Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling

Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization. Additionally, bacterial cell numbers and bacterial production were assessed. Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs) affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas "Pelagibacterales" were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads) was affiliated with "Pelagibacterales" and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads) was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community.

Ice formation and growth shape bacterial community structure in Baltic Sea drift ice

Drift ice, open water and under-ice water bacterial communities covering several developmental stages from open water to thick ice were studied in the northern Baltic Sea. The bacterial communities were assessed with 16S rRNA gene terminal-restriction fragment length polymorphism and cloning, together with bacterial abundance and production measurements. In the early stages, open water and pancake ice were dominated by Alphaproteobacteria and Actinobacteria, which are common bacterial groups in Baltic Sea wintertime surface waters. The pancake ice bacterial communities were similar to the open-water communities, suggesting that the parent water determines the sea-ice bacterial community in the early stages of sea-ice formation. In consolidated young and thick ice, the bacterial communities were significantly different from water bacterial communities as well as from each other, indicating community development in Baltic Sea drift ice along with ice-type changes. The thick ice was dominated by typical sea-ice genera from classes Flavobacteria and Gammaproteobacteria, similar to those in polar sea-ice bacterial communities. Since the thick ice bacterial community was remarkably different from that of the parent seawater, results indicate that thick ice bacterial communities were recruited from the rarer members of the seawater bacterial community.

Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea

Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 10⁷ cells mL⁻¹. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO₂ fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based ¹³C and ¹⁵N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.

Distribution of the verrucomicrobial clade Spartobacteria along a salinity gradient in the Baltic Sea

A recent pyrosequencing study along the whole Baltic Sea salinity transect identified members of the Verrucomicrobia class Spartobacteria as an important component of Baltic Sea bacterioplankton. In this study, catalysed reporter deposition-fluorescence in situ hybridization was used for cellular quantification. The published probes VER47 and SPA714 were optimized for samples from the Baltic Sea and a new, specific probe (SPA476) was used to quantify the dominant spartobacterial lineage ‘LD29’. The results confirmed that in the brackish surface waters of the Baltic Sea Spartobacteria comprise an important component, constituting up to 12% of all bacteria. The positive correlation and physical association of Spartobacteria with phytoplankton suggest their involvement in the utilization of phytoplankton-derived organic matter in the Baltic Sea.

Significance of archaeal nitrification in hypoxic waters of the Baltic Sea

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread, and their abundance in many terrestrial and aquatic ecosystems suggests a prominent role in nitrification. AOA also occur in high numbers in oxygen-deficient marine environments, such as the pelagic redox gradients of the central Baltic Sea; however, data on archaeal nitrification rates are scarce and little is known about the factors, for example sulfide, that regulate nitrification in this system. In the present work, we assessed the contribution of AOA to ammonia oxidation rates in Baltic deep basins and elucidated the impact of sulfide on this process. Rate measurements with (15)N-labeled ammonium, CO(2) dark fixation measurements and quantification of AOA by catalyzed reporter deposition-fluorescence in situ hybridization revealed that among the three investigated sites the highest potential nitrification rates (122-884 nmol l(-1)per day) were measured within gradients of decreasing oxygen, where thaumarchaeotal abundance was maximal (2.5-6.9 × 10(5) cells per ml) and CO(2) fixation elevated. In the presence of the archaeal-specific inhibitor GC(7), nitrification was reduced by 86-100%, confirming the assumed dominance of AOA in this process. In samples spiked with sulfide at concentrations similar to those of in situ conditions, nitrification activity was inhibited but persisted at reduced rates. This result together with the substantial nitrification potential detected in sulfidic waters suggests the tolerance of AOA to periodic mixing of anoxic and sulfidic waters. It begs the question of whether the globally distributed Thaumarchaeota respond similarly in other stratified water columns or whether the observed robustness against sulfide is a specific feature of the thaumarchaeotal subcluster present in the Baltic Deeps.

N and O isotope fractionation in nitrate during chemolithoautotrophic denitrification by Sulfurimonas gotlandica

Chemolithoautotrophic denitrification is an important mechanism of nitrogen loss in the water column of euxinic basins, but its isotope fractionation factor is not known. Sulfurimonas gotlandica GD1(T), a recently isolated bacterial key player in Baltic Sea pelagic redoxcline processes, was used to determine the isotope fractionation of nitrogen and oxygen in nitrate during denitrification. Under anoxic conditions, nitrate reduction was accompanied by nitrogen and oxygen isotope fractionation of 23.8 ± 2.5‰ and 11.7 ± 1.1‰, respectively. The isotope effect for nitrogen was in the range determined for heterotrophic denitrification, with only the absence of stirring resulting in a significant decrease of the fractionation factor. The relative increase in δ(18)ONO3 to δ(15)NNO3 did not follow the 1:1 relationship characteristic of heterotrophic, marine denitrification. Instead, δ(18)ONO3 increased slower than δ(15)NNO3, with a conserved ratio of 0.5:1. This result suggests that the periplasmic nitrate reductase (Nap) of S. gotlandica strain GD1(T) fractionates the N and O in nitrate differently than the membrane-bound nitrate reductase (Nar), which is generally prevalent among heterotrophic denitrifiers and is considered as the dominant driver for the observed isotope fractionation. Hence in the Baltic Sea redoxcline, other, as yet-unidentified factors likely explain the low apparent fractionation.

Uncoupling of bacterial and terrigenous dissolved organic matter dynamics in decomposition experiments

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot efficiently utilize tDOM and that in subarctic estuaries other factors are responsible for the removal of imported tDOM.

Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea

Nitrogenase genes (nifH) from heterotrophic dinitrogen (N2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79 μmol O2 L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6 × 10(5) and 5.8 × 10(5) nifH gene copies L(-1) within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15 μmol O2 L(-1) and 186-194 μmol O2 L(-1) in the absence of combined N.

Impact of dissolved inorganic carbon concentrations and pH on growth of the chemolithoautotrophic epsilonproteobacterium Sulfurimonas gotlandica GD1T

Epsilonproteobacteria have been found globally distributed in marine anoxic/sulfidic areas mediating relevant transformations within the sulfur and nitrogen cycles. In the Baltic Sea redox zones, chemoautotrophic epsilonproteobacteria mainly belong to the Sulfurimonas gotlandica GD17 cluster for which recently a representative strain, S. gotlandica GD1(T), could be established as a model organism. In this study, the potential effects of changes in dissolved inorganic carbon (DIC) and pH on S. gotlandica GD1(T) were examined. Bacterial cell abundance within a broad range of DIC concentrations and pH values were monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for achieving maximal cell numbers was already reached at 800 μmol L(-1), which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6-7.1 there was no significant difference in substrate utilization; however, at lower pH values maximum cell abundance decreased sharply and cell-specific substrate consumption increased.

Pyruvate utilization by a chemolithoautotrophic epsilonproteobacterial key player of pelagic Baltic Sea redoxclines

Pelagic redoxclines of the central Baltic Sea are dominated by the epsilonproteobacterial group Sulfurimonas GD17, considered to be the major driver of chemolithoautotrophic denitrification in this habitat. Autecological investigations of a recently isolated representative of this environmental group, Sulfurimonas gotlandica str. GD1(T), demonstrated that the bacterium grows best under sulfur-oxidizing, denitrifying conditions. However, in the presence of bicarbonate, this strain is able to use pyruvate as both an additional carbon source and an alternative electron donor. These observations suggested that the environmental group GD17 actively metabolizes organic substrates in situ. To examine this possibility, we used RNA-based stable isotope probing (RNA-SIP) on a natural redoxcline community provided with ¹³C-labeled pyruvate. While in this experiment, we were able to identify putative heterotrophic microorganisms, the uptake of ¹³C-pyruvate in GD17 nucleic acids could not be established. To resolve these contradictory findings, combined incorporation experiments with ¹⁴C- and ¹³C-labeled pyruvate were carried out in cells of strain GD1(T) cultivated under chemolithoautotrophic conditions, which favor pyruvate uptake rather than oxidation. An analysis of the labeled biomolecules revealed that pyruvate was mostly incorporated in cellular components such as amino acids, whose synthesis requires only minimal transformation. Carbon transfer into nucleic acids was not observed, explaining the inability of RNA-SIP to detect pyruvate incorporation by strain GD1(T) and the environmental group GD17. Together, these findings suggest that by integrating organic compounds such as pyruvate into cellular components S. gotlandica GD1(T) is able to replenish chemolithoautotrophic growth and thus ensure its survival in nutrient-limited habitats such as marine pelagic redoxclines.

Impact of warming on phyto-bacterioplankton coupling and bacterial community composition in experimental mesocosms

Global warming is assumed to alter the trophic interactions and carbon flow patterns of aquatic food webs. The impact of temperature on phyto-bacterioplankton coupling and bacterial community composition (BCC) was the focus of the present study, in which an indoor mesocosm experiment with natural plankton communities from the western Baltic Sea was conducted. A 6 °C increase in water temperature resulted, as predicted, in tighter coupling between the diatom-dominated phytoplankton and heterotrophic bacteria, accompanied by a strong increase in carbon flow into bacterioplankton during the phytoplankton bloom phase. Suppressed bacterial development at cold in situ temperatures probably reflected lowered bacterial production and grazing by protists, as the latter were less affected by low temperatures. BCC was strongly influenced by the phytoplankton bloom stage and to a lesser extent by temperature. Under both temperature regimes, Gammaproteobacteria clearly dominated during the phytoplankton peak, with Glaciecola sp. as the single most abundant taxon. However, warming induced the appearance of additional bacterial taxa belonging to Betaproteobacteria and Bacteroidetes. Our results show that warming during an early phytoplankton bloom causes a shift towards a more heterotrophic system, with the appearance of new bacterial taxa suggesting a potential for utilization of a broader substrate spectrum.

Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters

Knowledge on Actinobacteria rhodopsin gene (actR) diversity and spatial distribution is scarce. The Baltic Sea is characterized by strong salinity gradients leading to the coexistence of marine and freshwater bacteria and hence is an ideal study area to elucidate the dispersion and phylogenetic affiliation of actR in dependence on salinity. ActR DGGE fingerprints in summer 2008 revealed between 3 and 19 distinct bands within a salinity range of 2.4-27 PSU. Environmental actR clone sequences were obtained from stations distributed along the whole salinity gradient. Overall, 20 different actR sequence groups (operational taxonomic units) were found, with up to 11 different ones per station. Phylogenetically, the actR sequences were predominantly (80%) affiliated with freshwater acI-Actinobacteria whose 16S rRNA gene accounted for 2-33% of total 16S rRNA genes in both the Bothnian Sea and central Baltic Sea. However, at salinities above 14 PSU, acI-16S rRNA gene accounted for less than 1%. In contrast, the diversity of actR remained high. Changes in actR gene diversity were significantly correlated with salinity, oxygen, silica or abundance of Synechococcus sp. Our results demonstrate a wide distribution of freshwater actR along the Baltic Sea salinity gradient indicating that some freshwater Actinobacteria might have adapted to higher salinities.

Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas

A psychro- and aerotolerant bacterium was isolated from the sulfidic water of a pelagic redox zone of the central Baltic Sea. The slightly curved rod- or spiral-shaped cells were motile by one polar flagellum or two bipolar flagella. Growth was chemolithoautotrophic, with nitrate or nitrite as electron acceptor and either a variety of sulfur species of different oxidation states or hydrogen as electron donor. Although the bacterium was able to utilize organic substances such as acetate, pyruvate, peptone and yeast extract for growth, these compounds yielded considerably lower cell numbers than obtained with reduced sulfur or hydrogen; in addition, bicarbonate supplementation was necessary. The cells also had an absolute requirement for NaCl. Optimal growth occurred at 15 °C and at pH 6.6–8.0. The predominant fatty acid of this organism was 16 : 1ω7c, with 3-OH 14 : 0, 16 : 0, 16 : 1ω5c+t and 18 : 1ω7c present in smaller amounts. The DNA G+C content was 33.6 mol%. As determined in 16S rRNA gene sequence phylogeny analysis, the isolate belongs to the genus Sulfurimonas, within the class Epsilonproteobacteria, with 93.7 to 94.2 % similarity to the other species of the genus Sulfurimonas, Sulfurimonas autotrophica, Sulfurimonas paralvinellae and Sulfurimonas denitrificans. However, the distinct physiological and genotypic differences from these previously described taxa support the description of a novel species, Sulfurimonas gotlandica sp. nov. The type strain is GD1^T ( = DSM 19862^T = JCM 16533^T). Our results also justify an emended description of the genus Sulfurimonas.

Acetate-utilizing bacteria at an oxic-anoxic interface in the Baltic Sea

Pelagic redoxclines represent chemical gradients of elevated microbial activities. While chemolithoautotrophic microorganisms in these systems are well known as catalysts of major biogeochemical cycles, comparable knowledge on heterotrophic organisms is scarce. Thus, in this study, identity and biogeochemical involvement of active heterotrophs were investigated in stimulation experiments and activity measurements based on samples collected from pelagic redoxclines of the central Baltic Sea in 2005 and 2009. In the 2009 samples, (13)C-acetate 16S rRNA stable isotope probing (16S rRNA-SIP) identified gammaproteobacteria affiliated with Colwellia sp. and Neptunomonas sp. in addition to epsilonproteobacteria related to Arcobacter spp. as active heterotrophs at the oxic-anoxic interface layer. Incubations from sulfidic waters were dominated by two phylogenetic subgroups of Arcobacter. In the 2005 samples, organics, manganese(IV), and iron(III) were added to the sulfidic waters, followed by the determination of metal reduction and identification of the stimulated organisms. Here, the same Arcobacter and Colwellia subgroups were stimulated as in 2009, with Arcobacter predominating in samples, in which manganese(IV) reduction was highest. Our results offer new insights into the heterotrophic bacterial assemblage of Baltic Sea pelagic redoxclines and suggest Arcobacter spp. as a heterotroph with presumed relevance also for manganese cycling.

Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces

Barrier zones between oxic and anoxic water masses (redoxclines) host highly active prokaryotic communities with important roles in biogeochemical cycling. In Baltic Sea pelagic redoxclines, Epsilonproteobacteria of the genus Sulfurimonas (subgroup GD17) have been shown to dominate chemoautotrophic denitrification. However, little is known on the loss processes affecting this prokaryotic group. In the present study, the protist grazing impact on the Sulfurimonas subgroup GD17 was determined for suboxic and oxygen/hydrogen sulphide interface depths of Baltic Sea redoxclines, using predator exclusion assays and bacterial amendment with the cultured representative 'Sulfurimonas gotlandica' strain GD1. Additionally, the principal bacterivores were identified by RNA-Stable Isotope Probing (RNA-SIP). The natural Sulfurimonas subgroup GD17 population grew strongly under oxygen/hydrogen sulphide interface conditions (doubling time: 1-1.5 days), but protist grazing could consume the complete new cell production per day. In suboxic samples, little or no growth of Sulfurimonas subgroup GD17 was observed. RNA-SIP identified five active grazers, belonging to typical redoxcline ciliates (Oligohymenophorea, Prostomatea) and globally widespread marine flagellate groups (MAST-4, Chrysophyta, Cercozoa). Overall, we demonstrate for the first time that protist grazing can control the growth, and potentially the vertical distribution, of a chemolithoautotrophic key-player of oxic/anoxic interfaces.

Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae

Background

Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities.

Results

Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches.

Conclusions

Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.

Phenotypic variation in Pseudomonas sp. CM10 determines microcolony formation and survival under protozoan grazing

Abstract We investigated the survival mechanism of the bacterium Pseudomonas sp. CM10 in the presence of a flagellate predator. The bacterium had been isolated from a continuous culture containing bacterivorous nanoflagellates. On agar plates, we found intraclonal dimorphism of Pseudomonas sp. CM10 colonies at high frequencies: The primary mucoid colony type generated a secondary non-mucoid form. Unlike the repeated generation of non-mucoid colonies from mucoid clones, we did not observe the occurrence of mucoid forms in non-mucoid populations. In semicontinuous and batch cultures, we investigated the ability of the two morphs to survive predation by the bacterivorous flagellate Ochromonas sp. under conditions of growth and starvation. In predator-free cultures, populations of both variants were unicellular but differed in some phenotypic characteristics such as cell motility and hydrophobicity. Grazing treatments revealed that the non-mucoid morph was reduced severely whereas the primary mucoid type survived due to the formation of inert suspended microcolonies stabilized by an extracellular matrix. Effectiveness and competitive trade-offs of microcolony formation were revealed by a competition experiment with the bacterium Pseudomonas putida MM1: Pseudomonas sp. CM10 was displaced in predator-free cultures but outgrew the defenseless and monomorphic competitor under flagellate grazing pressure. We conclude that intraclonal polymorphism may regulate the ability of Pseudomonas sp. CM10 to survive in situations of severe protistan grazing. The formation of inert microcolonies, however, is suggested to be detrimental to rapid growth and dispersal.

Chemolithoautotrophic denitrification of epsilonproteobacteria in marine pelagic redox gradients

Pelagic marine oxygen-depleted zones often exhibit a redox gradient, caused by oxygen depletion due to biological demand exceeding ventilation, and the accumulation of reduced chemical species, such as hydrogen sulfide. These redox gradients harbour a distinct assemblage of epsilonproteobacteria capable of fixing carbon dioxide autotrophically in the dark and potentially of utilizing hydrogen sulfide chemolithotrophically by oxidation with nitrate. Together, these two processes are referred to as chemolithoautotrophic denitrification. The focus of this study was the recently isolated and cultivated representative strain of pelagic epsilonproteobacteria, 'Sulfurimonas gotlandica' strain GD1, specifically dark carbon dioxide fixation and its substrate turnovers during chemolithotrophic denitrification. By connecting these processes stoichiometrically and comparing the results with those obtained for dark carbon dioxide fixation and nutrient concentrations measured in pelagic redox gradients of the Baltic Sea, we were able to estimate the role of chemolithoautotrophic denitrification in the environment. Evidence is provided for a defined zone where chemolithoautotrophic denitrification of these epsilonproteobacteria allows the complete removal of nitrate and hydrogen sulfide from the water column. This water layer is roughly equivalent in thickness to the average overlapping region of the two substrates, but slightly larger. Such a difference may be explained by a variety of reasons, including, e.g. utilization of substrates present at concentrations below the detection limit, alternative usage of other substrates as thiosulfate or nitrous oxide, or comparable activities of other microbes. However, the combined results of in vitro and in situ studies strongly suggest that epsilonproteobacteria are primarily responsible for hydrogen sulfide and nitrate removal from pelagic Baltic Sea redox gradients.

Unveiling trophic functions of uncultured protist taxa by incubation experiments in the brackish Baltic Sea

BACKGROUND

Our knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches.

METHODOLOGY/PRINCIPAL FINDINGS

A combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species.

CONCLUSIONS/SIGNIFICANCE

These findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater-freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

Factors affecting preference responses of the freshwater ciliate Uronema nigricans to bacterial prey

To enhance our understanding of the factors affecting feeding selectivity of bacterivorous protists in aquatic systems, we examined the preference responses of the freshwater ciliate Uronema nigricans towards three bacterial prey taxa, Pseudomonas luteola, Serratia rubidaea, and Aeromonas hydrophila. Potential factors influencing the predator-prey contact rate included the previous feeding history of the ciliate and physiological state of bacteria. Preference indexes were obtained from multiple-choice mazes in which ciliates moved preferentially towards alternative bacteria or the prey species on which they had been feeding. Uronema nigricans showed differential attraction towards the offered prey types, and these preferences varied as a function of the ciliate feeding history: U. nigricans growing on P. luteola showed lower preference responses towards the offered bacteria than U. nigricans growing on S. rubidaea. The bacteria in stationary phase elicited a higher degree of attraction than bacteria in exponential phase, probably due to a higher concentration of carbohydrates in the former. Therefore, this protist will preferentially swim towards bacteria in stationary growth phase, although the degree of this response will be affected by the recent feeding history of the ciliate.

Diversity of active chemolithoautotrophic prokaryotes in the sulfidic zone of a Black Sea pelagic redoxcline as determined by rRNA-based stable isotope probing

Marine pelagic redoxclines are characterized by pronounced activities of chemolithoautotrophic microorganisms. As evidenced by the high dark CO(2) fixation rates measured around the oxic-anoxic interface but also in the upper sulfidic zone, the accordant organisms participate in important biogeochemical transformations. Although Epsilonproteobacteria have been identified as an important chemoautotrophic group in these environments, detailed species-level information on the identity of actively involved prokaryotes is lacking. In the present study, active chemolithoautotrophic prokaryotic assemblages were identified in the sulfidic zone of a pelagic Black Sea redoxcline by applying rRNA-based stable isotope probing in combination with 16S rRNA gene single-strand conformation polymorphism analysis and 16S rRNA gene cloning. The results showed that a single epsilonproteobacterium, affiliated with the genus Sulfurimonas, and two different members of the gammaproteobacterial sulfur oxidizer (GSO) cluster were responsible for dark CO(2) fixation activities in the upper sulfidic layer of the Black Sea redoxcline. Phylogenetically, these organisms were closely related to microorganisms, distributed worldwide, that are thought to be key players in denitrification and sulfide oxidation. Together, these findings emphasize the importance of chemolithoautotrophic members of the Sulfurimonas and GSO groups in the carbon, nitrogen, and sulfur cycles of oxic-anoxic pelagic transition zones.