass, polyethylene or polystyrene substrata. The proportion of active bacteria was lower for free-living cells (53–82%) and those attached to polystyrene (53–76%) than for those attached to glass (77–99%) or polyethylene (73–96%). For bacteria attached to glass, assimilated labelled substrate was retained within the cell over 3 h, whereas with polyethylene, labelled material was released from the cells and adsorbed on the surrounding substratum. Hence the physiological activity of attached bacteria depended on the chemical composition of the substratum.     

Growth characteristics of small and large free-living and attached bacteria in Lake Constance

The growth characteristics of small (0.2–1.0m) and large (1.0–3.0 (m) free-living and attached bacteria were studied in Lake Constance by comparing the spatial and seasonal dynamics of their biomass turnover time (ratio of biomass/production). The biomass of small free-living bacteria usually turned over significantly faster than that of large free-living bacteria throughout the water column. The turnover of attached bacterial biomass was characterized by large fluctuations. Occasionally, in aphotic water layers, it was as long as that of large free-living bacteria, but when large amounts of decaying organic particles were present, it was shorter than that of small free-living cells. Biomass turnover times of free-living bacteria were in the same range as their generation times, which were estimated from the increase in bacterial abundance in 3m prefiltered samples. The biomass turnover time of actively metabolizing bacteria was comparable to the generation time of actively metabolizing cells. These results indicate that the biomass turnover time is a useful indicator of the growth of different bacterial fractions, as it reflects their different amounts of participation in microbial processes of aquatic ecosystems.     

Polar lipid biomarkers of free-living bacteria from oligotrophic marine waters

Free-living marine bacteria isolated from oligotrophic Mediterranean waters were enriched in culture to characterize their phospholipid fatty acids (PLFAs). Odd chain iso- and anteiso-FAMEs and n–16:0 were the predominant structural PLFAs, together with a homologous series identified as mid-chain methoxy FAMEs. The dominant methoxy fatty acids identified were 9-CH₃O-15:0, 9-CH₃-16:0 and 11-CH₃O-17:0, occuring as pairs of stereoimers. Methoxy fatty acids accounted for up to 37% of PLFAs of free-living bacteria, which sets them as promising new biomarkers for bacteria of oligotrophic waters. Although similar homologues have already been characterized in a variety of eukaryotes and prokaryotes, methoxy fatty acids are identified here for the first time in marine bacteria. Analytical difficulties that may hinder the characterization of these biomarkers are presented, and structural elucidation keys by gas chromotography coupled to mass spectrometry are discussed. Whilst bacterial branched fatty acids were transferred to storage lipids of bacterivorous flagellates methoxy acids were not transferred to higher trophic levels in the studied conditions.     

Amino Acid assimilation and electron transport system activity in attached and free-living marine bacteria

[This corrects the article on p. 818 in vol. 45.].     

Spatiotemporal variability in archaeal communities of tropical coastal waters

Spatiotemporal variations in the archaeal community structure from four locations along the central west coast of India were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling and sequencing of prominent bands on the DGGE gels. A total of 36 water samples were collected during pre-monsoon, post-monsoon and monsoon seasons from three depths (surface, mid-depth , and close to bottom ～20 m). The community DNA extracts from these samples were subjected to DGGE analysis. The results of this study clearly indicate a significant difference in the community structure between sampling locations and seasons. Location-wise variation was more pronounced during pre-monsoon and post-monsoon seasons. During monsoon, however, the depth-wise variation was pronounced, suggesting monsoon influence on archaeal community structure. Sequencing of DGGE bands suggested the presence of marine group I and II archaea. Canonical correspondence analysis indicated that nitrate, nitrite and chlorophyll a were the significant explanatory variables responsible for > 60 % variation in archaeal community in these coastal waters.     

Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages

Marine snow aggregates are microbial hotspots that support high bacterial abundance and activities. We conducted laboratory experiments to compare cell-specific bacterial protein production (BPP) and protease activity between free-living and attached bacteria. Natural bacterial assemblages attached to model aggregates (agar spheres) had threefold higher BPP and two orders of magnitude higher protease activity than their free-living counterpart. These observations could be explained by preferential colonization of the agar spheres by bacteria with inherently higher metabolic activity and/or individual bacteria increasing their metabolism upon attachment to surfaces. In subsequent experiments, we used four strains of marine snow bacteria isolates to test the hypothesis that bacteria could up- and down-regulate their metabolism while on and off an aggregate. The protease activity of attached bacteria was 10-20 times higher than that of free-living bacteria, indicating that the individual strains could increase their protease activity within a short time (2 h) upon attachment to surfaces. Agar spheres with embedded diatom cells were colonized faster than plain agar spheres and the attached bacteria were clustered around the agar-embedded diatom cells, indicating a chemosensing response. Increased protease activity and BPP allow attached bacteria to quickly exploit aggregate resources upon attachment, which may accelerate remineralization of marine snow and reduce the downward carbon fluxes.     

Specific uptake rates of amino acids by attached and free-living bacteria in a mesotrophic lake

Seasonal and spatial patterns of specific uptake rates of amino acids by bacteria in Lake Constance were studied. The total bacterial population was divided into small (0.2- to 1.0-micron) and large (1.0- to 3.0-micron) free-living bacteria and attached bacteria by fractionated filtration. Data for attached bacteria, received by retention on 3.0-micron-pore Nuclepore filters, were corrected for free-living bacteria in this fraction. Specific uptake rates based on autoradiography were also recorded. Specific uptake rates for attached bacteria ranged from 9.41 X 10(-11) to 6.11 X 10(-8) ng of C h-1 cell-1 and were therefore significantly greater than those for free-living bacteria during most time periods. However, they were not significantly different from those for cells proven to be active by autoradiography. Specific uptake rates for small free-living bacteria ranged between 7.68 X 10(-11) and 4.60 X 10(-9) ng of C h-1 cell-1. They were nearly in the same range of those for large free-living bacteria (5.10 X 10(-11) to 1.07 X 10(-8) ng of C h-1 cell-1), although both fractions exhibited pronounced differences in their seasonal and vertical distributions.     

Anaerobic dechlorination of carbon tetrachloride by free-living and attached bacteria under various electron-donor conditions

The dechlorination of carbon tetrachloride (CCl₄) by free-living and attached bacteria under anaerobic conditions was studied to examine the relationship between porous media and electron donor. Two batch-type experiments, the free-living and attached bacterial systems, were conducted with and without addition of 0.5-mm glass beads. Glucose and acetate were selected as the primary electron donors because they are easily biodegradable. Direct epifluorescence technology, the DAPI (4′ 6-diamidino-2-phenylindole) method, was used for counting the microbial activities. Adding glass beads could accelerate the dechlorination rate of CCl₄. Removals of 44 %–57 % were observed in free-living bacterial system. Whereas a two- to fivefold increase in the CCl₄ dechlorination rate was observed in the attached system. Experimental results and thermodynamic calculations indicated that glucose is a better supplementary substrate than acetate for stimulating the dechlorinating capability of microorganisms because of its relatively high available free energy. A higher concentration of substrate provided more reducing power for attached bacteria to initiate the dechlorination reaction. The pseudo-first-order rate constants of CCl₄ dechlorination ranged from 0.007 day⁻¹ to 0.017 day⁻¹ and from 0.011 day⁻¹ to 0.0625 day⁻¹ for free-living and attached bacterial systems respectively. Microscopic observation revealed a three- to eightfold difference of microbial number between the free-living and attached bacterial systems. On the basis of the results in this study, we can conclude that the presence of porous media and an electron donor can change the dechlorination capabilities of the microorganisms. This work will be valuable in the design of in situ bioremediation as it discusses the specific area of the medium and supplementation with an electron donor to stimulate the indigenous microflora. Received: 21 June 1996 / Received revision: 2 September 1996 / Accepted: 29 September 1996     

Specific uptake rates of amino acids by attached and free-living bacteria in a mesotrophic lake.

Seasonal and spatial patterns of specific uptake rates of amino acids by bacteria in Lake Constance were studied. The total bacterial population was divided into small (0.2- to 1.0-micron) and large (1.0- to 3.0-micron) free-living bacteria and attached bacteria by fractionated filtration. Data for attached bacteria, received by retention on 3.0-micron-pore Nuclepore filters, were corrected for free-living bacteria in this fraction. Specific uptake rates based on autoradiography were also recorded. Specific uptake rates for attached bacteria ranged from 9.41 X 10(-11) to 6.11 X 10(-8) ng of C h-1 cell-1 and were therefore significantly greater than those for free-living bacteria during most time periods. However, they were not significantly different from those for cells proven to be active by autoradiography. Specific uptake rates for small free-living bacteria ranged between 7.68 X 10(-11) and 4.60 X 10(-9) ng of C h-1 cell-1. They were nearly in the same range of those for large free-living bacteria (5.10 X 10(-11) to 1.07 X 10(-8) ng of C h-1 cell-1), although both fractions exhibited pronounced differences in their seasonal and vertical distributions.     

Comparison of extracellular enzyme activities and community composition of attached and free-living bacteria in porous medium columns

Free-living and surface-associated microbial communities in sand-packed columns perfused with groundwater were compared by examination of compositional and functional characteristics. The composition of the microbial communities was assessed by bulk DNA extraction, PCR amplification of 16S ribosomal DNA fragments, separation of these fragments by denaturing gradient gel electrophoresis, and sequence analysis. Community function was assessed by measurement of beta-glucosidase and aminopeptidase extracellular enzyme activities. Free-living populations in the aqueous phase exhibited a greater diversity of phylotypes than populations associated with the solid phase. The attached bacterial community displayed significantly greater beta-glucosidase and aminopeptidase enzyme activities per volume of porous medium than those of the free-living community. On a per-cell basis, the attached community had a significantly higher cell-specific aminopeptidase enzyme activity (1.07 x 10(-7) nmol cell(-1) h(-1)) than the free-living community (5.02 x 10(-8) nmol cell(-1) h(-1)). Conversely, the free-living community had a significantly higher cell-specific beta-glucosidase activity (1.92 x 10(-6) nmol cell(-1) h(-1)) than the surface-associated community (6.08 x 10(-7) nmol cell(-1) h(-1)). The compositional and functional differences observed between these two communities may reflect different roles for these distinct but interacting communities in the decomposition of natural organic matter or biodegradation of xenobiotics in aquifers.     

Spatio-temporal structure of tidally mixed coastal waters: variability and heterogeneity

In the tidally mixed coastal waters of the eastern English Channel,the vertical properties of temperature, salinity, in vivo fluorescence,turbidity and light were investigated along an inshore-offshoretransect, sampled in different tidal conditions. The verticaldistribution of these parameters was then characterized in termsof mean value, variability (i.e. standard deviation) and heterogeneity(i.e. fractal dimension), regarded as a quantitative characterizationof the structure of the vertical variability of both physicaland biological parameters. These different estimates were thensubjected to multivariate spatio-temporal analysis and showeda very specific spatio-temporal structure suggesting a differentialcontrol of the vertical properties of water masses associatedwith both inshore-offshore gradient and tidal advection. Inparticular, the fractal dimension (i.e. heterogeneity) of invivo fluorescence is higher during ebb for offshore waters,suggesting a density dependence of the phytoplankton biomassstructure. In contrast, the vertical variability of fluorescenceis higher during flood for inshore waters, leading to an inverserelationship between variability and heterogeneity of the verticaldistribution of phytoplankton biomass.     

Temporal variability in copepod fecundity during two different spring bloom periods in coastal waters off Plymouth (SW England)

The temporal variation in egg production of the planktonic copepodsCalanus helgolandicus, Temora longicornis and Pseudocalanuselongatus was studied during two different spring bloom periodsin 1989 and 1990 by weekly sampling at two permanent stationsin coastal waters off Plymouth (SW England). Copepod egg productionwas estimated in situ by incubating individual adult femalesin filtered seawater for 24 h (72 h until hatching for P.elongatus)at the field surface temperature. The relationship between copepodegg production rates and: (i) chlorophyll a concentration (totaland >10 µm size fraction), (ii) temperature and (iii)initial copepod gut pigment content was investigated. The springbloom periods were very different in both years, with the occurrenceof a Phaeocystis sp. bloom in 1990, which negatively affectedthe feeding and fecundity of copepods. Egg production ratesin spring 1989 were significantly correlated with chlorophylla concentration (particularly with the >10 µm fraction),field temperature and copepod gut pigment contents. In spring1990, egg production rates were also correlated with copepodgut pigment contents, but no significant correlations were obtainedwith temperature or with chlorophyll a concentration, as a consequenceof the lower egg production rates obtained during the Phaeocystissp. dominance period. These results show that food availabilityis the factor which mainly affects the fecundity of neriticcopepods in short time periods.     

Survey of petroleum-degrading bacteria in coastal waters of Sunderban Biosphere Reserve

A survey of petroleum-degrading bacteria was carried out in the Indian part of deltaic Sunderbans to evaluate the distribution of the naturally occurring petroleum-degrading aerobic bacteria. Bacteriological analysis of surface water samples collected from five different locations in the Hooghly–Matla river mouth showed that, depending on the location, 0.08–2.0% of the heterotrophic bacteria culturable in marine agar medium could degrade crude petroleum hydrocarbons as the sole source of carbon. In the entire study area, the number of heterotrophic bacteria ranged from 1 × 10³ to 3.8 × 10⁵ c.f.u/ml, amongst which 2.7 × 10¹ to 6 × 10³ c.f.u/ml were petroleum degraders. There was a maximum number of petroleum-degrading bacteria in the waters of Haldia Port and its surrounding areas, where the water is highly polluted by hydrocarbon discharges from a nearby oil refinery and from the ships docking at the port. Among the isolates, identified on the basis of their Gram reaction, morphological and biochemical tests including the use of API20E strips, Pseudomonas, Mycobacterium, Klebsiella, Acinetobacter, Micrococcus, and Nocardia were the most common petroleum degraders. Other heterotrophic bacteria included several species of Escherichia, Klebsiella, non-oil-degrading Pseudomonas, Vibrio, Streptococcus, Staphylococcus and Bacillus. Following preliminary selection, five strains, showing best growth in medium with oil fraction as sole carbon source, were chosen for estimation of the efficiency of crude oil biodegradation. The selected strains belonged to Pseudomonas (two strains), Mycobacterium (two strains), and Nocardia (one strain). These strains degraded 47–78% of Arab-Mix crude oil over a period of 20 days. The best oil-degrading isolate, a strain of Pseudomonas aeruginosa, (BBW1), was found to degrade and multiply more rapidly in crude oil than the rest. BBW1 showed profuse growth in Bushnell Haas medium containing crude oil (as sole source of carbon) at high concentrations ranging from 0.2 to 20% (v/v), with optimum at 10%. As much as 75% of the oil was degraded within 72 h of incubation with the bacteria. Physicochemical analysis showed considerable decrease in initial boiling point and carbon residue of the degraded oil. The ability to degrade crude oil was found to be associated with a single 70-kb plasmid, pBN70. Resistance to the metals Mn²⁺ (50 mM), Mg²⁺ (200 mM), Zn²⁺ (6 mM), Ni²⁺ (10 mM) and antibiotics like ampicillin (10 g/ml), cephalexin (30 g/ml), nitrofurantoin (300 g/ml) and penicillin (10 U/ml) were plasmid-mediated.     

Oil-oxidizing activity of bacteria isolated from south Sakhalin coastal waters

Ability of bacteria isolated from the southern coastal waters of the Sakhalin Island to degrade various hydrocarbons was studied. The population of marine microorganisms grown on oil was heterogeneous in terms of hydrocarbon degradation. The rate of bacterial degradation of oil hydrocarbons was shown to correlate with their growth rate on the model medium. The degradation rates were higher for aromatic hydrocarbons than for alkanes. Based on our data, the studied bacteria were conditionally assigned to three groups: active, intermediately active, and passive degraders. Ability to oxidize oil was previously not reported for members of the genus Cobetia.     

Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison

We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.     

Distribution and biodegradation potential of oil-degrading bacteria in North Eastern Japanese coastal waters

Abstract The distribution of oil-degrading microorganism in samples of surface water and sediment from North Eastern Japanese coastal waters was studied. Modified natural sea water (NSW) agar supplemented with emulsified crude oil (Arabian light, 5 g 1⁻¹) was used to enumerate oil-degrading bacteria. In addition, filtered samples were inoculated into NSW broth containing weathered crude oil. Incubation was carried out at 20°C for 7–10 days. Populations of oil-degrading microorganisms ranged from 3–230 CFU 100 ml⁻¹ in surface waters and 2.9 × 10³ to 1.2 × 10⁵ CFU g⁻ in sediment samples. Analysis of variance showed that oil-degraders were heterogenously distributed. Six mixed populations selected from 20 samples were studied to determine which of the constituent microflora were capable of crude oil biodegradation. Among 51 strains selected for identification, only 61% could be identified which formed 17 different bacterial species. Acinetobacter species (14 strains), Psychrobacter immobilis (9 strains) and Gram-positive cocci (10 strains) were the predominant types. Oil-degrading activity by various mixed populations (three each from water and sediment samples) was determined by using a conventional total weight reduction technique. Reduction in amount of various aliphatic and aromatic hydrocarbon substrates was verified using gas chromatography and high pressure liquid chromatography. Biodegradation of crude oil ranged from 35–58%. One mixed population of the sediment samples degraded more hydrocarbon (both aliphatic and aromatic) and the biodegradation of the aromatic hydrocarbon reached as high as 48%.     

Degradation and mineralization of petroleum by two bacteria isolated from coastal waters

Within the framework of a study on the oil biodegradation potential of the sea the ability of a Flavobacterium sp. and Brevibacterium sp. to metabolize a paraffinic crude oil and a chemically defined hydrocarbon mixture was investigated. Major components of the crude oil were identified by combination gas chromatography and mass spectrometry. The rate and extent of total hydrocarbon biodegradation was measured. In addition, CO₂ evolution from the crude oil was continuously monitored in a shaker-mounted gas train arrangement. Degradation started after a 2 to 4 day lag period, and reached its maximum within two weeks. At this time up to 60% of the crude oil and 75% of the model hydrocarbon mixture, each added at the level of 1 ml per 100 ml artificial sea water, were degraded. Mineralization(conversion to CO₂) was slightly lower due to formation of products and bacterial cell material. n-Paraffins were preferentially degraded as compared to branched chain hydrocarbons. Biodegradation of n-paraffins in the range of C₁₂ to C₂₀ was simultaneous; no diauxie effects were observed.     

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.