Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of ...knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.
COVID-19 has led to global population lockdowns that have had indirect effects on terrestrial and marine fauna, yet little is known on their effects on marine planktonic communities. We analysed the ...effect of the spring 2020 lockdown in a marine coastal area in Blanes Bay, NW Mediterranean. We compared a set of 23 oceanographic, microbial and biogeochemical variables sampled right after the strict lockdown in Spain, with data from the previous 15 years after correcting for long-term trends. Our analysis shows a series of changes in the microbial communities which may have been induced by the combination of the decreased nitrogen atmospheric load, the lower wastewater flux and the reduced fishing activity in the area, among other factors. In particular, we detected a slight decrease beyond the long-term trend in chlorophyll a, in the abundance of several microbial groups (phototrophic nanoflagellates and total prokaryotes) and in prokaryotic activity (heterotrophic prokaryotic production and β-glucosidase activity) which, as a whole, resulted in a moderate increase of oligotrophy in Blanes Bay after the lockdown.
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•COVID-19 lockdown effects on marine planktonic communities are still unknown.•A set of 23 variables were compared between spring 2020 and the 15 previous years.•Data show a decrease of some microbial groups, and a moderate increase in oligotrophy.•Induced, among others, by reduced fishing, wastewater flux and N atmospheric load
ABSTRACT
Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. ...We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes
Gammaproteobacteria
(44%),
Alphaproteobacteria
(26%), and
Bacteroidia
(17%). Isolates pertaining to class
Gammaproteobacteria
were the most abundant in all experiments, while
Bacteroidia
were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations.
IMPORTANCE
Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
We carried out monthly photosynthesis-irradiance (P-E) experiments with the 14C-method for 12 years (2003-2014) to determine the photosynthetic parameters and primary production of surface ...phytoplankton in the Blanes Bay Microbial Observatory, a coastal sampling station in the NW Mediterranean Sea. Our goal was to obtain seasonal trends and to establish the basis for detecting future changes of primary production in this oligotrophic area. The maximal photosynthetic rate PBmax ranged 30-fold (0.5-15 mg C mg Chl a-1 h-1), averaged 3.7 mg C mg Chl a-1 h-1 (±0.25 SE) and was highest in August and lowest in April and December. We only observed photoinhibition twice. The initial or light-limited slope of the P-E relationship, αB, was low, averaging 0.007 mg C mg Chl a-1 h-1 (μmol photons m-2 s-1)-1 (±0.001 SE, range 0.001-0.045) and showed the lowest values in spring (April-June). The light saturation parameter or saturation irradiance, EK, averaged 711 μmol photons m-2 s-1 (±58.4 SE) and tended to be higher in spring and lower in winter. Phytoplankton assemblages were typically dominated by picoeukaryotes in early winter, diatoms in late autumn and late winter, dinoflagellates in spring and cyanobacteria in summer. Total particulate primary production averaged 1.45 mg C m-3 h-1 (±0.13 SE) with highest values in winter (up to 8.50 mg C m-3 h-1) and lowest values in summer (summer average, 0.30 mg C m-3 h-1), while chlorophyll-specific primary production averaged 2.49 mg C mg Chl a-1 h-1 (±0.19, SE) and peaked in summer (up to 12.0 mg C mg Chl a-1 h-1 in August). 14C-determined phytoplankton growth rates varied between ca. 0.3 d-1 in winter and 0.5 d-1 in summer and were within 60-80% of the maximal rates of growth, based on PBmax. Chlorophyll a was a good predictor of primary production only in the winter and autumn. Seasonality appeared to explain most of the variability in the studied variables, while phytoplankton composition played a minor role. Daily integrated primary production was fairly constant throughout the year: similar to previous oxygen-based estimates in winter but considerably lower than these in summer. The difference between 14C- and oxygen-based estimates of primary production could be explained by community respiration. Annually integrated primary production amounted to a rather modest 48 g C m-2 yr-1 (equivalent to 130 mg C m-2 d-1). Although no interannual patterns were detected, our work soundly establishes the seasonal trends for the coastal NW Mediterranean, therefore setting the basis for future detection of change.
Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use ...and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates as an estimate of bacterial heterotrophic production (BHP) showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu⁻¹ h⁻¹) as compared to summer (around 150 pM Leu⁻¹ h⁻¹). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu⁻¹, with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 μg C l⁻¹ d⁻¹) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.
Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint ...of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, catalyzed reporter deposition fluorescence
hybridization subcommunity cell-counts or metagenomic-operational taxonomic units (OTUs). Our calculations unveil a broad range of growth rates (0.3-10 d
) with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the
communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.
We investigated the short-term effects of variable solar irradiance and spectrum on the gross biological production of dimethylsulfide (DMS), a trace gas with potential climatic effects, in eight ...experiments performed at different times of the year in a northwest Mediterranean coastal site. Experimentally determined net community DMS production, DMS photolysis, and dark microbial DMS consumption rates were used to calculate gross community DMS production by budgeting. In addition, the composition of the bacterioplankton and phytoplankton communities in the initial samples, and the photoinhibition of bulk bacterial heterotrophic activity and phytoplankton photosynthetic efficiency were monitored. Our results show that: (1) gross DMS production is irradiance dependent, with a maximum short-term stimulation factor of 2- to 6-fold compared to dark incubations; (2) its spectral shape is variable but generally similar to that of phytoplankton photoinhibition or photodamage, with more effective stimulation at shorter ultraviolet wavelengths; and (3) stronger stimulation occurs when samples are overexposed with respect to their prior exposure. Remarkably, the photoresponse of gross DMS production was in most cases strong enough to (at least) compensate the photochemical DMS loss at the water subsurface. Such response would prevent DMS depletion in stratified and highly irradiated waters. Since the initial microbial communities were representative of meso- to oligotrophic conditions, our observations should apply to a wide variety of oceanic regimes.
To understand dissolved organic carbon (DOC) seasonal dynamics in a coastal oligotrophic site in the north-western Mediterranean Sea, we monitored DOC concentrations monthly over 3 yr, together with ...the meteorological data and the food-web-related biological processes involved in DOC dynamics. Additional DOC samples were taken in several inshore–offshore transects along the Catalan coast. We found DOC concentrations of ~60 μmol C l−1in winter, with increasing values through the summer and autumn and reaching 100 to 120 μmol C l−1in November. There was high inter-annual variability in this summer DOC accumulation, with values of 36, 69 and 13 μmol C l−1for 2006, 2007 and 2008, respectively. The analysis of the microbial food-web processes involved in the DOC balance did not reveal the causes of this accumulation, since the only occasion on which we observed net DOC production (0.3 ± 1 μmol C l−1d−1on average) was in 2007, and the negative DOC balance of 2006 and 2008 did not prevent DOC accumulating. The DOC accumulation episodes coincided with low rates of water renewal (average 0.037 ± 0.021 d−1from May to October) compared with those of winter to early spring (average 0.11 ± 0.048 d−1from November to April). Indeed, the amount of DOC accumulated each year was inversely correlated with the average summer rainfall. We hypothesize that decreased DOC turn-over due to photochemical or biological processes—mostly active during the summer—and low water renewal rate combine to determine seasonal DOC accumulation and influence its inter-annual variability.
The effect of photosynthetically available radiation (PAR; 400–700 nm) and ultraviolet radiation (UVR; 280–400 nm) on marine bacterial heterotrophic activity was assessed monthly throughout a ...seasonal cycle in Blanes Bay (northwestern Mediterranean Sea). Seawater samples amended with ³H-leucine were exposed to solar radiation under three radiation treatments: PAR + UVR (280–700 nm), PAR + UVA (320–700 nm), and PAR only. Parallel reference incubations in the dark and under a fixed artificial light source (PAR only) were also performed. Exposure to high UVR doses caused strong inhibition of ³H-leucine incorporation rates (LIR), whereas natural PAR doses did not cause overall significant effects. Within UVR, UVA radiation accounted for most of the reduction in LIR, and this effect was modulated by the proportionality of the experimental light to the previous light exposure history of the samples. Constant (artificial) PAR-only exposure led to a general but seasonally variable increase in bacterial heterotrophic production compared to the dark controls, with large increases in spring and lower changes during summer. This pattern was likely caused by the stimulation of the bacterial group Gammaproteobacteria, which showed higher numbers of cells active in ³H-leucine uptake after light exposure. Again, the previous light history of the samples seemed to partly explain the measured effects. Overall, our results show variable responses of bacterial activities to light manipulations, depending on seasonally changing light conditions and communities, and stress the importance of realistic simulation of light exposure conditions for ecosystem-relevant photobiological studies with microbial plankton.
Bacterial community activity and structure are thought to be directly or indirectly related to phytoplankton development and, in particular, to the phytoplankton species dominating specific algal ...blooms. To test this hypothesis, we performed a mesocosm experiment designed to generate blooms of different types of phytoplankton through the additions of silicate, urea and phosphorus to oligotrophic water from the Blanes Bay Microbial Observatory (NW Mediterranean). Over 10 d of incubation bacterial activity, bacterial abundance, nutrient composition and free-living bacterial community structure were monitored, as well as phytoplankton composition and the fluorescence characteristics of dissolved organic matter (DOM). While we found clear effects of the different nutrient additions on chlorophyll levels, bacterial production and the type of dominant DOM, bacterial abundance followed a similar pattern across different nutrient treatments, which deviated from that observed in the control. While phytoplankton composition in the treatment with added silicate evolved differently with respect to the other treatments, free-living bacterial community structure (as determined with DGGE) did not show conspicuous differences between treatments. Our results reveal that the changes in bacterial community composition were mostly due to the variation in grazing pressure with time, with a small contribution from changes in bottom-up nutrient supply mediated by the shifts in phytoplankton composition.
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