Prokaryotic Biomass Research Articles

Exploring the Relationship between Macrofaunal Biodiversity and Ecosystem Functioning in the Deep Sea

The global scale of the biodiversity crisis has stimulated research into the relationship between biodiversity and ecosystem functioning (BEF). Even though the deep sea is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scant. Moreover, the small number of recent studies, which mostly focus on meiobenthic nematodes, report conflicting results that range from a very clear positive relationship to none at all. In this BEF study, the deep-sea macrofauna were used as a model to investigate the structural and functional diversity of macrofauna assemblages at three depths (1200, 1900, and 3000 m) in seven open-slope systems from the North-Eastern Atlantic Ocean to the Central-Eastern Mediterranean Sea. The presence and nature of BEF relationships were studied considering two spatial scales, the large and the basin scale, in different environmental settings. Total benthic biomass and macrofaunal predator biomass were used as proxies to assess ecosystem functioning. Ecosystem efficiency was expressed as macrofaunal biomass to biopolymeric carbon content ratio, macrofaunal biomass to prokaryotic biomass ratio, macrofaunal biomass to meiofaunal biomass ratio, and meiofaunal biomass to prokaryotic biomass ratio. On both large and basin spatial scales, some significant relationships between macrofaunal diversity and ecosystem functioning and efficiency were reported. When significant, the nature of BEF relations was positive and exponential or linear supporting the general idea that a higher diversity can enhance ecosystem functioning. Other BEF relationships were explained by the effect of environmental variables. More data from different deep-sea systems are needed, to better elucidate the consequences of biodiversity loss on the ocean floor.

Temperature regulation of marine heterotrophic prokaryotes increases latitudinally as a breach between bottom-up and top-down controls.

Planktonic heterotrophic prokaryotes make up the largest living biomass and process most organic matter in the ocean. Determining when and where the biomass and activity of heterotrophic prokaryotes are controlled by resource availability (bottom-up), predation and viral lysis (top-down) or temperature will help in future carbon cycling predictions. We conducted an extensive survey across subtropical and tropical waters of the Atlantic, Indian and Pacific Oceans during the Malaspina 2010 Global Circumnavigation Expedition and assessed indices for these three types of controls at 109 stations (mostly from the surface to 4,000m depth). Temperature control was approached by the apparent activation energy in eV (ranging from 0.46 to 3.41), bottom-up control by the slope of the log-log relationship between biomass and production rate (ranging from -0.12 to 1.09) and top-down control by an index that considers the relative abundances of heterotrophic nanoflagellates and viruses (ranging from 0.82 to 4.83). We conclude that temperature becomes dominant (i.e. activation energy >1.5eV) within a narrow window of intermediate values of bottom-up (0.3-0.6) and top-down 0.8-1.2) controls. A pervasive latitudinal pattern of decreasing temperature regulation towards the Equator, regardless of the oceanic basin, suggests that the impact of global warming on marine microbes and their biogeochemical function will be more intense at higher latitudes. Our analysis predicts that 1°C ocean warming will result in increased biomass of heterotrophic prokaryoplankton only in waters with <26°C of mean annual surface temperature.

Bacterial complexes of a high moor related to different elements of microrelief

The analysis of bacterial complexes, including the number, taxonomic composition, physiological state, and proportion of ecological trophic groups was performed in a high moorland related to different elements of the microrelief. The abundance of bacteria, their ability for hydrolysis of polymers and the share of r-strategists were found to be higher in the sphagnum hillocks than on the flat surfaces. The total prokaryote biomass was 4 times greater in the sphagnum samples from microhighs (hillocks). On these elements of the microrelief, the density of actinomycetal mycelium was higher. Bacteria of the hydrolytic complex (Cytophaga and Chitinophaga genera) were found only in microhigh samples.

Elevated trace metal content of prokaryotic communities associated with marine oxygen deficient zones

AbstractLittle is known about the trace metal content of marine prokaryotes, in part due to their co‐occurrence with more abundant particulate phases in the upper ocean, such as phytoplankton and biogenic detritus, lithogenic minerals, and authigenic Mn and Fe oxyhydroxides. We attempt to isolate these biomass signals in particulate data from the US GEOTRACES Eastern Pacific Zonal Transect (cruise GP16) in the Eastern Tropical South Pacific (ETSP), which exhibited consistent maxima in P and other bioactive trace metals, and minima in particulate Mn, in the oxygen deficient zones (ODZs) of 13 stations. Nitrite maxima and nitrate deficits indicated the presence of denitrifying prokaryotic biomass within ETSP ODZs, and deep secondary fluorescence maxima at the upper ODZ boundaries of 10 stations also suggested the presence of low‐light, autotrophic communities. ODZs were observed as far west as 99°W, more than 2300 km from the South American coast, where eolian lithogenic and lateral/resuspended sedimentary inputs were negligible, presenting a unique opportunity to examine prokaryotic metal stoichiometries. ODZ particulate P maxima can rival gyre mixed layer biomass concentrations, are highly sensitive to oxygen, and are in excess of amounts scavengable by local Fe oxyhydroxides and acid–volatile sulfides. Even after correction for lithogenic and ferruginous–scavenged metals, ODZ P‐maxima are often enriched in Cd, Co, Cu, Ni, V, and Zn, exhibiting particulate trace metal ratios to P that exceed mixed layer biomass ratios by factors of 2–9. ODZ prokaryotic communities may be largely hidden, TM–rich pools involved in the marine cycles of these bioactive trace metals.

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field.

Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.

A seasonal comparison of prokaryote numbers, biomass and heterotrophic productivity in waters of the KwaZulu-Natal Bight, South Africa

The KwaZulu-Natal Bight is a shallow indentation of the eastern seaboard of South Africa, characterised by a narrow (45 km wide) extension of the continental shelf, with a shelf break at about 100 m. It has a complex hydrography: the waters of the bight are derived from the fast-flowing, southward-trending Agulhas Current, which is fed mostly by the tropical and subtropical surface waters of the South-West Indian Ocean subgyre, which are generally oligotrophic in nature, notably depleted in reduced nitrogen and phosphate except at river mouths and during periodic upwelling of deeper nutrient-rich water. Despite this, the bight is believed to be relatively productive, and it is suggested that efficient nutrient recycling by prokaryotes may sustain primary productivity efficiently, even in the absence of new nutrient inputs. Here we have measured bacterial numbers, biomass and heterotrophic productivity during summer and winter in conjunction with phytoplankton standing stock and factors that influence it. Bacterial distribution closely matched phytoplankton distribution in surface waters, and was highest close to the coast. Bacterial standing stocks were similar to those of oligotrophic systems elsewhere (0.5–5.0 × 105 cells ml–1; 1 × 10–8 to 1.25 × 10–7 g C ml–1) and increased in association with the development of phytoplankton blooms offshore and with inputs of allochthonous material by rivers at the coast. Heterotrophic productivity in summer was lowest in the far south and north of the bight (0.5 × 10–10 g C ml–1 h–1) but higher close to the shore, over shallow banks, and in association with increased phytoplankton abundance over the midshelf (1.0–3.5 × 10–9 g C ml–1 h–1). There were marked seasonal differences with lower bacterial standing stocks (5 × 104 to 2 × 105 cells ml–1; 4–5 × 10–9 to 1–2 × 10–8 g C ml–1) and very low bacterial productivity (4 × 10–11 to 1 × 10–10 g C ml–1 h–1) in winter, probably resulting from lowered rates of primary productivity and dissolved organic matter release as well as reduced riverine allochthonous inputs during the winter drought.

Aurelia aurita Ephyrae Reshape a Coastal Microbial Community.

Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of microplankton and their impact on prokaryotic assemblages, by favoring blooms of copiotrophic taxa.

Major contribution of prokaryotes to carbon fluxes in the pelagic microbial food webs of the Mediterranean Sea

&lt;p&gt;In this study, we carried out dilution experiments at the surface and in the mesopelagic and bathypelagic layers at 15 sites in the Mediterranean Sea that covered a wide range of trophic conditions. The main aim was to test the hypothesis that prokaryotes, and particularly heterotrophic prokaryotes, are pivotal in sustaining both nanoplankton and microzooplankton energy requirements at all of the considered trophic states. These data highlight that bacterivory is the major pathway of organic carbon transfer in the oligotrophic and meso-eutrophic environments. The microzooplankton mostly feed on prokaryotes, directly or indirectly (through nanoplankton exploitation), rather than on microalgae. Under eutrophic conditions, herbivory is the main trophic pathway; however, the heterotrophic prokaryotes always represent an important source of carbon. The lowest food-web efficiency &lt;em&gt;(i.e&lt;/em&gt;., ratio between productivity of the highest trophic level and productivity of the lower trophic levels) was determined for the eutrophic status due to possible grazer satiation, which translates into an excess of autotrophic biomass available for export or transfer to higher trophic levels. The food-web efficiency is higher under mesoeutrophic and oligotrophic conditions, where the main pathway is bacterivory. In the mesopelagic and bathypelagic layers, only nanoplankton predation on heterotrophic prokaryotes was investigated. The food-web efficiency in these layers was relatively high and nanoplankton appear to efficiently exploit the available biomass of heterotrophic prokaryotes.&lt;/p&gt;

Distribution and seasonal variation of picoplankton in Sanggou Bay, China

Picoplankton abundance and biomass in Sanggou Bay, China, were investigated in 4 successive seasons (April, August and October 2011, January 2012). Different distribution patterns of picoplankton abundance and biomass were observed according to season and culture areas (bivalves or macroalgae). Synechococcus, picoeukaryotes and heterotrophic prokaryotes exhibited higher abundance and biomass in warm seasons (summer and autumn) than in cold seasons (spring and winter). Over all 4 seasons, picoplankton abundance was higher in the bivalve culture area than in the macroalgae culture area. Among picoplankton, picoeukaryotes contributed most to the carbon standing stock in summer and autumn. In spring and winter, the heterotrophic component biomass exceeded that of the autotrophic picoplankton. Picoeukaryotes were an important contributor (21-27%) to total phytoplankton carbon biomass in spring to autumn. In spring, heterotrophic prokaryote biomass accounted for more than 56% of total phytoplankton biomass, and even exceeded phytoplankton biomass at some stations. As revealed by multiple stepwise regression analysis, physicochemical factors and protist grazing were the most important variables that controlled picoplankton distribution and variation. The reduction in grazing pressure, as well as phosphorus release by bivalves, is likely to explain the higher abundance of picoplankton in the bivalve culture area of Sanggou Bay.

Impact of the biocide Irgarol on meiofauna and prokaryotes from the sediments of the Bizerte lagoon-an experimental study.

The biocide Irgarol 1051 has been reported to have negative effects on a large number of living components including non-target organisms, but information on its impact on the marine meiofauna and benthic prokaryotes is completely lacking. Here, we report the results of long-term experimental studies in which we determined the effects of increasing Irgarol concentrations (from 11.5 to 315ngg(-1) sediment dry weight) on meiofauna and benthic prokaryotes. We found that this biocide had a significant impact on meiofauna abundance, even at the lowest concentrations, causing a drastic decline in the abundance of nematodes (the dominant meiofaunal taxon) and an increase of the relative importance of oligochaetes. Even if no direct effects of Irgarol were found on prokaryotic abundance and biomass, the molecular fingerprinting analyses (automated ribosomal intergenic spacer analysis) showed that the prokaryotic diversity was significantly altered by the biocide. The results of the present study indicate that Irgarol 1051 in marine sediments has a significant impact on the smallest eukaryotic and microbial components also at very low concentrations (ca 12ngg(-1)).

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil.

Global warming significantly affects Arctic tundra, including permafrost thaw and soluble C release that may differentially affect tundra microbial growth. Using laboratory experiments, we report some of the first evidence for the effects of soluble glucose-C enrichment on tundra soil prokaryotes (bacteria and archaea) and fungi, with comparisons to microbial eukaryotes. Fungal increase in C-biomass was equivalent to 10% (w/w) of the added glucose-C, and for prokaryote biomass 2% (w/w), the latter comparable to prior published results. The C-gain after 14d was 1.3mg/g soil for fungi, and ~200μg/g for prokaryotes.

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of 7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined in the fractions permanent black fallow > permanent winter wheat. The greatest number of fungi was recorded in the fraction <0.25 mm from the soils of the permanent black fallow and in all the studied aggregate fractions in the variant with permanent wheat. The system of agricultural use affected more significantly the structure of the prokaryote community in the chernozem than the size of aggregate fractions did. The most diverse microbial community was recorded in the soil samples of the fallow; the statistically significant maximums of the Shannon diversity indices and indices of phylogenetic diversity (PD) were recorded in the fractions <0.25 and 2–5 mm from the fallow soil. On the whole, the fine soil fractions (<0.25 mm) were characterized by higher diversity indices in comparison with those of the coarser aggregate fractions.

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust.

Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)-by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.

Seasonal changes on microbial metabolism and biomass in the euphotic layer of Sicilian Channel

As a part of a wider project on fisheries ecology, several biological and environmental parameters were monitored during two oceanographic cruises (BANSIC 2012 and NOVESAR 2013) in the Sicily Channel, which connects the Western and Eastern Mediterranean basins.The prokaryotic abundances and biomass as well as hydrolysis rates on organic matter were investigated in the euphotic layer of a retention area for fish larval stages including anchovy (Engraulis encrasicolus, Linnaeus, 1758) with the aim to investigate the different biogeochemical signatures in two seasonal conditions. The environmental parameters, particulate organic carbon and nitrogen together with heterotrophic production were also measured.Results showed significant increases for most of the studied parameters with increasing temperature during summer. This had effects on the Carbon cycle and recycling of nutrients; in fact total prokaryotic abundance and biomass, as well as carbon hydrolyzed by two enzymes (Leucine aminopeptidase and β-glucosidase), increased significantly during summer. Conversely Alkaline phosphatase activity, Chlorophyll concentration and Oxygen increased during winter. The same environmental parameters affected also the presence of fish eggs. Moreover high percentages of free enzymes (i.e., enzymes not associated with cells) were measured, accounting for percentages variable from 12 to 95 % of the total enzymatic activity, with values generally higher in summer than in winter.In this oligotrophic environment, the prokaryotic biomass was supported by the C hydrolyzed by enzymatic activities. The ratio between the hydrolyzed C and prokaryotic biomass was higher in winter than in summer, indicating that alkaline phosphatase activity contribute to an efficient incorporation of C into biomass in winter.

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor

The deep-ocean interior contains the majority of microbes present on Earth. Most deep-sea microbes are concentrated in surface sediments, with abundances up to 4 orders of magnitude higher, per unit of volume, than in highly productive waters of the photic zone. To date, it has been shown that prokaryotic biomass largely dominates over all other biotic components, but the relative importance of Bacteria, Archaea and viruses to the global benthic biomass has not yet been quantified. Here, we report that the microbial abundance in the top 50 cm of deep-sea sediments of the world oceans is on the order of 1.5 ± 0.4 × 1029. This is largely represented by viruses (9.8 ± 2.5 × 1028), followed by Bacteria (3.5 ± 0.9 × 1028 cells) and Archaea (1.4 ± 0.4 × 1028 cells). The overall biomass in the top 50 cm of the deep-sea sediments is 1.7 ± 0.4 Pg C, largely represented by bacterial biomass (ca. 78%), followed by archaeal biomass (ca. 21%) and viruses (<1%). The bathymetric patterns of abundance and biomass of the 3 microbial components show differences: abundance and biomass of Bacteria decrease with increasing water depth, whereas those of Archaea and viruses remain constant. These results support the hypothesis that the role of Archaea and viruses could be more relevant in the deepest part of the ocean floor.

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.

A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China.

Mounting evidence suggests that Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles, yet the pattern and its ecological drivers of biogeographic distribution of archaeal community in estuarine ecosystem are still not well understood. Here, we investigated planktonic and benthic archaeal communities in the human-impacted Jiulong River estuary (JRE), southern China by using real-time PCR (RT-PCR) and Illumina 16S ribosomal RNA (rRNA) amplicon sequencing. RT-PCR analysis indicated that Archaea accounted for an average of 0.79 and 5.31% of prokaryotic biomass in water and sediment samples of the JRE, respectively. The diversity of planktonic archaeal community decreased gradually from the river runoff to seawater, whereas that of benthic community did not show the similar pattern. The results of taxonomic assignments indicated that Thaumarchaeota (Nitrosopumilus and Cenarchaeum), Methanocorpusculum, and Methanospirillum were significantly more abundant in planktonic than benthic communities, whereas the relative abundances of Miscellaneous Crenarchaeotic Group, Marine Benthic Group-B/-D, anaerobic methane-oxidizingArchaea -1/-2D, and South Africa Gold Mine Euryarchaeotic Group 1 were higher in sediments than in surface waters. Moreover, planktonic archaeal community composition varied significantly at broad and finer-scale taxonomic levels along the salinity gradient. Multivariate statistical analyses revealed that salinity is the main factor structuring the JRE planktonic but not benthic archaeal community at both total community and population level. SourceTrakcer analysis indicated that river might be a major source of archaea in the freshwater zone of the JRE. Overall, this study advances our understanding of the biogeographic patterns and its ecological drivers of estuarine archaeal communities.

Global abundance of planktonic heterotrophic protists in the deep ocean.

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml(-1) in mesopelagic waters down to 11±1 cells ml(-1) in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml(-1). The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

The carbon budget in the northern Adriatic Sea, a winter case study

AbstractThis paper presents a winter carbon budget for the northern Adriatic Sea, obtained through direct measurements during two multidisciplinary cruises and literature data. A box model approach was adopted to integrate estimates of stocks and fluxes of carbon species over the total area. The oligotrophy at the basin scale and the start of primary productivity well before the onset of spring stratification were observed. In winter, the system underwent a complete reset, as the mixing of water masses erased any signal of previous hypoxia or anoxia episodes. The northern Adriatic Sea was phosphorus depleted with respect to C and N availability. This fact confirms the importance of mixing with deep‐sea water for P supply to biological processes on the whole. Despite the abundant prokaryotic biomass, the microbial food web was less efficient in organic C production than phytoplankton. In the upper layer, the carbon produced by primary production exceeded the fraction respired by planktonic community smaller than 200 µm. On the contrary, respiration processes prevailed in the water column below the pycnocline. The carbon budget also proved that the northern Adriatic Sea can be an effective sink for atmospheric CO2 throughout the entire winter season.

Distinctive patterns in prokaryotic community composition in response to viral lysis and flagellate grazing in freshwater microcosms

Summary We conducted microcosm experiments to examine the effect of viruses and heterotrophic nanoflagellates (together referred to as top‐down factors) on prokaryotic standing stock and prokaryotic community composition during the clear water phase (autumn season) in the oligotrophic Lake Pavin in France. In the experimental treatments containing viruses and viruses plus flagellates, the dissolved organic matter released through top‐down activity appeared to stimulate prokaryotic biomass production and viral proliferation. About 68% of the total prokaryotic abundance detected by fluorescence in situ hybridization (FISH) revealed the dominance of typical freshwater groups, which included Beta‐proteobacteria, Actinobacteria and Cytophaga‐Flavobacterium subgroups at the start of the experiments. The manipulation of viruses and flagellates (presence or absence) was successful in inducing significant changes in prokaryotic community composition at a broad phylogenetic level, suggesting that prokaryotic lifestyles are influenced by top‐down factors. The Beta‐proteobacteria subgroup, which outgrew other prokaryotic groups in the absence of viruses and flagellates, was strongly suppressed and vulnerable to mortality in the presence of both the factors. Alpha‐proteobacteria and Actinobacteria subgroups grew significantly in the presence of top‐down factors, suggesting that the dissolved organic matter (regenerated nutrients) released through their activity favoured the development of these groups. The Cytophaga‐Flavobacterium subgroup failed to show any functional response in the presence or absence of top‐down factors. Low prokaryotic diversity in the experimental treatment containing viruses and high diversity in the presence of both top‐down factors were observed. We found synergistic interactions in treatments when both top‐down factors were present, suggesting that the process of nutrient regeneration was crucial in sustaining stable prokaryotic communities.