Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability

Abundance of Live and Dead Bacteriopsammon Inhabiting Sandy Ecosystems of Recreational Marine Beaches of the Southern Baltic Sea

The study was carried out on four non-tidal sandy marine beaches located on the Polish part of the southern Baltic Sea coast. We applied a LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen™) method to determine the abundance of live and dead bacteriopsammon. Live psammon bacteria cells constituted 31-53% of the total number of bacteria inhabiting sand of the studied beaches. Abundance of live and dead psammon bacteria generally differed along the horizontal profile in all beaches. The maximum density of bacteria was noted in the dune and the middle part of the beach (dry zones) and the minimum in wet zones, i.e., under seawater surface and at the swash zone. Generally along the vertical profile, the highest numbers of two studied bacterial groups were noted in the surface sand layer, while with increasing sediment depth their numbers significantly decreased. The abundance of live and dead bacteria showed a distinct seasonal variation.

Sediment Microbial Communities and Their Potential Role as Environmental Pollution Indicators in Xuande Atoll, South China Sea

In this study, 39 sediment samples were collected from Qilian Island, Iltis Bank, and Yongxing Island in Xuande Atoll in the South China Sea (SCS), and the microbial community structures and distribution were analyzed. The microbial community was influenced by both natural environmental factors and human activities. The abundance of genera Vibrio and Pseudoalteromonas, which are associated with pathogenicity and pollutant degradation, were significantly higher in Qilian Island than in Yongxing Island and Iltis Bank, suggesting possible contamination of Qilian Island area through human activities. Pathogenic or typical pollutants-degrading bacteria were found to be negatively correlated with most of the commonly occurring bacterial populations in marine sediment, and these bacteria were more likely to appear in the sediment of deep water layer. This co-occurrence pattern may be due to bacterial adaptation to environmental changes such as depth and contaminations from human activities, including garbage disposal, farming, and oil spills from ships. The findings of this study could help in understanding the potential influences of human activities on the ecosystem at the microbial level.

Drivers of Bacterial α- and β-Diversity Patterns and Functioning in Subsurface Hadal Sediments

Oceanic trenches at hadal (>6,000 m) depths are hot spots of organic matter deposition and mineralization and can host abundant and active bacterial assemblages. However, the factors able to shape their biodiversity and functioning remain largely unexplored, especially in subsurface sediments. Here, we investigated the patterns and drivers of benthic bacterial α- and β-diversity (i.e., OTU richness and turnover diversity) along the vertical profile down to 1.5 m sediment depth in the Izu-Bonin Trench (at ~10,000 m water depth). The protease and glucosidase enzymatic activity rates were also determined, as a proxy of organic matter degradation potential in the different sediment layers. Molecular fingerprinting based on automated ribosomal intergenic spacer analysis (ARISA) indicated that the α-diversity of bacterial assemblages remained high throughout the vertical profile and that the turnover (β-) diversity among sediment horizons reached values up to 90% of dissimilarity. Multivariate distance-based linear modeling (DISTLM) pointed out that the diversity and functioning of the hadal bacterial assemblages were influenced by the variability of environmental conditions (including the availability of organic resources and electron donors/acceptors) and of viral production rates along the sediment vertical profile. Based on our results, we can argue that the heterogeneity of physical-chemical features of the hadal sediments of the Izu-Bonin Trench contribute to increase the niches availability for different bacterial taxa, while viruses contribute to maintain high levels of bacterial turnover diversity and to enhance organic matter cycling in these extremely remote and isolated ecosystems.

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities

Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.

Biodegradation and toxicity of melamine at high activated sludge concentrations in a membrane bioreactor

Melamine is recalcitrant and toxic to bacteria in conventional activated sludge systems. In this study, we investigated the degradation and toxicity of melamine in a membrane bioreactor (MBR) system operated at high activated sludge concentrations (∼8.5 g TSS/L). Melamine was dosed at 3 mg/L for about 100 days. The average melamine removal efficiency in the MBR system was 20 ± 11%. Meanwhile, batch studies showed the acclimated sludge from the MBR had higher removal efficiencies after the depletion of readily biodegradable substrate (acetate) while non-acclimated sludge did not remove any melamine. As acclimated sludge had removal efficiencies ranging from 33 ± 6% (by 1.7 g TSS/L biomass) to 41 ± 10% (by 8.5 g TSS/L biomass), microbial specialists with unique hydrolytic enzymes in the acclimated sludge were likely responsible for melamine degradation. Since bacteria prefer to use readily biodegradable substrates for growth in the MBR, the population of microbial specialists capable of degrading melamine or the capability of cometabolism appeared not to increase with an increase in biomass concentration. Nevertheless, because of high sludge concentrations and thus low mass ratio of toxic melamine to biomass in the MBR, the long-term melamine exposure did not affect MBR activated sludge performance.

Seasonal rather than spatial variability drives planktonic and benthic bacterial diversity in a microtidal lagoon and the adjacent open sea

Coastal lagoons are highly productive ecosystems, which are experiencing a variety of human disturbances at increasing frequency. Bacteria are key ecological players within lagoons, yet little is known about the magnitude, patterns and drivers of diversity in these transitional environments. We carried out a seasonal study in the Venice Lagoon (Italy) and the adjacent sea, to simultaneously explore diversity patterns in different domains (pelagic, benthic) and their spatio-temporal variability, and test the role of environmental gradients in structuring assemblages. Community composition differed between lagoon and open sea, and between domains. The dominant phyla varied temporally, with varying trends for the two domains, suggesting different environmental constraints on the assemblages. The percentage of freshwater taxa within the lagoon increased during higher river run-off, pointing at the lagoon as a dynamic mosaic of microbial taxa that generate the metacommunity across the whole hydrological continuum. Seasonality was more important than spatial variability in shaping assemblages. Network analyses indicated more interactions between several genera and environmental variables in the open sea than the lagoon. Our study provides evidences for a temporally dynamic nature of bacterial assemblages in lagoons and suggests that an interplay of seasonally influenced environmental drivers shape assemblages in these vulnerable ecosystems.

Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin

BACKGROUND

Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters.

RESULTS

Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pH_i; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 g_COD L^-1 d^-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm^-1), while marine conditions resembled brine waters (>47 mS cm^-1). Enrichments at optimal conditions of OLR 5 g_COD L^-1 d^-1 and pH_i 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 g_COD L^-1 d^-1, which was later increased to OLR 10 g_COD L^-1 d^-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm^-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities.

CONCLUSIONS

Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.

Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin

BACKGROUND

Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters.

RESULTS

Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pH_i; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 g_COD L^-1 d^-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm^-1), while marine conditions resembled brine waters (>47 mS cm^-1). Enrichments at optimal conditions of OLR 5 g_COD L^-1 d^-1 and pH_i 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 g_COD L^-1 d^-1, which was later increased to OLR 10 g_COD L^-1 d^-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm^-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities.

CONCLUSIONS

Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.

Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea

Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.

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.

Bacterial diversity and community composition from seasurface to subseafloor

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China

The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction) and vertical (sediment depth) gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH⁺₄ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments

We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems.

Fate and toxicity of melamine in activated sludge treatment systems after a long-term sludge adaptation

Melamine is a nitrogen-rich (67% nitrogen by mass) heterocyclic aromatic compound that could significantly increase effluent total nitrogen concentrations. In this study, we investigated the degradation of melamine and its impact on activated sludge operations by employing two common activated sludge processes, namely the Modified Ludzack-Ettinger (MLE) process and the continuous stirred tank reactor (CSTR) process. Melamine was dosed continuously from day 125 in both activated sludge treatment systems at an influent concentration of 3 mg/L for about 100 days. Even after such a long period of sludge adaptation, melamine appeared not to be easily biodegradable. The average melamine removal efficiencies in the CSTR and MLE systems were 14 ± 10% and 20 ± 15%, respectively. There was no significant difference in melamine removal between the two different activated sludge processes. The long-term input of melamine resulted in a decrease in the nitrifying bacterial activities (by 82 ± 8%) and population in both systems. Short-term microtiter assay results also showed that melamine reduced activated sludge growth by 80% when supplied at a concentration of 75.6 mg/L. These results suggest that sludge adaptation plays a minimal role in melamine degradation, as the enzymes responsible for hydrolytic deamination of melamine in activated sludge are not easily induced. The insignificant biodegradation of melamine is also attributed to bacterial growth inhibition under long-term dosing conditions with melamine, resulting in a significant decrease in effluent water quality.

Interactions between Zn and bacteria in marine tropical coastal sediments

PURPOSE

The main goals of this study were (1) to examine the effects of zinc on the microbial community structure of anthropogenically impacted sediments in a tropical coastal ecosystem and (2) to determine whether these microbial benthic communities may enhance the adsorption of zinc.

METHODS

The interactions between zinc and bacteria in tropical sediments were studied in sediment microcosms amended with 2.5 mg L⁻¹ of Zn in the water phase and incubated for 8 days under different environmental conditions, oxic/anoxic and glucose addition. At the end of incubation, microbial structure was assessed by molecular fingerprints (T-RFLP) analysis and Zn speciation in the sediment was determined by sequential extraction.

RESULTS

In the three studied sediments, Zn spiking resulted in only slight changes in bacterial community structure. In contrast, the addition of low concentrations of glucose (5 mM) strongly modified the bacterial community structure: <20% of similarity with the initial structure concomitant with a strong diminution of the specific richness. Overall, these results suggest that highly labile organic matter has a larger impact on microbial structure than heavy metal. These weak impacts of Zn on bacteria diversity might be partly explained by (1) the strong adsorption of Zn in the presence of bacteria and/or (2) the incorporation of Zn into a nonbioavailable fraction. Nevertheless, Zn spiking resulted in significant changes in nutrient cycles, suggesting that bacterial metabolisms were impacted by the heavy metal. This led to an increase in nutrient supplies to the water column, potentially enhancing eutrophication in a nutrient-limited, oligotrophic ecosystem.

The effect of substratum type, orientation and depth on the development of bacterial deep-sea biofilm communities grown on artificial substrata deployed in the Eastern Mediterranean

An increasing number of deep-sea studies have highlighted the importance of deep-sea biofouling, especially in relation to the protection of deep-sea instruments. In this study, the microbial communities developed on different substrata (titanium, aluminum, limestone, shale and neutrino telescope glass) exposed for 155 days at different depths (1500 m, 2500 m, 3500 m and 4500 m) and positions (vertical and horizontal) in the Eastern Mediterranean Deep Sea were compared. Replicated biofilm samples were analyzed using a Terminal Restriction Fragment Length Polymorphisms (T-RFLP) method. The restriction enzymes CfoI and RsaI produced similar total numbers (94, 93) of different T-RFLP peaks (T-RFs) along the vertical transect. In contrast, the mean total T-RF number between each sample according to substratum type and depth was higher in more samples when CfoI was used. The total species richness (S) of the bacterial communities differed significantly between the substrata, and depended on the orientation of each substratum within one depth and throughout the water column (ANOVA). T-RFLP analyses using the Jaccard similarity index showed that within one depth layer, the composition of microbial communities on different substrata was different and highly altered among communities developed on the same substratum but exposed to fouling at different depths. Based on Multidimensional Scaling Analyses (MDS), the study suggests that depth plays an important role in the composition of deep-sea biofouling communities, while substratum type and orientation of substrata throughout the water column are less important. To the authors' knowledge, this is the first study of biofilm development in deep waters, in relation to the effects of substratum type, orientation and depth.

Isolation and characterisation of bacteria from the Eastern Mediterranean deep sea

The Eastern Mediterranean deep sea is one of the most oligotrophic regions in the world's ocean. With the aim to classify bacteria from this special environment we isolated 107 strains affiliating to the Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria and Bacteroidetes from sediments of the Eastern Mediterranean Sea. As determined by 16S rRNA gene sequence analysis, Actinobacteria and Firmicutes, in particular members of the genus Bacillus, were dominant and represented a remarkable diversity with 27 out of a total of 33 operational taxonomic units obtained from the untreated sediment. The considerable percentage of operational taxonomic units (42%) which may be considered to be new species underlines the uniqueness of the studied environment. In order to selectively enrich bacteria which are adapted to the deep-sea conditions and tolerate broad pressure ranges, enrichments were set up with a sediment sample under in situ pressure and temperature (28 MPa, 13.5°C) using N-acetyl-D: -glucosamine as substrate. Interestingly Gammaproteobacteria were significantly enriched and dominant among the strains isolated after pressure pre-incubation. Obviously, Gammaproteobacteria have a selective advantage under the enrichment conditions applied mimicking nutrient supply under pressure conditions and cope well with sudden changes of hydrostatic pressure. However, under the continued low nutrient situation in the Eastern Mediterranean deep-sea sediments apparently Firmicutes and Actinobacteria have a clear adaptative advantage.

Vertical distribution of bacteria in a lake sediment from Antarctica by culture-independent and culture-dependent approaches

Bacterial diversity of the subsurface (18-22 cm), middle (60-64 cm) and bottom (100-104 cm) of a 136-cm-long sediment core sampled from a freshwater lake in Antarctica was determined by the culturable approach, T-RFLP and 16S rRNA gene clone libraries. Using the culturable approach, 41 strains were isolated and, based on phylogenetic analysis, they could be categorized into 14 groups. Representatives of the 14 groups varied in their growth temperature range (4-30 °C), in their tolerance to NaCl (0-2 M NaCl) and in the growth pH range (5-11). Eleven of fourteen representative strains exhibited either amylase, lipase, protease and (or) urease activities at 4 °C. Bacterial diversity at the phyla level using T-RFLP and 16S rRNA clone libraries was similar and clones were affiliated with Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. TRFs affiliated with Spirochaetes were detected only by the T-RFLP approach and clones affiliated with Caldiserica only in the clone libraries. Stratification of bacteria along the depth of the sediment was observed both with the T-RFLP and the 16S rRNA gene clone library methods, and results indicated that stratification was dependent on the nature of the organism, aerobic or anaerobic. For instance, aerobic Janthinobacterium and Polaromonas were confined to the surface of the sediment, whereas anaerobic Caldisericum was present only in the bottom portion of the core. It may be concluded that the bacterial diversity of an Antarctic lake sediment core sample varies throughout the length of the core depending on the oxic-anoxic conditions of the sediment. Furthermore, these psychrophilic bacteria, due to their ability to produce extracellular cold active enzymes, might play a key role in the transformation of complex organic compounds.

Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable

Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.

Influence of microorganisms on the removal of nickel in tropical marine sediments (New Caledonia)

The removal of nickel in marine tropical sediments (New Caledonia) was studied in microcosms. Removal of Ni(2+) was strongly enhanced by the presence of bacteria, with rates up to twofold higher than those observed under sterilized conditions. After 8 days of incubation, Ni(2+) concentration in the water column ranged from 30% to 50% of the initial concentration according to sediment origin. Addition of glucose stimulated bacterial processes and resulted in a complete disappearance of Ni(2+) in the water phase. Incubation under anoxic conditions slightly affects the microbial structure inferred from T-RFLP analysis irrespective of Ni(2+) spiking, whereas incubation under oxic conditions resulted to moderate modification of the microbial structure, changes that might be more marked in the presence of Ni(2+). Five different T-RFs were observed in almost all microcosms with relative abundance between 5% and 30%. Incubation with glucose resulted in the dominance of a common T-RF, with relative abundance up to 39%.

Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

Short-term effect of capping on microbial communities in freshwater sediments

Because biogas bubbles can influence cap integrity, the effect of capping and cap material on the ebullition potential in sediments must be studied. The goal of this comprehensive study was to determine the short-term effect of capping regime on the activity, metabolic potential, and community structure of sediment microorganisms. To evaluate the effect of capping (sand, synthetic aggregate, and no cap) on microbial communities (i.e., nitrifiers and methanogens), sediments were collected from the Anacostia River (Washington, D.C.). Microbial communities in sand-capped sediments exhibited the highest activity (tetrazolium redox dye, fluorescein diacetate hydrolysis assay, and biogas production), while communities in uncapped sediments exhibited the highest metabolic diversity. Substantial changes in microbial community structure (denaturing gradient gel electrophoresis) did not occur as a result of capping. Our data showed that the nature and magnitude of the effect that capping can have on microbial activity (biogas production) will likely be dependent on the capping materials chosen.

Temporal variations of microbial activity and diversity in marine tropical sediments (New Caledonia lagoon)

Temporal variations of oxygen consumption, sensitivity to metal spiking, and microbial diversity were investigated during a one-year survey at the sediment-water interface in the tropical lagoon of New Caledonia. Sediment oxygen consumption (SOC) exhibited strong variations with time with maximum rates during February (Austral summer) and minimum values during July (cold period). SOC was strongly positively correlated with temperature, with an apparent activation energy (E (a)) of 41 kJ mol(-1), corresponding to an apparent Q (10)(20-30 degrees C) of 1.75. Strong short-term variations of SOC were also observed with ratios between two consecutive samplings reaching up to twofold of magnitude within one week, whereas the maximum/minimum ratio over the whole year was equal to 2.73. In most cases, metal spiking led to a strong decrease of SOC; however, in a third of sampling dates, spiking did not significantly decrease activity. These periods of apparent metal tolerance were not characterized by a particular bacterial community structure. Bacterial community structure estimated from terminal restriction fragment length polymorphism (T-RFLP) analysis exhibited strong variations over the one-year survey, and no seasonality was observed for bacterial richness. However, on average, the Whittaker similarity index between two consecutive T-RFLP profiles was above 60% suggesting a relative stability of the bacterial community structure on the short timescale with prominent T-RFs representing on average more than 67% of relative abundance occurring over most of the year, whereas other T-RFs only occurred during some periods.

Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean

Two bacterial strains, BBH6T and BBH9, were isolated from a deep-sea sediment sample collected from the Chagos Trench, Indian Ocean, at a depth of 5904 m. The two strains were closely related in their 16S rRNA gene sequences (99.7 %), belonged to one genomic species and were virtually identical at the phenotypic level. Microbacterium barkeri DSM 20145T was the nearest phylogenetic neighbour to the new isolates, with 16S rRNA gene sequence similarity levels of 97.2–97.4 %. The new isolates exhibited levels of DNA–DNA relatedness of 32–34 % to M. barkeri and differed from it in a number of phenotypic characteristics. Therefore, it is suggested that strains BBH6T and BBH9 represent a novel species of the genus Microbacterium, for which the name Microbacterium indicum sp. nov. is proposed. The type strain is BBH6T (=LMG 23459T=IAM 15355T).

Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands

Sediment bacteria play important roles in the biogeochemistry of ocean sediments; however, factors influencing assemblage composition have not been extensively studied. We examined extractable sediment bacterial abundance, the composition of bacterial assemblages using a high-throughput molecular fingerprinting approach, and several sediment biogeochemical parameters (organic matter content and alkaline phosphatase activity), along a 35 km transect from Point Fermin, Southern California, to Santa Catalina Island, across the approximately 900-m-deep San Pedro Basin. Automated rRNA intergenic spacer analysis (ARISA) demonstrated that in two spatially isolated shallow (approximately < 60 m, on opposite sides of the channel) sediment environments, assemblages were more similar to each other than to deeper communities. Distinct communities existed in deeper and shallower sediments, and stations within the deep basin over 2 km apart contained remarkably similar assemblage fingerprints. The relative contribution to total amplified DNA fluorescence of operational taxonomic units (OTUs) was significantly correlated to that of other OTUs in few comparisons (2.7% of total), i.e. few bacterial types were found together or apart consistently. The relative proportions within assemblages of only a few OTU were significantly correlated to measured physicochemical parameters (organic matter content and wet/dry weight ratio of sediments) or enzyme (alkaline phosphatase) activities. A low percentage of shared OTU between shallow and deep sediments, and the presence of similar, but spatially isolated assemblages suggests that bacterial OTU may be widely dispersed over scales of a few kilometres, but that environmental conditions select for particular assemblages.

Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.

Carbon speciation and composition of natural microbial communities in polluted and pristine sediments of the Eastern Mediterranean Sea

Sediment samples collected from polluted (Augusta Bay) and pristine regions of the Eastern Mediterranean Sea (South Ionian Sea, Thracian Sea) were analyzed for black carbon, aliphatic hydrocarbons and phospholipid ester-linked fatty acids (PLFA). The aim of the study was to investigate the anthropogenic and biogenic inputs into the Eastern Mediterranean Sea and to evaluate the effects of refractory organic matter (e.g. black carbon) and the level of hydrocarbon contamination on benthic microbial community composition. Black carbon, generally considered to be chemically and biologically inert, comprised a significant but highly variable fraction of the sedimentary carbon pool in the analyzed sediments with a ratio to total organic carbon ranging from 0.02 to 0.66. Principal component analysis of the chemical characteristics of the sediments (organic carbon content, black carbon, bioavailable organic carbon, chlorophyll a, phaeopigments, aliphatic hydrocarbons) revealed clustering of samples along a gradient from the most productive and contaminated region of Augusta Bay to the carbon-poor and pristine sediments of the Thracian Sea. PLFA analysis revealed that gram-negative bacteria and microeukaryotes were most abundant in Augusta Bay and in the most impacted station of the Thracian Sea. The high levels of branched and odd-chain fatty acids recorded for these stations is probably linked to the elevated amounts of hydrocarbons at these stations; e.g. microbial communities may have developed the ability to degrade either naturally occurring aliphatic hydrocarbons or hydrocarbons derived from oil contamination.

Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments

Eastern Mediterranean sediments are characterized by the occurrence of distinct, organic-rich layers, called sapropels. These harbour elevated microbial numbers in comparison with adjacent carbon-lean intermediate layers. A recently obtained culture collection from these sediments was composed of 20% of strains closely related to Rhizobium radiobacter, formerly classified as Agrobacterium tumefaciens. To prove and quantify the in situ abundance of R. radiobacter, a highly specific quantitative polymerase chain reaction (PCR) protocol was developed. To convert quantification results into cell numbers, the copy number of rrn operons per genome was determined. Southern hybridization showed that our isolates contained four operons. Finally, quantitative PCR was applied to 45 sediment samples obtained across the eastern Mediterranean. Rhizobium radiobacter was present in 38 of 45 samples indicating an almost ubiquitous distribution. In total, 25-40 000 cells per gram of sediment were detected, corresponding to 0.001-5.1% of the bacterial cells. In general, the relative and absolute abundance of R. radiobacter increased with depth and was higher in sapropels than in intermediate layers. This indicates that R. radiobacter forms an active population in up to 200 000 years old sapropels. The present study shows for the first time that a cultivated subsurface bacterium is highly abundant in this environment.

DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments

In order to evaluate whether different DNA extraction procedures can affect estimates of benthic bacterial diversity, based on 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique, we compared two in situ lysis procedures (a SDS-based protocol and a commercial kit for DNA recovery) and one cell-extraction protocol on a variety of marine sediments. Despite the two in situ lysis procedures resulted in significantly different DNA yields (highest with the SDS in situ lysis), estimates of bacterial diversity provided a not significantly different ribotype richness, as well as similar values of the Shannon-Wiener (H') and Margalef (d) indices of biodiversity and of evenness (Pielou index, J). Conversely, the cell-extraction procedure for DNA extraction resulted always in a significantly lower ribotype richness and diversity. The analysis of similarities (anosim) among the T-RFLP electropherograms allowed concluding that ribotypes composition did not change significantly using different protocols. However, the analysis of beta-diversity (turnover diversity) revealed that a large number of ribotypes was observed exclusively with one of the three protocols utilized. When unshared ribotypes from in situ lysis and cell extraction were pooled together, total ribotype richness resulted much higher (up to 80%). Our results indicate that estimates of ribotype diversity based on a single protocol of DNA extraction can significantly underestimate the total number of bacterial ribotypes present in the benthic domain. We recommend that future studies will not only integrate different DNA extraction procedures, but also will explore the possibility of integrating two or more different genetic markers in order to increase our ability to detect the actual bacterial diversity in environmental samples.

Bacterial communities associated with benthic organic matter in headwater stream microhabitats

Bacterial communities associated with a variety of benthic detritus types were studied in three streams in the context of the chemical characteristics of the sediment material and the stream water. A cell purification assay was developed for a quantitative microscopic evaluation of bacterial community structure in detritus samples by fluorescence in situ hybridization (FISH). The efficiency of FISH with fluorescently monolabelled probes was compared with FISH with signal amplification by catalysed reporter deposition (CARD-FISH). In detritus types poor in organic carbon and nitrogen, the numbers of prokaryotes were related to the chemical characteristics of the stream water column, whereas no such relationship was found for detritus types rich in organic carbon and nitrogen. These results might help to provide criteria for the selection of detritus types for river ecosystem assessment and monitoring. The percentage of bacteria detected by FISH with monolabelled probes was correlated with the detritus total organic matter (OM). This is likely attributed to a higher ribosome content of microbial cells on substrates rich in OM. Cell detection by CARD-FISH did not show any correlation with OM content, indicating that this technique renders the results more independent from the activity state of cells. Fluorescence in situ hybridization with four group-specific probes suggested a relationship between substrate quality and the composition of the microbial assemblages on the various types of detritus. The improved protocol for cell purification and CARD-FISH may facilitate future investigations on the relationship between the riverine benthic detritus quality and microbial community composition.