Aquatic Microbial Ecology Research Papers (original) (raw)

2025, Helgoland Marine Research

Marine zooplanktic organisms, such as copepods, are usually associated with large numbers of bacteria. Some of these bacteria live attached to copepods' exoskeleton, while others prevail in their intestine and faecal pellets. Until now, general conclusions concerning the identity of these bacteria are problematic since the majority of previous studies focused on cultivable bacteria only. Hence, to date little is known on whether copepod genera or species harbour distinct bacterial populations and about the nature of this association. To shed more light on these copepod/bacteria consortia, the focus of this study was the development and evaluation of a suitable approach to extract bacterial DNA from different North Sea copepod genera. Furthermore, the bacterial DNA was analysed by PCR-DGGE and subsequent sequencing of excised bands. The result of this work was an appropriate extraction method for batches of ten to one copepod specimens and offered first insights as to which bacteria are attached to the copepods Acartia sp. and Temora sp. from Helgoland Roads (German Bight) and a laboratory-grown Acartia tonsa culture. It revealed the prevalence of Alphaproteobacteria.

2025, FEMS Microbiology Ecology

We investigated the occurrence of Planktotalea frisia strain SH6-1 T , a member of the Roseobacter clade, in the North Sea, and interactions with phytoplankton algae with a special emphasis on the carbohydrate metabolisms. This bacterium was present in May 2006 throughout the North Sea. Planktotalea frisia SH6-1 was further present in the German Bight between February and early July, with distinct peaks during and after phytoplankton blooms. The highest abundances, as detected by quantitative PCR, were 0.5-0.9% of total bacterial abundance. Comparison by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) with a set of highly specific probes confirmed the high values in one sample. Between mid-July and October, P. frisia SH6-1 was not detected throughout the North Sea. Experimental studies in which P. frisia SH6-1 was grown in the presence of axenic cultures of the algae Phaeocystis globosa, Leptocylindrus danicus and Thalassiosira rotula exhibited distinctly different responses, with the best growth together with P. globosa and T. rotula and very low growth together with L. danicus. The algae greatly differed in the composition of their exuded carbohydrates and in the fact that P. frisia SH6-1 was rather selective in consumption of algae, suggesting that the distinct carbohydrate metabolisms are a key feature to explain the seasonal occurrence of this bacterium in the North Sea.

2025, Aquatic Microbial Ecology

Toxic Cyanobacteria-dominated blooms are a global phenomenon that poses a health risk to humans and animals. These blooms harbor a diverse range of heterotrophic bacteria which are involved in growth-promoting and decomposition processes. In the present study, we investigated microbial communities and microcystins in a lake cyanobacterial scum at a single point in time. The outer edges of the scum (ca. 500 cm from shore) were freshly formed, while those closest to the shore showed signs of cyanobacterial cell lysis and degradation. Samples were collected from 5 sites across the scum and from 2 separate bays. We hypothesized that cyanobacterial genera, bacterial communities and microcystin quota (toxin content per cell) would be significantly different in the degrading scums versus where the scum had freshly formed. Samples were analyzed using 16S rRNA metabarcoding (DNA and RNA), and a range of physicochemical para meters were determined. Microcystis transcripts were more abundant than Dolichospermum in the breaking-down scum, suggesting they are better suited to tolerating the harsh physicochemical conditions encountered within scums. Multivariate analysis of operational taxonomic units (excluding Cyanobacteria) showed significant differences in bacterial community structures across the scums. Proteobacteria was the most abundant phylum, among which Aeromonas, Caulobacter and Brevundimonas dominated. No relationships were observed between microcystin quotas and bacterial community structure or position in the scum.

2025, The ISME journal

Coral reef ecosystems are highly sensitive to microbial activities that result from dissolved organic matter (DOM) enrichment of their surrounding seawater. However, the response to particulate organic matter (POM) enrichment is less studied. In a microcosm experiment, we tested the response of bacterioplankton to a pulse of POM from the mass-spawning of Orbicella franksi coral off the Caribbean coast of Panama. Particulate organic carbon (POC), a proxy measurement for POM, increased by 40-fold in seawater samples collected during spawning; 68% degraded within 66 h. The elevation of multiple hydrolases presumably solubilized the spawn-derived POM into DOM. A carbon budget constructed for the 275 µM of degraded POC showed negligible change to the concentration of dissolved organic carbon (DOC), indicating that the DOM was readily utilized. Fourier transform ion cyclotron resonance mass spectrometry shows that the DOM pool became enriched with heteroatom-containing molecules, a trend ...

2025, Frontiers in Microbiology

Current models and observations indicate that bacterial respiration should increase and growth efficiency (BGE) should decrease with increasing temperatures. However, these models and observations are mostly derived from data collected in temperate regions, and the tropics are under-represented. The aim of this work was to compare bacterial metabolism, namely bacterial production (BP) and respiration (BR), bacterial growth efficiency (BGE) and bacterial carbon demand (BCD) between tropical and temperate ecosystems via a literature review and using unpublished data. We hypothesized that (1) tropical ecosystems have higher metabolism than temperate ones and, (2) that BGE is lower in tropical relative to temperate ecosystems. We collected a total of 498 coupled BP and BR observations (N total = 498; N temperate = 301; N tropical = 197), calculated BGE (BP/(BP+BR)) and BCD (BP+BR) for each case and examined patterns using a model II regression analysis and compared each parameter between the two regions using nonparametric Mann-Whitney U test. We observed a significant positive linear regression between BR and BP for the whole dataset, and also for tropical and temperate data separately. We found that BP, BR and BCD were higher in the tropics, but BGE was lower compared to temperate regions. Also, BR rates per BP unit were at least two fold higher in the tropics than in temperate ecosystems. We argue that higher temperature, nutrient limitation, and light exposure all contribute to lower BGE in the tropics, mediated through effects on thermodynamics, substrate stoichiometry, nutrient availability and interactions with photochemically produced compounds. More efforts are needed in this study area in the tropics, but our work indicates that bottom-up (nutrient availability and resource stoichiometry) and top-down (grazer pressure) processes, coupled with thermodynamic constraints, might contribute to the lower BGE in the tropics relative to temperate regions.

2025, Aquatic Microbial Ecology

Spatial and seasonal variation in sediment properties, benthic metabolism (O 2 and TCO 2 fluxes) and nitrogen (N) cycling (dinitrogen gas [N 2 ], dissolved inorganic N [DIN] and organic N [DON] fluxes) in western Moreton Bay, Queensland, Australia, were investigated using spatially intensive sediment core incubations. Principal component analysis (PCA) showed that variation in the dataset was best explained by 2 components representing heterotrophic and autotrophic processes respectively. Heterotrophic respiration was most closely associated with sediment chlorophyll c, indicating that benthic labile organic carbon (OC) was dominated by phytodetritus (diatoms) and viable phytoplankton cells. The supply of this OC to the sediments was controlled by a combination of phytoplankton biomass and hydrodynamic circulation patterns. Autotrophic benthic production across the study area was closely associated with light attenuation, which varied according to depth and turbidity. DIN fluxes were most closely associated with the autotrophic component, indicating the importance of N assimilation by benthic microalgae. N 2 fluxes were negatively associated with the heterotrophic component, most likely due to the increasing inhibition of coupled nitrificationdenitrification and/or an increase in N fixation as OC loading increases. DON fluxes dominated N fluxes overall and were controlled by autotrophic/heterotrophic DON production and heterotrophic DON consumption. Cluster analysis identified 3 basic states that describe the spatial and temporal variation in benthic processes across western Moreton Bay: reactive nearshore sediments underlying phytoplankton bloom centres (Cluster 1), less reactive sediments further offshore which receive a lesser supply of phytodetritus (Cluster 2) and a new suite of sediment properties, metabolism and N fluxes at the nearshore sites following a post-flood phytoplankton bloom (Cluster 3).

2025, Aquatic Microbial Ecology

Marine picoeukaryotes show high phylogenetic diversity worldwide, notably in oligotrophic waters. In the Gulf of Gabès (south-eastern Mediterranean), characterized by oligotrophic conditions and a complex water mass circulation, information on picoeukaryotic diversity is still lacking. In this study, we investigated the diversity and spatial variability of picoeukaryotic assemblages in relation to nutrient availability, physical parameters and water masses in 3 cruises carried out in the Gulf of Gabès in June of 2008, April of 2009 and November of 2009. Highthroughput sequencing revealed a dominance of sequences from non photosynthetic picoeukaryotes, mostly represented by the presumably parasitic marine alveolate MALV-II (33.20%) and the bacterivorous Bicosoecida (13.56%). Differences in picoeukaryotic assemblages were higher between coastal and open-sea stations, and depth in the water column also affected community differences, with surface (5 m), intermediate (25-100 m) and mesopelagic (> 200 m) samples forming separate groups. A clear temporal variability was also evident, particularly for communities collected from the surface layer and open-sea stations. Co-inertia analysis revealed that picoeukaryotic groups were more affected by salinity in deep waters, whereas at the surface, they were dependent on nutrients and temperature. During the November cruise, samples that shared similar water mass properties generally clustered together. The Levantine water mass, observed for the first time in this area, was characterized by the presence of Acantharia and Polycystinea. Our study highlights the role of physical and chemical features, such as water mass origin, the wide continental shelf and trophic status, in determining the diversity of marine picoeukaryotes.

2025

The production and mortality of prokaryotes were assessed over a latitudinal gradient in the North Atlantic Ocean during summer stratification. Heterotrophic production was uncoupled from phytoplankton biomass and closely tied to nutrient availability suggesting nutrient limitation played an important role in regulating host production dynamics. Viruses were the dominate mortality factor regulating prokaryotic losses in the surface waters of the Northeast Atlantic Ocean. Wherein, lytic viral production was the favored life strategy for prokaryotic viruses in the mixed layer, independent of system trophic status, with rates ranging from 0.9 to 57.0 x109 viruses l-1 d-1. Lytic VP in the surface waters was correlated to heterotrophic production and the nitrogen to phosphorus ratio. Lysogeny was important only within the deep chlorophyll maximum layer of oligotrophic stations wherein prophage induction decreased hyperbolically from 16.0 to 0.2 x109 viruses l-1 d-1 with latitude and Chl ...

2025, Aquatic Microbial Ecology

The structure and activity of prokaryotic communities were determined in marine snow and in the ambient water of the northern Adriatic Sea in different seasons (autumn, spring and summer). The seasonal variation in the composition of marine-snow-associated and ambientwater bacterial communities was assessed by T-RFLP (Terminal Restriction Fragment Length Polymorphism) on the 16S rRNA gene (16S rDNA) and 16S rRNA transcript (16S rRNA) level. On the 16S rDNA level, the bacterial community composition of the marine snow and ambient water was similar in summer and autumn, but not in spring. In contrast, on the 16S rRNA level, indicative of the active bacterial community, the marine-snow-associated bacterial community was different from that of the ambient-water, and different from the bacterial community on the 16S rDNA level, except in autumn. To phylogenetically characterize the bacterial and archaeal community composition associated with marine snow and the ambient water, clone libraries of 16S rDNA and 16S rRNA were constructed from 2 contrasting seasons. Phylogenetic profiling re vealed a higher similarity among bacterial communities in summer compared to late autumn. Certain bacterial and archaeal groups were exclusively associated with summer or autumn marine snow, suggesting that marine-snow-associated prokaryotic communities are subjected to successional changes similar to ambient-water communities. Moreover, the presence of bacterial groups enriched in marine snow including Vibrionales and sulphate-reducing bacteria is consistent with niche partitioning and metabolic adaptations of the particle-associated microbiota. KEY WORDS: Marine snow • Free-living bacteria • Marine snow-associated bacteria • Archaea • T-RFLP • 16S rRNA • 16S rDNA • Northern Adriatic Sea

2025, Aquatic Microbial Ecology

Bioassays in natural water-based batch cultures were performed to identify factors that could control the development of the toxic heterocystous cyanobacterium Cylindrospermopsis raciborskii in Lake Guiers (North Senegal). Without dissolved inorganic nitrogen, C. raciborskii was unable to grow, unless EDTA was supplied. The addition of P, S, Fe, B, Ca, Co, Cu, Mg, Mn, Mo and Zn did not restore its growth. Variations in the percentages of heterocysts found in bioassays, in the concentrations of major and trace elements in Lake Guiers, and in the computed chemical speciation of all dissolved species using MINEQL+ software, led us to deduce that, after N, Fe was the second greatest growth-limiting nutrient. Assuming that the 'Free Ion Model' is valid for the indigenous species of phytoplankton, the concentrations of bioavailable Fe 3+ were within the range of 10 -19 to 10 -22 M and were limited by the very low solubility of Fe-hydroxides. At such negligible concentrations, C. raciborskii is unable to take up the Fe necessary to ensure efficient nitrogenase functioning. The addition of EDTA led to the production of (III) Fe-EDTA complexes, which acted as an iron buffer that, in turn, increased the bioavailability of Fe 3+ and the growth of C. raciborskii. These bioassays suggest that, in Lake Guiers, the primary limiting factor for cyanobacterial growth is nitrogen. They also demonstrate the lack of a sufficient concentration of complexing agents, which limits the bioavailability of Fe, and then the nitrogenase activity and diazotrophy of C. raciborskii. This cascading limitation could account for the seasonal fluctuations of this cyanobacterial population in Lake Guiers.

2025, Geobiology

Stromatolites date back some 3.5 billion years and constitute the most common and conspicuous fossils through the Proterozoic. These organosedimentary structures decreased dramatically in diversity and abundance by the late Neoproterozoic, a phenomenon often ascribed to destructive grazing by newly evolved metazoans. We investigated the concurrent processes of microbial calcification and metazoan bioerosion in one of the few locations (Rio Mesquites, Cuatro Ciénegas, Coahuila, Mexico) where living freshwater stromatolites, formed by cyanobacteria and diatoms, coexist with significant populations of metazoan grazers. We used microsensor chemical profiling and monitoring of bulk water Ca 2+ concentrations to determine calcification rates and their dependence on microbial metabolism. The bioerosive impact resulting from grazing by endemic hydrobiid gastropods was assessed by gravimetric quantification of carbonaceous faecal pellet production. Calcification was clearly light-dependent, reaching maximal rates (saturation) at low incident light intensity, and was surprisingly efficient, with O 2 /Ca 2+ exchange ratios well above unity, and with absolute rates similar to those found in corals. However, the erosive action of grazing snails removed most of these carbonate inputs from the oncolites. Thus, a precarious balance between constructive and destructive geobiological processes was at play in the system. The fact that accretion barely exceeded bioerosion in an environment highly conducive to calcification supports the potential impact of faunal grazing as causal agent in the demise of stromatolites in the late Proterozoic. Our findings indicate that a search for fossil evidence of bioerosive grazing in the form of carbonaceous faecal pellets associated with fossil stromatolites may provide a means to test that hypothesis directly.

2025, Aquatic Microbial Ecology

The productivity of most marine ecosystems is limited by the availability of dissolved nitrogen (N) and phosphorus (P). Nutrient recycling is therefore a key process for ecosystem functioning. Fish recycle nutrients through the excretion of ammonia and phosphate and can influence the abundance and community structure of primary producers such as phytoplankton. However, the effect of fish on other plankton compartments, and whether all fish species have similar effects, is largely unknown. We used a tank experiment to test how 2 Mediterranean fish species, gilthead seabream Sparus aurata and golden mullet Chelon auratus, with distinctly different N and P excretion rates, can affect the abundance and community structure of 3 plankton compartments: phytoplankton, bacterioplankton, and microzooplankton. We found that the nutrients released by seabream (whose excreta had an N:P molar ratio greater than the Redfield ratio of 16:1) induced a substantial increase in the abundance of all plankton compartments. In addition, with seabream, the relative abundance of diatoms in the phytoplankton communities increased. However, no significant change was observed with mullet, which had a low excreta N:P molar ratio, suggesting that the growth of microbial plankton was limited by the availability of N. Our results demonstrate that nutrient excretion by fish affects the microbial food web through a speciesspecific bottom-up effect on the total abundance and community structure of the phytoplankton, bacterioplankton, and microzooplankton communities.

2025, General and Comparative Endocrinology

The growth hormone (GH) gene has been characterized for a number of fishes and used to establish phylogenetic relationships and population structures. Analysis of tetraploid fishes, such as salmon and some Asian cyprinids, has shown the presence of two GH genes. Fishes in the sucker family (Catostomidae, Cypriniformes) are also tetraploid, and the present study reports the isolation and characterization of two GH cDNAs from a representative species, the smallmouth buffalofish (Ictiobus bubalus). The GH cDNAs of smallmouth buffalofish are 1272 and 1273 nt in length, and each codes for a polypeptide of 210 amino acids, predicted to be cleaved to a final product of 188 aa. The GH cDNAs of smallmouth buffalofish are 6% divergent in nt sequence in the coding region, and there are 16 differences in predicted aa sequence. Because the cDNAs have distinct sequences in coding regions and in UTRs, which differed by more than 10%, they were identified as GHI and GHII. The predicted GHI protein contains 4 Cys residues, homologous to other vertebrate GH sequences. On the other hand, GHII has 5 Cys residues, homologous to other ostariophysan sequences. GHI and GHII are most similar to other cypriniform fishes for both nt and protein sequences. Phylogenetically, the sequences of smallmouth buffalofish GH consistently grouped with Asian cyprinids, but not loaches, consistent with morphological evidence suggesting that suckers are most closely related to minnows.

2025

In this study has been analyzed the genetic potential (rDNA) versus expression (crDNA) of microbial populations associated to gills of living mussel Mytilus galloprovincialis (Bivalvia: Mytilidae) in natural environment. Data obtained (16S rDNA/crDNA clones libraries) showed as sequences mainly related to Bacteroides/ Chlorobi, Firmicutes and Gamma-Proteobacteria groups are specific in live mussels. It is presumed that further studies of microbial population structure with culture-independent methods will demonstrate the active interactions (symbiosis) between filter-feeding organisms and gill-associated bacteria.

2025, Aquatic Microbial Ecology

A unique chemoautotrophic system of floating microbial mats was examined in a subterranean cave in southern Romania. Oxygen measurements were made with a recently developed technique applying micro-optodes. The oxygen uptake rate of the anoxic and sulfidic cave waters over the atmosphere/water interface was as high as 103.3 i 9.1 mm01 O2 m-2 d-l. Floating microbial mats consisting primarily of sulfide oxidizers and fungal mycelia were found to be adapted to reduced oxygen supply and thrived even under strict anoxia. These 2 mm thick mats were inhabited by 5 different species of nematodes, reaching densities of 9.8 X 106 ind. m-2 Possible alternative pathways for growth of the mats and also for the persistence and reproduction of nematodes under strict anoxic conditions are discussed.

2025, Aquatic Microbial Ecology

2025, Frontiers in Microbiology

2025, Aquatic Microbial Ecology

In situ dissolved B 12 concentration in marine ecosystems is controlled by the balance between rates of release of B 12 by prokaryotes, uptake by prokaryotes and eukaryotes, and abiotic degradation. We used chemostats at a range of specific growth rates (μ, d -1 ; 0.1 to 1) with natural communities of prokaryotes and monospecific cultures of a B 12 producer, Dinoroseobacter shibae. We measured the dissolved B 12 concentration produced in the culture (B 12-d ), the B 12 in the particulate fraction (B 12-p ), cell concentration, respiration rate, particulate organic carbon and nitrogen (POC, PON), and the 16S amplicon composition. Total dissolved B 12 concentrations (0.92 to 4.90 pmol l -1 ) were comparable to those found in the surface ocean. B 12-p concentration was 6 to 35 times higher than B 12-d . B 12-d , B 12-p , and community composition showed no relation to μ for either natural populations or D. shibae. The chemostats allowed calculation of the rates of production: B 12-d (0.34 ± 0.28 pmol l -1 d -1 ) and B 12-p (5.65 ± 2.34 pmol l -1 d -1 ), and the B 12 cell quota (900 to 3300 molecules cell -1 ). In multispecies and D. shibae cultures, B 12 production rates per cell increased with respiration rates (volumetric or per cell), and with rates of cellular organic carbon and nitrogen production. Rates increased with μ, but not the concentrations of B 12-d or of B 12-p . To understand the physiological and ecological dynamics of B 12 , concentrations alone are insufficient since they do not provide rates, which are important in understanding the dynamics between producers and consumers.

2025, Aquatic Microbial Ecology

We examined the effect of light attenuation, due to floating plants, on the community structure of the main phagotrophic protists and their grazing rates in a wetland in the Lower Paraná Basin. Ingestion experiments (winter and summer) were conducted at 2 sites in the same shallow lake that had contrasting light scenarios: open waters (light) and under profuse macrophyte coverage (dark: light attenuation ~97%). We compared the rates at which protists ingested 3 types of tracer prey: fluorescently labelled heterotrophic bacteria (FLB), picocyanobacteria (FLC) and picoeukaryotic algae (FLA). Light influenced both the structure of the microbial communities and the protistan grazing rates. Heterotrophic flagellates (HF) were more abundant under the macrophytes, whereas mixotrophic algae (cryptophytes) and autotrophic and heterotrophic picoplankton populations attained higher abundances in open waters. Specific grazing rates (SGRs) of mixotrophs on heterotrophic bacteria (HB) were higher in the light (7.9 to 15.5 prey cells grazer -1 h -1 ), than in darkness (0.1 to 5.1 prey cells grazer -1 h -1 ); the same trend was observed on picocyanobacteria (Pcy) (1.1 and 0.2 prey cells grazer -1 h -1 , light and dark). SGRs of HF were 1.0 to 7.3 cells grazer -1 h -1 (on HB) and 0.01 to 1.8 prey cells grazer -1 h -1 (on Pcy), with highest values in summer and no pattern in relation to light. SGRs of ciliates were higher in summer and in darkness. Clearance rates (CR) on Pcy were higher than on HB, for both HF and mixotrophic algae. In winter, cryptophytes contributed up to 93% of the microbial grazing in the light, whereas HF were more important in darkness; in summer, bacterivory was dominated by heterotrophs in both light scenarios. Our experimental results highlight the importance of light conditions in structuring bacterial grazing by protists.

2025

In recent years great progress has been made in developing approaches for characterizing microbial communities in natural environments through the application of modern molecular methods. It is possible to "fingerprint" natural communities by extracting their stable low molecular weight RNA (SLMW RNA) and to establish relationships between environmental factors and differences in community composition. Because of the "noise" in such environmental data, we have applied neural net analysis to detect patterns in community data and obtain quantitative data that can be used for statistical analysis and establishment of relationships. Applied to samples from the Chesapeake Bay, microbial communities were shown to vary temporally and spatially. Particle-associated and freeliving communities differed in the winter, but not in the summer, and there was little overlap in summer and winter communities.

2025, Aquatic Microbial Ecology

Mixed blooms of 4 species of harmful raphidophytes (Chattonella cf. verruculosa, Chattonella subsalsa, Heterosigma akashiwo, and Fibrocapsa japonica) occur in the shallow (1 to 2 m) Delaware Inland Bays (DIB), USA. Raphidophytes vertically migrate in other deeper water ecosystems to utilize deep nutrient stocks at night, and thus obtain an advantage over non-migrating algae. Anoxic DIB sediments release high levels of bioavailable phosphate, which could potentially be used by vertically migrating flagellates. This study aimed to characterize and understand the migration patterns of DIB raphidophytes, and determine whether benthic phosphate fluxes could provide the cells with P. We demonstrated vertical migration of isolated DIB raphidophyte cultures in the laboratory, where differences in the response of C. subsalsa and H. akashiwo to light:dark period manipulations suggested possible differences in external versus endogenous regulation of migration behavior in the 2 species. Natural blooms in the field (enclosed in a mesocosm system) also exhibited patterns of diel vertical migration, as determined by quantitative real-time PCR (QPCR) used to enumerate the diel vertical distributions of each species. Our data suggested that these 2 photoautotrophic species spend daylight hours near the surface and are found directly on the sediment surface at night. However, diel changes in particulate C:P ratios did not support the hypothesis that there is preferential uptake of sedimentary phosphate at night. Our results also suggested that the migration behavior may have important implications for designing sampling strategies for monitoring programs. QPCR has a number of decisive advantages over traditional microscopic counting methods, making this a powerful tool for fine spatial and temporal scale detection and enumeration of vertically migrating harmful algal species.

2025, Aquatic Microbial Ecology

Seawater cultures were conducted in large volume (36 1) gas impermeable tri-laminate bags for the purpose of empirically deriving bacterial growth efficiency (BGE) and carbon conversion factors (CCF) in the south central Ross Sea. Thls experimental design allowed for concomitant nleasurements of metabolic reactants (loss of total and dissolved organic carbon [TOC and DOC]) and products (gain of total carbon dioxide [TCOz] and bacterial biomass) to be made from a single incubation vessel. Some previous studies have relied on proxy measurements (e.g. 02, 3H-thymidine incorporation and cell abundance) to determine BGE and CCF rather than direct carbon measurements. Our experimental design enabled a complete carbon budget to be constructed and eliminated variability associated with normally employed parallel bottle incubations. Uhlization of TOC was well balanced by the production of TC02, in 7 of 8 experiments, validating the use of tri-laminate bags for measuring microbial respiration. In 3 experiments, where TOC, DOC, TCOzand bacterial biovolume were directly measured, carbon mass balance yielded BGE estimates of 12, 32 and 38% and bacterial CCF of 77, 95 and 134 fg C pm-3 In experiments where independent DOC measurements were not made we used our empirically derived CCF values to determine bacterial carbon production and calculated DOC concentrations and BGE for these remaining experiments. The BGE derived from all the bag experiments conducted throughout the austral spring and summer 1995-1997 ranged from 9 to 38%. Our experimental design and carbon mass balance approach could be applied to other aquatic systems to empirically derive the BGE and CCF, factors essential for determining carbon flux through bacterioplankton. KEY WORDS: DOC remineralization . Bacterial respiration . TCOz . Growth efficiency . Carbon conversion factor . Tri-laminate bags . Seawater culture

2025, Aquatic Microbial Ecology

Top: Autumnal leaves shed in a temperate stream. Bottom (right): Mycelium, conidiophores and conidia of aquatic hyphomycetes (mostly of Tetrachaetum elegans) developed on a leaf blade. Bottom (left): Conidia from the species used: (a) Articulospora tetracladia, (b) Clavariopsis aquatica, (c) Lemon niera terrestris, (d) T. elegans, (e) Tetra cladium mar chalianum, (f) Tricladium chaetocladium

2025, Aquatic Microbial Ecology

The bacterioplankton composition of 67 Finnish lakes was characterised by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, and subsequent sequence analyses of major fragments. The DGGE patterns grouped as a function of environmental characteristics describing the trophic status of the lakes, such as total phosphorus (TP), total nitrogen (TN), TN:TP, chlorophyll a, Secchi depth and water colour. Most sequences retrieved represented Verrucomicrobia, Actinobacteria and Cyanobacteria, while those representing Alpha-and Gammaproteobacteria, Chloroflexi and Acidobacteria were less frequent. The presence of several sequences could be linked to the trophic status of the lakes, while that of others was more common and thus unrelated to the trophic status. These results suggest that individual responses towards environmental factors may occur among the bacterioplankton at the level of phyla as well as phylotypes.

2025, Aquatic Microbial Ecology

The effects of phosphate limitation and of the presence of marine bacteria during phosphate limitation on growth and polysaccharide production in the diatom Cylindrotheca fusiformis grown in batch cultures are described in this paper. Growth of C. fusiformis was inhibited under low Pi (inorganic phosphate) conditions, corresponding to an increasing N/P ratio, and higher amounts of polysaccharides were extruded in the medium, in particular during the stationary phase of growth. The presence of bacteria reduced phytoplankton cell density only when the phosphate added corresponded to 1/6 of the initial amount. Even when diatom cell growth was not affected, the presence of bacteria stimulated a higher polysaccharide production. These results are interpreted in the light of the fact that nutrient-stressed phytoplankton cells produced and released a higher amount of polysaccharides and, as bacteria exhibited a better utilization of phosphate than algal cells, their presence accentuated the Pi depletion, resulting in a higher polysaccharide production.

2025, HAL (Le Centre pour la Communication Scientifique Directe)

Contributions of filamentous and picoplanktonic cyanobacteria to the phytoplankton community structure were examined in New Caledonian waters during the 2001-2003 El Niño period at three stations. Morphometric characteristics of diazotrophic filamentous cyanobacteria are given as well as the seasonal and inter-annual variations of their surface areas and integrated abundances. Trichodesmium tenue and T. thiebautii were the dominant species followed by T. erythraeum, altogether accounting for more than 51-80 % of the biomass of the free-living filamentous cyanobacteria. Katagnymene spp. accounted for a smaller percentage (<13.8 % at ocean stations, <3.6 % in the lagoon). R. intracellularis biomass was relatively small (<1 % of total surface area and volume of Trichodesmium trichomes) with the highest ! concentration observed in summer (735 trichomes l -1 ). Colonies of unidentified cyanobacteria composed of spherical cells accounted on average for <1 % of the Trichodesmium biomass, with values exceeding 4000 cells l -1 . Abundance of filamentous cyanobacteria varied according to environmental factors, with summer 2001-2002 characterized by low filamentous diazotroph abundance and summer 2003, occurring at the peak of the 2001-2003 El Niño, particularly rich in filamentous cyanobacteria (with a maximum Trichodesmium spp abundance of 4500 trichomes l -1 in the Loyalty Channel). A similar variability pattern was observed for large diatoms and dinoflagellates, and for all picoeukaryotic populations. Different biomass estimators are provided as cell abundances, pigment concentrations including chlorophylls and phycoerythrin, and carbon content. The filamentous communities dominated in summer in oceanic waters while

2025

El deterioro del agua del embalse de Bellús, ha ocasionado procesos de eutrofización, dando como resultado que la calidad de sus aguas sea pésima para su uso. En este estudio se ha desarrollado la modelación matemática de la calidad del... more

2025, Aquatic Microbial Ecology

Assessment of the role of viral lysis in aquatic microbial communities requires a robust means of estimating viral production (VP). Here, 3 incubation-based VP methods (fluorescently labeled viruses [FLV], dilution [DIL], and thymidine incorporation [TdR]) were evaluated in water samples from the Delaware and Chesapeake Bays. In Chesapeake Bay samples, average VP rates were 10-fold higher for FLV and DIL (~3 to 25 × 10 10 viruses l -1 d -1 ) than for TdR (~0.2 to 3 × 10 10 viruses l -1 d -1 ). Estimates of viral-mediated bacterial mortality (VMM) indicate that FLV overestimates VP in eutrophic waters, since >100% of bacterial production (BP) would have been consumed through viral lysis. DIL and TdR VP methods gave more realistic estimates of VMM with respect to BP. The FLV method provides estimates of both VP and virus removal rates; however, it requires preparation of a viral tracer and twice as many microscopic enumerations as the DIL method. DIL was the least difficult and most efficient method; however, bacterial loss during vacuum diafiltration resulted in poor replicability. TdR gave similar VP estimates to DIL, but requires use of a large and poorly constrained conversion factor. With methodological improvements in bacterial cell recovery, DIL should be the most widely applicable method for estimation of VP in highly productive estuarine waters.

2025, Aquatic Microbial Ecology

), concentrations of dissolved inorganic P are gen erally below 1 μM in the surface ocean (Karl 2014), which limits phytoplankton productivity (Tyrrell 1999). Marine phytoplankton respond to chronic P deficiency by investing resources in... more

2025, Aquatic Microbial Ecology

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2025, Aquatic Microbial Ecology

Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities.

2025, Aquatic Microbial Ecology

The following parameters were determined in the photic zone of Lake Kinneret from January 2001 through December 2002: primary production (PP), community respiration (CR), bacterial biomass production (BBP), bacterial numbers (BN) and biological oxygen demand (BOD 5 ). Average values over the 2 yr period for these parameters in the photic zone (0 to 15 m) were PP, 1539 mg C m -2 d -1 ; CR, 1653 mg C m -2 d -1 ; BBP, 887 mg C m -2 d -1 ; BN, 4.6 × 10 6 cells ml -1 ; and BOD 5 , 6366 mg C m -2 . We used these data together with literature-based assumptions about the ratio of net to gross primary production, bacterial and zooplankton respiration to estimate bacterial growth efficiencies (BGE) ranging from 44 to 64%. Bacterial specific growth rates averaged 0.33 d -1 , ranging from 0.13 to 0.93 d -1 . CR was significantly correlated with both PP and BBP. A significant correlation was found between BBP and BOD 5 , suggesting that the indigenous bacterial populations were strongly dependent on substrates measured by BOD 5 . The potentially labile fractions of TOC, as quantified by BOD 5 , were rapidly cycled by heterotrophic bacteria, within ~4 d on average. With the exception of 6 to 8 wk in early summer, the photic zone of this warm mesotrophic-eutrophic lake, with low inputs of allochthonous organic carbon, was net autotrophic. BBP and BGE values were high in comparison to those reported from even more eutrophic aquatic systems. Our results indicate that bacteria are by far the major biological agents of organic carbon cycling in Lake Kinneret, and contradict the general perception that the microbial loop plays a less important role in carbon cycling in eutrophic than in oligotrophic aquatic systems.

2025, Aquatic Microbial Ecology

polysaccharides of the marine microalga Phaeocystis can be degraded in enrichment cultures. In this paper we report on the characterization of the microbial community in such enrichments. Denaturing gradient gel electrophoresis (DGGE) profiles that were obtained during mucopolysaccharide degradation showed a substantial number of sequence types, suggesting the occurrence of multiple bacterial species in the enrichments. Only after the rate of mucopolysaccharide degradation had slowed down to less than 5% of its initial value could a significant change in the relative abundance of certain bacterial species in the enrichments be detected. Therefore, degradation of this complex substrate does not seem to require a succession of bacterial populations. Several mucopolysaccharide-degrading enrichments obtained by inoculation from different sources (colony mucus, the water column and sediments), and grown under either oxic or anoxic conditions, appeared to contain very different microbial communities with only a few overlapping species. Therefore, the selection pressure imposed by mucopolysaccharides as growth substrates is only one of the factors shaping the species composition in the enrichments. Attempts to isolate pure cultures of bacteria capable of mucopolysaccharide degradation using plating and dilution techniques failed. However, following a new approach which couples community analysis (using DGGE) and the physiological capability of the enrichment to degrade mucopolysaccharides, bacteria involved in the degradation process could be identified. This was based on the correlation between inhibition of mucopolysaccharide degradation and absence of certain bands from DGGE profiles when enrichment cultures were incubated at an elevated temperature. Phylogenetic analysis on clones of DNA fragments that were excised from DGGE gels, placed the putative mucopolysaccharide degraders in the α and γ subdivisions of the Proteobacteria, the Cytophaga-Flexibacter cluster, and the Planctomyces and Verrucomicrobiales clade. These findings directly link representatives of these abundant bacterial clusters with the degradation of complex algal polymers in the sea.

2025, Aquatic Microbial Ecology

2025

La responsabilità dei dati scientifici e tecnici è dei singoli autori.

2025, Boletín de Investigaciones Marinas y Costeras

Se estimaron abundancia, biomasa, biovolumen y forma del bacterioplancton en tres estaciones de la bahía de Gaira (costa Caribe colombiana) en los períodos denidos para este estudio como: “lluvioso” (julio, agosto; 2003), “transición” (abril, octubre; 2004) y “seco” (febrero, marzo; 2004). Las muestras del bacterioplancton fueron tomadas a 0.5 y 42 m de profundidad, ltradas sobre ltros de policarbonato de 0.22 μm y cuanticadas utilizando microscopía de epi!uorescencia con naranja de acridina y análisis de imagen. La abundancia bacteriana varió entre 1.3 x 105-2.9 x 106 células mL-1 en el período lluvioso, 8.8 x 104-2.2 x 106 células mL-1 en el período de transición y 6.7 x 104-3.9 x 105 células mL-1 en el período seco, la abundancia promedio fue de 4.4 x 105 células mL-1. Las diferencias en abundancia fueron estadísticamente signicativas entre períodos, estaciones y profundidades, las diferencias en biovolumen fueron signicativas entre períodos y estaciones, nalmente, las diferencias en biomasa fueron signicativas entre estaciones y profundidades (ANOVA, p<0.05). Predominaron las células cocoides y de biovolumen pequeño (0.01-0.08 μm3 célula-1). Durante el muestreo la biomasa bacteriana promedio varió entre 0.88 y 32.1 μg C L-1, el valor máximo se observó durante el período lluvioso. Los resultados sugieren que los valores de abundancia y biomasa bacterianas se incrementan en el período lluvioso, probablemente como consecuencia del incremento en la descarga del río Gaira y de la Ciénaga Grande de Santa Marta. La hipótesis planteada señala que la dinámica de la comunidad bacteriana en la bahía está siendo afectada por la disponibilidad de nutrientes orgánicos (COD).

2025, Aquatic Microbial Ecology

2025, Marine Ecology Progress Series

Recent field studies indicate that dinoflagellates are key degraders of copepod fecal pellets. This study is the first to publish direct evidence of pellet grazing by dinoflagellates. Feeding and growth on copepod fecal pellets were studied for both heterotrophic (4 species) and mixotrophic dinoflagellates (3 species) using a combination of classic incubation experiments and video recordings of feeding behavior. Fecal pellets were produced by adult Acartia tonsa feeding on Rhodomonas salina. Two mixotrophic species (Karlodinium armiger, a gymnodinoid dinoflagellate, Gy1) and all heterotrophic dinoflagellates (Gyrodinium dominans, Gyrodinium spirale, Diplopsalis lenticula, Protoperidinium depressum) studied fed on fecal pellets. Using natural concentrations of dinoflagellates and copepod fecal pellets, average ingestion rates of 0.2 and 0.1 pellets cell -1 d -1 and clearance rates of between 0.2 and 0.3 ml cell -1 d -1 were obtained for G. spirale and P. depressum, respectively. Pellet feeding resulted in average growth rates of 0.69 and 0.08 d -1 with growth yields of 0.58 and 0.50 for G. spirale and P. depressum. Important factors for the grazing impact of the dinoflagellates on fecal pellets in this study were: dinoflagellate concentration, the dinoflagellate-to-pellet size ratio, the feeding mechanism, pellet food source, and pellet age. This study reveals a new trophic role for dinoflagellates as detritivores, and shows that large (> 20 µm) heterotrophic dinoflagellates alone can account for reported pellet degradation rates in field studies. Thus, dinoflagellates can function as an effective 'protozoan filter' for fecal pellets in the water column.

2025, Journal of Plankton Research

The Mediterranean coast receives large inputs of dust with a potential fertilization effect. We evaluated the effect of a wet dust deposition event on microbial abundance and activity, community structure and metabolic balance. Dust collected during a dust storm event was added to a series of microcosms. We added a realistic concentration (0.05 g L 21 ) based on the phosphorus concentration contained in the dust and, in addition, we included a P amended tank to distinguish the effect of dust from that of the phosphorus in the dust. We also included a higher dust concentration tank (0.5 g L 21 ). Dust increased the initial water-phosphorus concentration by 0.3 mM and the dissolved organic carbon (DOC) concentration by 14 mM, and increased bacterial abundance (1.8-fold) and bacterial production (5-fold). At the end of the experiment, primary production and community respiration were stimulated by dust and by P, but the net result of the addition of low amounts of dust was an initial switch towards heterotrophy, whereas the net result of the high-dust (DH) additions and the P addition was a shift towards autotrophy. Bacterial community structure changed little between P and low dust, but these were very different from the control and the DH communities.

2025, Aquatic Microbial Ecology

Bioassay experiments were performed to identify how growth of key groups within the microbial community was simultaneously limited by nutrient (nitrogen and phosphorus) availability during spring in the Gulf of Aqaba's oceanic waters. Measurements of chlorophyll a (chl a) concentration and fast repetition rate (FRR) fluorescence generally demonstrated that growth of obligate phototrophic phytoplankton was co-limited by N and P and growth of facultative aerobic anoxygenic photoheterotropic (AAP) bacteria was limited by N. Phytoplankton exhibited an increase in chl a biomass over 24 to 48 h upon relief of nutrient limitation. This response coincided with an increase in photosystem II (PSII) photochemical efficiency (F v /F m ), but was preceded (within 24 h) by a decrease in effective absorption crosssection (σ PSII ) and electron turnover time (τ). A similar response for τ and bacterio-chl a was observed for the AAPs. Consistent with the up-regulation of PSII activity with FRR fluorescence were observations of newly synthesized PSII reaction centers via low temperature (77K) fluorescence spectroscopy for addition of N (and N + P). Flow cytometry revealed that the chl a and thus FRR fluorescence responses were partly driven by the picophytoplankton (<10 µm) community, and in particular Synechococcus. Productivity of obligate heterotrophic bacteria exhibited the greatest increase in response to a natural (deep water) treatment, but only a small increase in response to N and P addition, demonstrating the importance of additional substrates (most likely dissolved organic carbon) in moderating the heterotrophs. These data support previous observations that the microbial community response (autotrophy relative to heterotrophy) is critically dependent upon the nature of transient nutrient enrichment.

2025

We collected particles on quartz filters with High Volume Samplers. The we extracted the particles from fhe filters. We added 0.8 mg L -1 to 15 or 10 L containers with 150 µm screened natural seawater. We monitored biomass, activity and community composition over several days. Experiments were done at 3 different sites in the NW Mediterranean of increasing oligotrophy (Barcelona: BCN, Blanes: BLA, and offshore (OFF), and at different times of the year. Nitrate, ammonium, phosphate, silicate, TOC, POC, chlorophyll, heterotrophic bacterial abundance and production, and prokaryotic community composition were among the variables tracked.