Prokaryotic Abundance Research Articles

Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits

Abstract Rumen DNA viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen DNA virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high versus low carcass weight cattle and high versus low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.

Consistent prokaryotic successional dynamics across contrasting phytoplankton blooms

AbstractHeterotrophic prokaryotes play a vital role in organic matter cycling in the ocean and have been observed to undergo substrate‐controlled successions during phytoplankton blooms. However, there is limited understanding of the succession patterns during blooms triggered by upwelling events of different characteristics. Here we simulated eight upwelling scenarios of varying intensity and duration (single vs. recurring pulses) by adding nutrient‐rich mesopelagic waters into large‐scale mesocosms containing oligotrophic surface waters from the subtropical North Atlantic. Over a monitoring period of nearly 6 weeks, we observed that phytoplankton blooms displayed diverging outcomes depending on the upwelling mode: treatments with single upwelling pulses presented a unique, short‐lived bloom, whereas recurring upwelling resulted in blooms that were sustained over time. Prokaryotic abundances were positively related to upwelling intensity and presented three similar abundance cycles in all treatments, whereas heterotrophic activity differed between the two upwelling modes. The successional dynamics of free‐living and particle‐associated communities were consistent regardless of upwelling intensity and mode, with four or five prokaryotic assemblages sequentially proliferating during the experiment. Yet, some differences were observed in the taxa that formed the assemblages in both upwelling modes. Together, our results suggest that, despite differences in activity, prokaryotes seemed to be more influenced by processes taking place within the community than by phytoplankton bloom patterns, with similar succession dynamics even under widely distinct blooms. These findings can help advance our understanding on prokaryotic ecology and its relation to organic matter cycling across different upwelling scenarios.

Properties of Biofilm Prokaryotic and Eukaryotic Communities in a Representative Hypereutrophic Urban River

ABSTRACT Biofilms play an important role in nutrient and food web dynamics of shallow aquatic ecosystems. Multiple prokaryotic and eukaryotic microorganisms within biofilms interact with each other to shape the community structure and their functional attributes. However, there is no clear understanding of varied patterns of biofilm prokaryotic versus eukaryotic microbial abundances, diversities and communities, which limit our understanding of how biofilm communities and functions in hypereutrophic urban river ecosystems are changing. To elucidate the properties of biofilm communities and controls on biofilm communities in a hypereutrophic urban river, we conducted a one‐year study to investigate the seasonal and water‐depth variations on the abundance/biomass, diversity and structure of biofilm prokaryotic and eukaryotic communities. The structure and dynamics of biofilm prokaryotic and eukaryotic communities were determined by high‐throughput sequencing based on the 16S and 18S rRNA gene. Sequencing revealed that Proteobacteria, Bacteroidota and Cyanobacteria were the three dominant phyla in biofilm prokaryotic communities, and Rotifera, Chlorophyta, Annelida and Bacillariophyta were the four dominant phyla in biofilm eukaryotic communities. Biofilm bacterial abundance depended mainly on the water temperature, whereas biofilm algal biomass correlated with rotifer grazing and light levels. Prokaryotic communities had higher species richness and diversity than eukaryotic communities. Species richness and diversity displayed significant seasonal variations with minima for prokaryotic communities in winter and eukaryotic communities in summer, which were linked to water temperature and rotifer grazing, respectively. Variations in biofilm prokaryotic and eukaryotic community composition were mainly related to ammonia concentration and water temperature, respectively. The co‐occurrence network analysis suggested that rotifer grazing could considerably decrease the complexity of the biofilm network in summer, and the algal groups, especially for Chlorophyta and Bacillariophyta, were the key to the formation of stable biofilm networks. There were significant differences in seasonal and water‐depth heterogeneity of biofilm prokaryotic and eukaryotic community composition. Our findings indicate that variations in water temperature, light level, rotifer grazing and nutrients (especially ammonia) appreciably contribute to changes in the abundance, diversity and composition of biofilm prokaryotic versus eukaryotic communities in the hypereutrophic urban river. These findings increase our understanding of biofilm community characteristics in hypereutrophic urban rivers and provide insights for water pollution remediation strategies.

Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences

Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.

Differential impacts of temperature increase on prokaryotes across temperature regimes in subtropical coastal waters: insights from field experiments

AbstractProkaryotic communities play a dominant role in driving biogeochemical cycling in marine ecosystems. How short‐term temperature increase impacts prokaryotes in subtropical coastal waters is still largely unknown. Here, 14 field experiments were conducted to investigate the response of prokaryotes in subtropical coastal waters to temperature increases of 3°C and 6°C, encompassing a range of ambient temperatures from 17°C to 31°C. We found that responses of prokaryotic growth, grazing pressure, community, and transcriptomes to increased temperatures were largely affected by ambient temperatures. Increased temperatures enhanced the growth rate and grazing pressure of heterotrophic prokaryotes when ambient temperatures were below 26–28°C. The increased temperatures had greater negative effects on the grazing rate compared to the growth rate; therefore, the abundance of heterotrophic prokaryotes generally increased after temperature increase across all temperature regimes. Metatranscriptomics analysis showed that at an ambient temperature of 30°C, genes involved in the adenosine triphosphate synthase were significantly downregulated by the increased temperature. This could be a major factor contributing to the decreased prokaryotic growth rate. In comparison, autotrophic prokaryotes (Synechococcus) exhibited better performance in response to elevated temperatures, thriving up to 35°C, beyond which their growth rate experienced a dramatic decline. When exposing to extremely high temperatures, genes involved in photosynthesis significantly decreased. These findings highlight the differential ecological impacts of temperature increase on prokaryotic communities, varying across different ambient temperatures and taxa in subtropical coastal waters.

Microbial distribution in Mudbank regions off Alappuzha, South-West coast of India.

The coastal waters of Kerala, in the South Eastern Arabian Sea (SEAS), are unique during the Southwest monsoon season due to the concurrent occurrence of two physical processes, the upwelling and Mudbanks. However, little is known about the viral ecology and activity in a system where upwelling and Mudbanks coexist, though it is generally recognized that microbial assemblages play a vital role in the food web dynamics of marine systems, particularly in upwelling. Water samples were taken from monsoon and pre-monsoon period from three locations, (M1, M2, and M3) off Alappuzha, on the southwest coast of India to examine the viral activity and distribution. The dissolved oxygen levels showed the incursion of hypoxic waters in all the stations during the peak upwelling period. Upwelling signals were prominent in all the stations, but Mudbank and upwelling co-occurred at M2 alone during monsoon. The abundance of viruses ranged from 0.86 to 15.68 × 106 Viral-like Particles (VLPs mL-1) and prokaryotic abundance ranged from 2.73-16.26 × 105 cells mL-1. Viral and prokaryotic abundance was significantly higher in the monsoon compared to pre and late-monsoon. Based on Transmission electron microscopy (TEM) results, the non-tailed viruses constituted the major (43%) proportion of the total viruses in this study region. However, the viral production rates and viral-mediated bacterial mortality were high in the pre-monsoon compared to the monsoon and late-monsoon periods. There was no obvious effect of Mudbanks on viral dynamics and the observed variations in virological and hydrological features were governed mainly by coastal upwelling.

Компоненты микробной пищевой сети в пелагиали фьордов о. Западный Шпицберген в современных климатических условиях

The spatial variability of quantitative indicators of prokaryotes and virus-like particles in the waters of three Arctic fjords was studied in connection with the structure of their dominant water masses in the summer. A comparison of the abundance and biomass of prokaryotes showed that their average value in mesotrophic surface waters (0.60 million cells/ml and 28.64 mg/m3, respectively) exceeded the values in deeper oligotrophic waters – intermediate (0.33 million cells/ml and 16.82 mg/m3) and winter (0.32 million cells/ml and 19.72 mg/m3). The abundance of virus-like particles in different trophic conditions positively correlated with the parameters of prokaryotic communities and in the isolated water masses averaged 1.01 million, 0.09 million and 1.31 million per ml respectively. The factors determining the distribution of the most abundant representatives of the microbial food web and the nature of their interaction are considered.

Impact of Viruses on Prokaryotic Communities and Greenhouse Gas Emissions in Agricultural Soils.

Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe-virus interactions and advance current knowledge on soil virusecology.

Bacterioplankton of the Western Part of the Kara Sea

Data on the structural and production characteristics of bacterioplankton in the western part of the Kara Sea at the beginning and in the middle of summer are presented. In the region of the St. Anna Trough slope, the average abundance of prokaryotes for the water column was (594–708) × 103 cells/ml (26.4–36.5 mgC/m3) in June and (247–517) × 103 cells/ml (12–28 mgC/m3) at the beginning of August. On the transect along Novaya Zemlya, the average abundance of bacterioplankton in the water column was (186–554) × 103 cells/mL (8.5–30 mgC/m3) within a week after the seasonal ice and (169–443) × 103 cells/mL (8–21 mgC/m3) in the midsummer. Bacterial specific growth rate did not exceed 1.28 day–1; its high values were observed in the upper warm water layer, above the halocline, and also at the near-bottom depths. At the beginning of summer, the production of bacterioplankton tended to decrease in the northeast direction. The distribution of prokaryotes abundance was determined by temperature and water saturation with oxygen, possibly as an indirect indicator of past phytoplankton “bloom”.

Regenerative soil management practices no‐till and sheep grazing induce significant but contrasting short‐term changes in the vineyard soil microbiome

Societal Impact StatementWinegrape production is an essential cultural heritage and economic engine of many regions of the world. Regenerative management, which is gaining traction with industry and consumers alike, relies on soil biodiversity for agroecosystem function, reducing external inputs and increasing ecosystem resilience to climate change. We evaluated the effects of no‐till and sheep integration on vineyard soil biodiversity and soil ecosystem function. No‐till had stronger effects on microbial diversity, while sheep grazing stimulated microbial functioning. By providing a better understanding of the practices, we provide fundamental information for growers that want to embrace regenerative principles, ultimately contributing to the sustainability and resilience of the winegrape industry.Summary Regenerative management aims to optimize soil microbial function and diversity for enhanced agroecosystem functionality. Understanding the effects of management practices on soil microorganisms is crucial in the context of growing societal interest in this type of management. This study evaluated the short‐term effects of two soil conservation practices: sheep grazing and no‐till, on abundance, diversity, activity, and network complexity of prokaryotes and fungi in a vineyard soil. Four treatments were applied for 3 years: (1) grazed and tilled, (2) grazed and non‐tilled, (3) non‐grazed and tilled, and (4) non‐grazed and non‐tilled. We hypothesized that stacking of conservation practices (grazing and no‐till) would increase microbial diversity, function, and network complexity. Grazing had strong effects on microbial function, increasing the α‐glucosidase, β‐glucosidase, cellulase, phosphatase, and β‐xylosidase enzymatic activity by 82%, 48%, 61%, 39%, and 55%, respectively, compared to non‐grazed soils, while not causing significant changes in soil microbial diversity. Tillage had strong effects on soil prokaryotic and fungal diversity. For prokaryotes, significant interactions in alpha diversity were found between tillage and grazing, and between tillage and sampling location (tractor row and under vine). Fungal Shannon diversity index was higher in the subsoil (15–30 cm) while a significant interaction between depth, location, tillage, and grazing was found for the Chao‐1 index. Microbial network properties were only significantly affected by sampling depth. This study shows that the lack of disturbance in non‐tilled and non‐grazed soils resulted in a more diverse soil community, while grazing stimulated microbial function, thus showing a decoupling between diversity and function in vineyard soil ecosystems.

Biotechnological Potential of the Soil Microbiome

Molecular biological techniques and bioinformatic analysis were used to investigate the phylogenetic and functional diversity of the prokaryotic complex of soil microcosms. The dominant organisms of the hydrolytic community were different in the samples from different climatic zones. In the soils subject to anthropogenic or abiogenic load, apart from decreased diversity and abundance of prokaryotes, the number of the genes marking the ability to degrade xenobiotics, as well as those encoding nitrogen conversion and metabolism of vitamins and cofactors, was found to increase. Under heavy oil contamination, the bacterial community was capable of nitrification; its role increased in the lower horizons of the soil profile. The patterns revealed in the work indicate high metabolic potential of the prokaryotic component of the studied soils.

Significant correlations between heavy metals and prokaryotes in the Okinawa Trough hydrothermal sediments

Prokaryotes play crucial roles in hydrothermal vent ecosystems, yet their interactions with heavy metals are not well understood. This study explored the diversity of prokaryotic communities and their correlations with heavy metals and nutrient elements in hydrothermal sediments from Okinawa Trough. A total of 117 bacterial genera in 26 bacterial phyla and 10 archaeal classes in 3 archaeal phyla were identified, including dominant prokaryotic phyla Planctomycetes, Acidobacteria, Verrucomicrobia, and Euryarchaeota. Furthermore, Fe (39.61 mg/g), Mn (2.84 mg/g) and Ba (0.36 mg/g) were found to be the most abundant heavy metals in the Okinawa hydrothermal sediments. Notably, the concentrations of Zn, Ba, Mn, total organic carbon, and total nitrogen significantly increased, whereas the total sulfur concentration distinctively decreased at sampling sites farther from hydrothermal vents. These changes corresponded with reductions in prokaryotic abundance and diversity. Most heavy metals, including Mn, Fe, Co, Cu and As, presented significant positive correlations with a number of prokaryotic genera in the nearby sediment samples. In contrast, both positive and negative correlations with prokaryotes were observed in remote sediment. The keystone taxa include Magnetospirillum, GOUTA19, Lysobacter, Kaistobacter, Treponema, and Clostridium were detected through prokaryote interspecies interactions. The functional predictions revealed significant genes involved in carbon fixation, nitrogen/sulfur cycling, heat shock protein, and metal resistance pathways. Structural equation modeling confirmed that metal and nutrient elements directly influence the composition of prokaryotic communities, which in turn affects the relative abundance of functional genes.

A semi-automated image processing method for analysing the taxonomic composition of algal biofilms

Benthic phototrophic communities play a crucial role in the functioning of shallow lake ecosystems. The complexity of benthic algal communities poses challenges for exploring their fine structures using traditional methods such as light microscopy. However, confocal laser scanning microscopy (CLSM) offers the potential for microscale-level structural investigation of phototrophic biofilms, thereby contributing to a deeper understanding of the structural and compositional changes within these communities. The primary objective of this study was to develop a relatively rapid, semi-automated, and freely available image processing method to facilitate the tracking of spatio-temporal alterations in intact biofilms. To evaluate our image processing method, we conducted an eight-week long outdoor mesocosm experiment, manipulating temperatures based on two global warming scenarios (assuming intermediate- and high degree of greenhouse gas emission), with increases of 3°C and 5°C, respectively, compared to the reference/unheated mesocosms. Eight limestone cubes were placed on the bottom of each mesocosm to provide 'natural' surfaces for phytobenthos colonization, which was subsequently analysed by confocal microscopy. We hypothesized that increasing water temperature might have a significant impact on the taxonomic composition of algal biofilms, particularly on the abundance of phototrophic prokaryotes and eukaryotes. The designed 'FIJI macro' efficiently analysed the recorded images, including single images, series of Z-stack images, and projection images. Our image processing method effectively discriminated photosynthetic prokaryotes and eukaryotes based on their pigment composition and proved suitable for the high-throughput analysis of structural and compositional changes in algal biofilms. Moreover, this study confirmed that climate-induced warming can lead to an increasing dominance of cyanobacteria in benthic phototrophic communities at the expense of eukaryotic algae.

Cobalt effects on prokaryotic communities of river biofilms: Impact on their colonization kinetics, structure and functions

Although cobalt (Co) plays a significant role in the transition to low-carbon technologies, its environmental impact remains largely unknown. This study examines Co impacts on the prokaryotic communities within river biofilms to evaluate their potential use as bioindicators of Co contamination. To this end, biofilms were cultivated in artificial streams enriched with different environmental Co concentrations (0.1, 0.5, and 1 μM Co) over 28 days and examined for prokaryotic abundance and diversity via quantitative PCR and DNA-metabarcoding every 7 days. The prokaryotic community's resilience was further investigated after an additional 35 days without Co contamination. The prokaryotic communities were affected by 0.5 and 1 μM Co from the onset of biofilm colonization. The biofilm biomass was comparable between treatments, but the community composition differed. Control biofilms were dominated by Cyanobacteria and Planctomycetes, whereas Bacteroidetes dominated the Co-contaminated biofilms. Potential functional redundancy was observed through the implementation of carbon fixation alternatives by non-photosynthetic prokaryotes in biofilms exposed to high Co concentrations. No structural resilience was observed in the biofilms after 35 days without Co contamination. Measuring the prokaryotic community structural response using molecular approaches appears to be a promising method for assessing shifts in water quality owing to Co contamination.

The global distribution and climate resilience of marine heterotrophic prokaryotes

Heterotrophic Bacteria and Archaea (prokaryotes) are a major component of marine food webs and global biogeochemical cycles. Yet, there is limited understanding about how prokaryotes vary across global environmental gradients, and how their global abundance and metabolic activity (production and respiration) may be affected by climate change. Using global datasets of prokaryotic abundance, cell carbon and metabolic activity we reveal that mean prokaryotic biomass varies by just under 3-fold across the global surface ocean, while total prokaryotic metabolic activity increases by more than one order of magnitude from polar to tropical coastal and upwelling regions. Under climate change, global prokaryotic biomass in surface waters is projected to decline ~1.5% per °C of warming, while prokaryotic respiration will increase ~3.5% ( ~ 0.85 Pg C yr−1). The rate of prokaryotic biomass decline is one-third that of zooplankton and fish, while the rate of increase in prokaryotic respiration is double. This suggests that future, warmer oceans could be increasingly dominated by prokaryotes, diverting a growing proportion of primary production into microbial food webs and away from higher trophic levels as well as reducing the capacity of the deep ocean to sequester carbon, all else being equal.

First observations on airborne prokaryotes in a subArctic Atlantic marine area

Among extreme environments, bioaerosol includes a wide range of primary atmospheric organic particles associated with and emitted by living and dead organisms. Bioaerosol samples were collected along two transects at a subArctic Atlantic spatial scale, including the eastern Fram Strait and the Greenland, Norwegian, and North Seas. This study was aimed at first estimating microscopically the prokaryotic abundance, biomass and phenotypic traits, along with the number of potential viable and respiring cells. Moreover, physiological profiles at community level were assessed. Prokaryotic abundance ranged from 104 to 107 cells m−3, with the predominance of small sized cells (0.1 μm3). Prokaryotic biomass reached higher values (mean value 233 μg C m−3) in relation to the occurrence of large sized rods. Overall, the percentage of the viable cells was lower than the dead ones, while respiring cells were in lower abundance than total cells. The physiological profiles revealed various potential metabolic pathways among the samples, highlighting the utilization of phosphate-carbon, carboxylic and amino acids. These first results on the metabolism and physiology of microbes, which survived transport in the atmosphere of the Northern Hemisphere, suggest that bioaerosol constitutes an extremely dynamic environment of remarkable ecological interest, also considering future global warming scenarios.

Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones

Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.

Patterns of prokaryotic activity along the marine planktonic matter continuum

Prokaryotic abundance and activity are commonly assessed by dividing them into two size-fractions: free-living and attached to particles. Nevertheless, organic matter, essential for the growth of heterotrophic prokaryotes, is present in the environment in a continuum of sizes, from purely dissolved to large particles. Therefore, defining the activity of the prokaryotic community would be more accurate by considering all the distinct size fractions. To achieve this, we measured prokaryotic abundance (PA), heterotrophic prokaryotic activity (as leucine incorporation) and extracellular enzyme activities at a coastal site in the NW Mediterranean Sea. We conducted measurements in both bulk seawater and size fractionated samples sequentially passing through 5 different filter types: 0.2–0.8–3–5–10 μm pore size. Our results indicate that the fraction <0.8 μm contained the highest percentage of cells (91.6 ± 1.1 %) and leucine incorporation rates (72.2 ± 3.5 %). Most of the extracellular enzyme activity appeared in the dissolved fraction (<0.2 μm; 19.8–79.4 %), yet the specific activity of the enzymes (per cell activity) was 100–1000 times higher in the particulate (>0.8 μm) than in the free-living (0.2–0.8 μm) fraction. The size fraction with highest specific activities for leucine incorporation and most of the enzyme activities (β-glucosidase, esterase, Leu-aminopeptidase and alkaline phosphatase) was the 5–10 μm fraction. In contrast, the higher specific chitobiase activity in the >10 μm fraction, suggests that the prokaryotic community colonizing large particles might be more specialized in the hydrolysis of organic matter of zooplanktonic origin than the community colonizing smaller particles.

Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation.

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

A hydrothermal plume on the Southwest Indian Ridge revealed by a multi-proxy approach: Impact on iron and manganese distributions (GEOTRACES GS02)

Iron (Fe) and manganese (Mn) are crucial micronutrients that limit oceanic primary productivity in the Southern Ocean. It has been recently suggested that hydrothermal activity may be an important source of oceanic dissolved iron, yet, this contribution is still not fully understood and only one active hydrothermal site has been reported on the Southwest Indian Ridge (SWIR), south of 40°S.Using a multi-proxy approach, this study demonstrates the occurrence of hydrothermal venting on the SWIR in the near vicinity of the location 44°51.690 S, 36°10.460 E, which is likely to be a low or moderately high temperature fluid. Indeed, we report high values of dissolved methane to manganese ratios (up to 11.1 ± 1.2 mol mol−1), low particulate iron (pFe) and manganese (pMn) concentrations (with maximum values of 0.7 nmol L−1 and 0.06 nmol L−1, respectively) associated with the presence of few oxyhydroxides, as well as high 223Radium (Ra) and 224Ra activities near the seafloor. The Fe and Mn data revealed a significant enrichment at depths influenced by hydrothermal circulation on the seafloor, within the Upper Circumpolar Deep Water. Dissolved Fe (dFe) and dissolved Mn (dMn) concentrations were enriched by 3- and 7-fold, respectively, and pFe and pMn by 2- and 1.5-fold, respectively, compared to a reference station located outside the SWIR. They were however lower than concentrations reported so far near high temperature vents, suggesting a weaker influence of this hydrothermal system on deep Fe and Mn reservoirs. We show that a large fraction of the dFe could be stabilized by organic complexation with humic substances (eHS, estimated 27–60% of dFe). High prokaryotic abundance related to the proximity of the hydrothermal vent suggests that other Fe-complexing ligands of biological origin might also stabilize Fe in its dissolved form. Collectively, these measurements integrated within the concept of a “multi-proxy approach”, helped painting a more detailed picture of the complex interactions and processes in this region of the SWIR. Although the system is a source of both dFe and dMn to the deep ocean, the low current velocities and the bathymetry likely limit the fertilization of surface water by dFe and dMn along this section of the SWIR.