Phylogenetic characterization of the heterotrophic bacterial communities inhabiting a marine recirculating aquaculture system

Aims: The aim of the present work was to characterize the heterotrophic bacterial community of a marine recirculating aquaculture system (RAS). Methods and Results: An experimental RAS was sampled for the rearing water (RW) and inside the biofilter. Samples were analysed for bacterial abundances, community structure and composition by using a combination of culture‐dependent and ‐independent techniques. The most represented species detected among biofilter clones was Pseudomonas stutzeri, while Ruegeria spp. and Roseobacter spp. were more abundant among isolates. In comparison, the genera Roseobacter and Ruegeria were well represented in both the biofilter and the RW samples. A variety of possible bacterial pathogens (e.g. Vibrio spp., Erwinia spp. and Coxiella spp.) were also identified in this study. Conclusions: Results revealed that the bacterial community in the RW was quite different to that associated with the biofilter. Moreover, data obtained suggest that the whole bacterial community can be involved in maintaining an effective and a stable rearing environment (shelter effect). Significance and Impact of the Study: Improving the reliability and the sustainability of RAS depends on the correct management of the bacterial populations inside it. This study furnishes more accurate information on the bacterial populations and better clarifies the existing relationships between the bacterial flora in the RW and that associated with the biofilter.     

Viral influence on aquatic bacterial communities

Bacterial viruses, or bacteriophages, have numerous roles in marine systems. Although they are now considered important agents of mortality of bacteria, a second possible role of regulating bacterial community composition is less well known. The effect on community composition derives from the presumed species-specificity and density-dependence of infection. Although models have described the "kill the winner" hypothesis of such control, there are few observational or experimental demonstrations of this effect in complex natural communities. We report here on some experiments that demonstrate that viruses can influence community composition in natural marine communities. Although the effect is subtle over the time frame suitable for field experiments (days), the cumulative effect over months or years would be substantial. Other virus roles, such as in genetic exchange or microbial evolution, have the potential to be extremely important, but we know very little about them.     

Significance of bacterial ectoenzymes in aquatic environments

The report presents studies on temporal and spatial variations of kinetics (Vmax and Km) of bacterial ectoenzyme activity (-glucosidase - Glc, leucine aminopeptidase - Leu-amp) in the naturally eutrophic Plusee. Glc and Leu-amp activity were positively correlated with the flux of polymeric materials (polysaccharides, proteins) in the lake. Glc activity was low when algal populations grew actively, but during the algal bloom breakdown Glc activity increased rapidly. Leu-amp displayed the highest rates of activity in the epilimnion and was tightly coupled to bacterial production. The synthesis of studied ectoenzymes was under control of a repression/derepression mechanism. The significance of ectoenzymes for the transformation and bacterial utilization of organic matter, and their role in the microbial loop in aquatic environments is discussed.     

Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica

Heterotrophic bacteria isolated from five aquatic microbial mat samples from different locations in continental Antarctica and the Antarctic Peninsula were compared to assess their biodiversity. A total of 2,225 isolates obtained on different media and at different temperatures were included. After an initial grouping by whole-genome fingerprinting, partial 16S rRNA gene sequence analysis was used for further identification. These results were compared with previously published data obtained with the same methodology from terrestrial and aquatic microbial mat samples from two additional Antarctic regions. The phylotypes recovered in all these samples belonged to five major phyla, Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus, and included several potentially new taxa. Ordination analyses were performed in order to explore the variance in the diversity of the samples at genus level. Habitat type (terrestrial vs. aquatic) and specific conductivity in the lacustrine systems significantly explained the variation in bacterial community structure. Comparison of the phylotypes with sequences from public databases showed that a considerable proportion (36.9%) is currently known only from Antarctica. This suggests that in Antarctica, both cosmopolitan taxa and taxa with limited dispersal and a history of long-term isolated evolution occur.     

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments

Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to “species”) using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms.     

Molecular characterization of carotenogenic yeasts from aquatic environments in Patagonia, Argentina

Fifteen aquatic environments (lakes, lagoons and rivers) of glacial origin in the northern Andean Patagonia (Argentina) were surveyed for the occurrence of red yeasts. Subsurface water samples were filtered and used for colony counting and yeast isolation. A preliminary quantitative analysis indicated that total yeast counts ranged between 0 and 250 cells l⁻¹. A polyphasic approach including physiological and molecular methods was used for the identification of 64 carotenogenic yeast strains. The molecular characterisation of the isolates was based on the mini/microsatellite-primed PCR technique (MSP-PCR) employing the (GTG)₅ and the M13 primers. Comparison of representative fingerprints of each group with those of the type strains of pigmented yeasts allowed the expeditious identification of 87.5% isolates. The sequence analysis of the D1/D2 domains of the 26S rDNA was employed to confirm identifications and in the characterization of the unidentified MSP-PCR groups. Teleomorphic yeast species were detected by performing sexual compatibility assays. The isolates corresponded to 6 genera and 15 yeast species, including four new yeast species of the genera Cryptococcus (1), Rhodotorula (1) and Sporobolomyces (2). Rhodotorula mucilaginosa was found in the majority of the samples and represented ca. 50% of the total number of isolates. However, this yeast was not detected in aquatic environments with very low anthropic influence. Other frequent yeast isolates were teleomorphic yeast species of Rhodosporidium babjevae, R. kratochvilovae and Sporidiobolus salmonicolor. This study represents the first report on red yeast occurrence and biodiversity in northwestern Patagonia. This revised version was published online in June 2006 with corrections to the Cover Date.     

Differential utilization of carbon substrates by aggregate-associated and water-associated heterotrophic bacterial communities

The capacity to utilize carbon substrates is fundamental to the functioning of heterotrophic microbial communities in aquatic environments. Carbon-source utilization within the water column, however, is not a bulk property because microbial communities are patchily distributed on suspended organic aggregates (i.e., marine snow, marine aggregates, river aggregates, organic detritus, and bioflocs). In this study, Biolog Ecoplates were used to evaluate the metabolic capacity of heterotrophic bacterial communities associated with aggregates compared to communities in the surrounding water. Overall, aggregate-associated microbial communities demonstrated higher levels of metabolism, metabolic versatility, and functional redundancy, and a more consistent pattern of carbon-source utilization compared with water-associated communities. In addition, aggregate-associated communities more effectively exploited available resources, including representatives from several biochemical guilds and nitrogen-containing carbon sources. Within the aggregate-associated microbial community, metabolic activity was significantly higher in the presence of polymers, amino acids, and carbohydrates relative to amines and carboxylic acids. In comparison, metabolic activity of water-associated communities exceeded a threshold value for only two of the five guilds (polymers and carbohydrates) evaluated. These results suggest that compared with their free-living counterparts, aggregate-associated communities have a greater capacity to respond to a wider array of carbon inputs. Results also underscore the importance of targeting organic aggregates to better understand the role of microbial processes in ecosystem functioning.     

Effect of dispersed oil on heterotrophic bacterial communities in cold marine waters

Mesocosm studies were conducted to evaluate the effect of dispersed oil on total and heterotrophic bacterial communities of under-ice seawater from the St. Lawrence Estuary. A regular survey of bacterial changes in the oil-contaminated seawater was performed during a two week period. The bacterial community structure was investigated by carrying out 27 morphological and biochemical tests on 168 isolated strains. The results show a detectable but transient response of the bacterial community to crude oil addition. While total bacterial counts were approximately constant during the experiment, dispersed oil induced an increase in heterotrophic bacterial microflora (from 10⁴ to 10⁵ bacteria ml^-1 after two weeks of contamination). The dispersed oil appeared to have an inhibitory effect on some components of the bacterial community. A decrease of most probable number values was observed just after addition of crude oil in the most polluted tanks and one day later in the less polluted tank. However, except for the most polluted tank, this adverse effect disappeared rapidly. While the dispersed oil induced a total disappearance of some components of the bacterial community in the most polluted tank, the structure of the bacterial community in the less polluted tank appeared relatively unchanged after 14 days of contamination.Offprint requests to: Daniel Delille     

Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress

The effects of mercury contamination of lake sediments on the phenotypic and genotypic mercury resistance of the indigenous heterotrophic aerobic bacterial communities were investigated. Strong positive correlations between mercury sediment concentration and the frequency of the gene coding for mercury volatilization (mer) (r = 0.96) or the phenotypic mercury resistance (r = 0.86) of the studied communities suggested that the inheritance via selection or genetic exchange of the mer gene had promoted bacterial adaptation to mercury. Failure to detect the mer gene in one mercury-contaminated sediment where phenotypic expression was low suggested that other mechanisms of resistance may partially determine the presence of mercury-resistant organisms in mercury-contaminated sediment or that the mercury in this particular sediment was very chemically limited in its availability to the microorganisms.     

It's all relative: ranking the diversity of aquatic bacterial communities

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.     

Complete oxidation of linear alkylbenzene sulfonate by bacterial communities selected from coastal seawater.

Anionic surfactants, especially alkylbenzene sulfonates, are discharged into marine areas in great quantities. Because of their poor biodegradability, linear alkylbenzene sulfonates accumulate in seawater and sediments. Bacterial communities that can degrade surfactants were selected from coastal seawater contaminated by urban sewage. All the isolated strains consisted of gram-negative, strictly aerobic rods or helical bacteria. Some of these, though isolated from coastal seawater, did not need sodium for growth and appeared to be related to the genera Alcaligenes and Pseudomonas. Complete surfactant biodegradation was achieved by three important steps: terminal oxidation of the alkyl chain, desulfonation, and aromatic-ring cleavage. Only a few strains were able to carry out the first two steps. The aromatic ring was then cleaved by other strains that possess very specific enzymatic activities. Finally, a number of strains grew on short acids that were end-of-metabolism products of the others.     

Complete oxidation of linear alkylbenzene sulfonate by bacterial communities selected from coastal seawater.

Anionic surfactants, especially alkylbenzene sulfonates, are discharged into marine areas in great quantities. Because of their poor biodegradability, linear alkylbenzene sulfonates accumulate in seawater and sediments. Bacterial communities that can degrade surfactants were selected from coastal seawater contaminated by urban sewage. All the isolated strains consisted of gram-negative, strictly aerobic rods or helical bacteria. Some of these, though isolated from coastal seawater, did not need sodium for growth and appeared to be related to the genera Alcaligenes and Pseudomonas. Complete surfactant biodegradation was achieved by three important steps: terminal oxidation of the alkyl chain, desulfonation, and aromatic-ring cleavage. Only a few strains were able to carry out the first two steps. The aromatic ring was then cleaved by other strains that possess very specific enzymatic activities. Finally, a number of strains grew on short acids that were end-of-metabolism products of the others.     

Effects of selected root exudate components on soil bacterial communities

Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.     

Mechanisms determining the fate of dispersed bacterial communities in new environments

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

Population dynamics of heterotrophic bacterial communities associated withFucus vesiculosus andUlva rigida in an estuary

The heterotrophic bacterial communities associated with the seaweedsFucus vesiculosus andUlva rigida in an estuary were studied. Changes in these communities were monitored by monthly sampling during the year. The isolated strains were identified at the genus level and grouped into 14 clusters by their similarities. Seasonal changes in genera and clusters as well as variations in diversity were related to primary production periods and fluctuation of salinity levels. TheFlavobacterium group was the major inhabitant of algal surfaces, being dominant after the primary production peaks occurred in spring and autumn. The decrease of dissolved organic matter after these peaks yielded an increase in diversity. Important alterations in these bacterial communities were observed during a period of large decrease in the salinity of estuarine water. In general, the epiphytic communities of both seaweeds were similar in their composition and dynamics, but they were very different from the surrounding water communities.     

Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress.

The effects of mercury contamination of lake sediments on the phenotypic and genotypic mercury resistance of the indigenous heterotrophic aerobic bacterial communities were investigated. Strong positive correlations between mercury sediment concentration and the frequency of the gene coding for mercury volatilization (mer) (r = 0.96) or the phenotypic mercury resistance (r = 0.86) of the studied communities suggested that the inheritance via selection or genetic exchange of the mer gene had promoted bacterial adaptation to mercury. Failure to detect the mer gene in one mercury-contaminated sediment where phenotypic expression was low suggested that other mechanisms of resistance may partially determine the presence of mercury-resistant organisms in mercury-contaminated sediment or that the mercury in this particular sediment was very chemically limited in its availability to the microorganisms.     

High performance liquid chromatography detection of phototrophic bacterial pigments in aquatic environments

Pigment extracts of phototrophic bacteria isolated from Lake Kinneret (Rhodopseudomonas palustris, Thiocapsa roseopersicina, Prosthecochloris aestuaris andChlorobium phaeobacteroides) were studied by means of high performance liquid chromatography (HPLC). An absorption wavelength of 360 nm provided the best resolution among the pigments of the species tested and between them and chlorophylla. Signature pigments were identified for each of these species, and their presence was thereby monitored in lake water samples.C. phaeobacteroides, which was observed in the anaerobic hypolimnion and predominated in the metalimnion, was recognized by a characteristic cluster of major chlorophyllous pigment peaks. The spectral qualities of these pigments were close but not identical to published data on bacteriochlorophylle, presumably due to the use of different solvents for extraction. The intensity of these pigment peaks was employed to determine the depth of the greatest phototrophic bacterial biomass, which was not related to that of algae.     

Physiological and ecological responses of plants and plant communities in dryland environments

Landscape and Ecological Engineering -     

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments

Although bacteria are ubiquitous in the near-surface atmosphere and they can have important effects on human health, airborne bacteria have received relatively little attention and their spatial dynamics remain poorly understood. Owing to differences in meteorological conditions and the potential sources of airborne bacteria, we would expect the atmosphere over different land-use types to harbor distinct bacterial communities. To test this hypothesis, we sampled the near-surface atmosphere above three distinct land-use types (agricultural fields, suburban areas and forests) across northern Colorado, USA, sampling five sites per land-use type. Microbial abundances were stable across land-use types, with ∼10⁵–10⁶ bacterial cells per m³ of air, but the concentrations of biological ice nuclei, determined using a droplet freezing assay, were on average two and eight times higher in samples from agricultural areas than in the other two land-use types. Likewise, the composition of the airborne bacterial communities, assessed via bar-coded pyrosequencing, was significantly related to land-use type and these differences were likely driven by shifts in the sources of bacteria to the atmosphere across the land-uses, not local meteorological conditions. A meta-analysis of previously published data shows that atmospheric bacterial communities differ from those in potential source environments (leaf surfaces and soils), and we demonstrate that we may be able to use this information to determine the relative inputs of bacteria from these source environments to the atmosphere. This work furthers our understanding of bacterial diversity in the atmosphere, the terrestrial controls on this diversity and potential approaches for source tracking of airborne bacteria.     

Nutrient effects on the genetic and functional diversity of aquatic bacterial communities

Studies on the effects of biodiversity on ecosystem functioning have generally revealed a positive asymptotic relationship between biodiversity and single functions, suggesting species redundancy with respect to these functions. However, most research was performed on specific processes and did not consider ecosystem 'multifunctionality'. There is also little information on the relationship between genetic and functional diversity. To analyze this relationship, we performed a microcosm experiment on a complex lake assemblage of decomposers, in the presence of the green alga Scenedesmus obliquus, which acted as carbon source for decomposers. By manipulating nutrient enrichment and the N : P input ratio, we observed that the structures of particle-associated and free bacterial assemblages were highly predictable in response to stoichiometric constraints. For a given treatment, the taxonomic compositions of free and particle-associated bacterial communities appeared close to each other only when phosphorus was not depleted. A coinertia analysis revealed a clear coupling between the genetic diversity of the microbial community, assessed using PCR-denatured gradient gel electrophoresis, and its potential functional diversity, studied with Biolog Ecoplates. This suggests that an ecologically relevant fraction of bacterial communities is characterized by lower level of redundancy than frequently thought, highlighting the necessity of exploring further the role of biodiversity in multifunctionality within ecosystems.