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Auteur : Grafiati
Publié le 25 mai 2024

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1

Ochi Agostini, Vanessa, Letícia Terres Rodrigues, Alexandre José Macedo et Erik Muxagata. « Comparison of techniques for counting prokaryotes in marine planktonic and biofilm samples ». Scientia Marina 85, no 3 (2 septembre 2021) : 211–20. http://dx.doi.org/10.3989/scimar.05117.019.

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Though a large number of techniques are available for the study of aquatic bacteria, the aim of this study was to establish a technique for analysing free-living and biofilm prokaryotic cells through laboratory assays. In particular, we wished to analyse the efficiency of ultrasound to detach and disrupt biofilm, to obtain an efficient stain treatment for quantifying free-living and biofilm prokaryotes in flow cytometry (FC), and to compare epifluorescence microscopy (EFM), scanning electron microscopy (SEM) and FC for quantifying free-living and biofilm prokaryotes#. Marine-grade plywood substrates were immersed in natural marine water that was conditioned for 12 days. At 6 and 12 days, water aliquots and substrates were removed to estimate free-living and biofilm prokaryote density. Ultrasound efficiently removed marine biofilm from substrates (up to 94%) without cell damage. FC analysis (unstained) reliably quantified marine plankton and young or mature biofilm prokaryotes compared with other staining (acridine orange, 4′,6-diamidino-2-phenylindole, propidium iodide and green fluorescent nucleic acid), EFM or SEM techniques. FC and SEM achieved similar results, while a high variability was observed in the EFM technique. FC was faster and more precise than SEM because the count is not dependent on the observer.
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Wild, Christian, Christian Laforsch et Markus Huettel. « Detection and enumeration of microbial cells within highly porous calcareous reef sands ». Marine and Freshwater Research 57, no 4 (2006) : 415. http://dx.doi.org/10.1071/mf05205.

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In order to assess and to compare the abundances of prokaryotes in coral sands from three different areas in the Indo-Pacific, a technique was developed and evaluated for enumeration of prokaryotes living on and within calcareous grains. Propidium iodide labelling of prokaryotes and consecutive confocal laser scanning microscopy showed microbial colonisation within pores and small fissures of the coral sands. This embedded microbial colonisation required at least four extractions with weak acetic acid to dissolve the grain surface layer in order to detach 97% of the prokaryotic cells. Microbial enumeration based on this technique revealed that the abundance of prokaryotes in the carbonate sands were not significantly different among the three sites, but were about one order of magnitude higher than reported for silicate sands of a similar grain size spectrum. A possible reason for this high abundance of prokaryotes is the complex surface structure of the biogenic calcareous grains, their correspondingly highly porous matrix and the associated ability of prokaryotes to penetrate into carbonate grains. Our results highlight the role of calcareous reef sands as a substratum with a large specific surface area for prokaryotic colonisation and emphasise the contribution of calcium carbonate reef sands for element cycles in subtropical and tropical ecosystems.
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Garuglieri, Elisa, Jenny Marie Booth, Marco Fusi, Xinyuan Yang, Ramona Marasco, Tumeka Mbobo, Emanuela Clementi, Luciano Sacchi et Daniele Daffonchio. « Morphological characteristics and abundance of prokaryotes associated with gills in mangrove brachyuran crabs living along a tidal gradient ». PLOS ONE 17, no 4 (14 avril 2022) : e0266977. http://dx.doi.org/10.1371/journal.pone.0266977.

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Due to the chemico-physical differences between air and water, the transition from aquatic life to the land poses several challenges for animal evolution, necessitating morphological, physiological and behavioural adaptations. Microbial symbiosis is known to have played an important role in eukaryote evolution, favouring host adaptation under changing environmental conditions. We selected mangrove brachyuran crabs as a model group to investigate the prokaryotes associated with the gill of crabs dwelling at different tidal levels (subtidal, intertidal and supratidal). In these animals, the gill undergoes a high selective pressure, finely regulating multiple physiological functions during both animal submersion under and emersion from the periodical tidal events. We hypothesize that similarly to other marine animals, the gills of tidal crabs are consistently colonized by prokaryotes that may quantitatively change along the environmental gradient driven by the tides. Using electron microscopy techniques, we found a thick layer of prokaryotes over the gill surfaces of all of 12 crab species from the mangrove forests of Saudi Arabia, Kenya and South Africa. We consistently observed two distinct morphotypes (rod- and spherical-shaped), positioned horizontally and/or perpendicularly to the gill surface. The presence of replicating cells indicated that the prokaryote layer is actively growing on the gill surface. Quantitative analysis of scanning electron microscopy images and the quantification of the bacterial 16S rRNA gene by qPCR revealed a higher specific abundance of prokaryote cells per gill surface area in the subtidal species than those living in the supratidal zone. Our results revealed a correlation between prokaryote colonization of the gill surfaces and the host lifestyle. This finding indicates a possible role of prokaryote partnership within the crab gills, with potential effects on animal adaptation to different levels of the intertidal gradient present in the mangrove ecosystem.
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Parada, Verónica, Gerhard J. Herndl et Markus G. Weinbauer. « Viral burst size of heterotrophic prokaryotes in aquatic systems ». Journal of the Marine Biological Association of the United Kingdom 86, no 3 (10 avril 2006) : 613–21. http://dx.doi.org/10.1017/s002531540601352x.

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Viral burst size (BS), i.e. the number of viruses released during cell lysis, is a critical parameter for assessing the ecological and biogeochemical role of viruses in aquatic systems. Burst size is typically estimated by enumerating the viral particles in bacteria using transmission electron microscopy. Here, we review the average BS reported for different aquatic systems, present several hypotheses on the control of the BS and evaluate whether there are relationships between BS and bacterial activity parameters across systems. Based on reports from a variety of different aquatic environments, we calculated a mean BS of 24 and 34 for marine and freshwater environments, respectively. Generally, the BS increased with the trophic status of the environment and with the percentage of infected cells in marine populations. When diel dynamics were investigated or averages from large-scale environments were used, BS was positively related to bacterial production but no trend was detectable across systems. The across systems' finding that BS was significantly related to the frequency of infected cells (FIC) could be due to co-infection or superinfection. At any given site, BS seems to be influenced by a number of factors such as the size of the host cell and the viruses, the metabolic activity of the host and phage and host diversity. Thus, based on the available data collected over the past two decades on a variety of aquatic systems, some relations between BS and bacterial variables were detectable.
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Weinbauer, MG, C. Griebler, HM van Aken et GJ Herndl. « Viral infection of prokaryotic plankton during early formation of the North Atlantic Deep Water ». Aquatic Microbial Ecology 84 (4 juin 2020) : 175–89. http://dx.doi.org/10.3354/ame01934.

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Viral abundance was assessed in different water masses of the NW Atlantic, and the development of viral abundance, lytic viral infection and lysogeny was followed for the first ca. 5000 km (corresponding to ca. 50 yr in the oceanic conveyor belt) of the western branch of the North Atlantic Deep Water (NADW). Viral abundance was significantly higher in the 100 m layer than in the NADW (2400-2700 m depth) and the Denmark Strait Overflow Water (2400-3600 m depth). The virus-to-prokaryote ratio (VPR) increased with depth, ranging from 32-43 for different water masses of the bathypelagic ocean, thus corroborating the enigma of high viral abundance in the dark ocean. The O2-minimum layer (250-600 m) also showed high viral abundance and VPRs. Viral abundance, a viral subgroup and VPRs decreased in a non-linear form with distance from the NADW origin. Viral production (range: 0.2-2.4 × 107 viruses l-1) and the fraction of lytically infected cells (range: 1-22%) decreased with increasing distance from the formation site of the NADW. Conservative estimations of virus-mediated mortality of prokaryotes in the NADW averaged 20 ± 12%. The fraction of the prokaryotic community with lysogens (i.e. harboring a functional viral DNA) in the NADW averaged 21 ± 14%. Hence, we conclude that (1) viral abundance and subgroups differ between water masses, (2) virus-mediated mortality of prokaryotes as well as lysogeny are significant in the dark ocean and (3) the lysogenic life strategy became more important than the lytic life style during the early formation of the NADW.
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Ant�n, Josefa, Ram�n Rossell�-Mora, Francisco Rodr�guez-Valera et Rudolf Amann. « Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns ». Applied and Environmental Microbiology 66, no 7 (1 juillet 2000) : 3052–57. http://dx.doi.org/10.1128/aem.66.7.3052-3057.2000.

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ABSTRACT It is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain Archaea, while Bacteriaare not considered to be relevant in this kind of environment. Here, we report the high abundance and growth of a new group of hitherto-uncultured Bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. In the present study, these Bacteria constituted from 5 to 25% of the total prokaryotic community and were affiliated with theCytophaga-Flavobacterium-Bacteroides phylum. Growth was demonstrated in saturated NaCl. A provisional classification of this new bacterial group as “Candidatus Salinibacter gen. nov.” is proposed. The perception that Archaea are the only ecologically relevant prokaryotes in hypersaline aquatic environments should be revised.
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Zubkov, M. V. « Photoheterotrophy in marine prokaryotes ». Journal of Plankton Research 31, no 9 (18 juin 2009) : 933–38. http://dx.doi.org/10.1093/plankt/fbp043.

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Dando, P. R., et A. J. Southward. « Chemoautotrophy in Bivalve Molluscs of the Genus Thyasira ». Journal of the Marine Biological Association of the United Kingdom 66, no 4 (novembre 1986) : 915–29. http://dx.doi.org/10.1017/s0025315400048529.

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The bivalves Thyasiraflexuosa and T. sarsi have enlarged gills which contain numerous prokaryotes. Gills from freshly collected animals contain high concentrations of elemental sulphur. Homogenates of gill tissue show activity for ribulosebisphosphate carboxylase, adenylylsulphate reductase, sulphate adenylyltransferase and sulphate adenylyltransferase (ADP), indicating that the prokaryotes are sulphur-oxidizing autotrophs. Both species can burrow to depths of 8 cm below the sediment surface and use their vermiform feet to construct channels penetrating deeper into the sediment. T.flexuosa and T. sarsi are scarce in sediments with high hydrogen sulphide concentrations and are not found in sediments where the sulphide zone is below their burrowing depth.
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Elloumi, Jannet, Wassim Guermazi, Habib Ayadi, Abderrahmen Bouain et Lotfi Aleya. « Abundance and biomass of prokaryotic and eukaryotic microorganisms coupled with environmental factors in an arid multi-pond solar saltern (Sfax, Tunisia) ». Journal of the Marine Biological Association of the United Kingdom 89, no 2 (29 juillet 2008) : 243–53. http://dx.doi.org/10.1017/s0025315408002269.

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The distribution of abundance and biomass of prokaryotes, flagellates, ciliates and phytoplankton, were studied in five ponds of increasing salinity in the Sfax solar saltern (Tunisia) coupled with environmental factors. The results showed that abundance of eukaryotic microorganisms decreased with increasing salinity of the ponds whereas prokaryotes (heterotrophic bacteria and Archaea) were abundant in the hyper-saline ponds. Phototrophic picoplankton was found in a large range of salinity values (70 and 200‰). Phototrophic non-flagellated nanoplankton which dominated in the first sampled pond was substituted by phototrophic flagellated nanoplankton in the other ponds. Heterotrophic nanoplankton dominated in the crystallizer pond but its quantitative importance declined in the less saline ponds. Diatoms and dinoflagellates were the major contributors to phytoplankton abundance in the first ponds (>90% of total abundance). Ciliated protozoa were found in all the ponds except in the crystallizer in which prokaryotes proliferated. Oligotrichida and Heterotrichida were the most abundant ciliate groups. Overall, species richness decreased with salinity gradient. We propose a simplified diagram of the Sfax saltern's food web showing the dominant role of the microbial loop along the salinity gradient.
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Euler, Sebastian, Luke C. Jeffrey, Damien T. Maher, Derek Mackenzie et Douglas R. Tait. « Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient ». PLOS ONE 15, no 11 (24 novembre 2020) : e0242339. http://dx.doi.org/10.1371/journal.pone.0242339.

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In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%– 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane–a potent greenhouse gas.
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McNair, HM, et S. Menden-Deuer. « Protist grazing contributes to microbial food web at the upper boundary of the twilight zone in the subarctic Pacific ». Marine Ecology Progress Series 636 (20 février 2020) : 235–41. http://dx.doi.org/10.3354/meps13246.

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Grazing by herbivorous protists (microzooplankton) is a major loss pathway of primary production in the surface ocean, yet its impact below the well-lit surface ocean is largely unknown. The upper boundary of the twilight zone is critically important to understanding carbon cycling and is often the depth of highest attenuation of particulate carbon flux. Available measurements of primary production and grazing below the well-lit surface ocean suggest that the upper boundary of the twilight zone may harbor active but poorly constrained food web processes. Previous grazing rates from the base of the euphotic zone were measured in subtropical and tropical environments. Thus, the impact of protist grazing on prey populations remains unknown in colder conditions at higher latitudes. To advance understanding and provide mechanistic insight into processes occurring at the base of the euphotic zone (0.4-0.7% PAR), we measured predation rates on both phytoplankton and heterotrophic prokaryotes in the North Pacific, using a novel method that amplified the grazing signal by concentrating the predator community, enabling detection of grazing rates far below previous limits. Protists consumed 0.6% of the phytoplankton population daily and 12% of daily heterotrophic prokaryote growth. These conservative rate measurements document marginal removal of phytoplankton even in these colder regimes, implying flows of energy from single-cell primary producers and prokaryotes to single-cell protists at rates far below previous detection limits in this twilight region of a low-productivity system.
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Brum, JR, GF Steward, SC Jiang et R. Jellison. « Spatial and temporal variability of prokaryotes, viruses, and viral infections of prokaryotes in an alkaline, hypersaline lake ». Aquatic Microbial Ecology 41 (2005) : 247–60. http://dx.doi.org/10.3354/ame041247.

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Jeong, Gaeul, Hyun-Jung Kim, Kang Eun Kim, Yu Jin Kim, Taek-Kyun Lee, Won Joon Shim et Seung Won Jung. « Selective attachment of prokaryotes and emergence of potentially pathogenic prokaryotes on four plastic surfaces : Adhesion study in a natural marine environment ». Marine Pollution Bulletin 193 (août 2023) : 115149. http://dx.doi.org/10.1016/j.marpolbul.2023.115149.

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González-Pazmiño, José, Krizia Maribell Pretell, Karina Zapata-Vidaurre, Maribel Lucero Mesones, Juan Quimí-Mujica et Benoit Diringer. « Microbial characterization of a natural biofilm associated with Peruvian scallop (Argopecten purpuratus) larvae settlement on artificial collector by confocal imaging, microbiology, and metagenomic analysis ». Latin American Journal of Aquatic Research 49, no 1 (1 mars 2021) : 86–96. http://dx.doi.org/10.3856/vol49-issue1-fulltext-2547.

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Biofilms strongly influence bivalve settlement patterns on artificial substrates; however, their structure and taxonomic composition remains a black box. We characterized a natural biofilm composition that exhibits a large settlement of larvae of the Peruvian scallop Argopecten purpuratus by culture-dependent and culture-independent methods. Thirty-two different strains, representing six genera (10 strains of Bacillus, 9 of Vibrio, 6 Acinetobacter, 4 Staphylococcus, 2 Photobacterium, and 1 Exiguobacterium) were isolated. Those strains represented only 1.09% of the relative abundance compared with the total microbiota obtained by 16S rRNA high-throughput sequencing. The metagenomic analysis identified 441 species. Prokaryotes were predominant (93.4%) over eukaryotes (6.6%), with Pelobacter (13.4%), Lewinella (5.6%), Marinobacter (5.4%), Hoeflea (4.2%), and Microcystis (3.1%) being the most representative genera. Laser scanning confocal microscopy (LSCM) imaging evidenced an irregular and heterogeneous biofilm with an average thickness of 35 μm, where the heterotrophic prokaryotic community (3.4×106 cell cm-2) dominate the photoautotrophic communities (2.3×105 cell cm-2). For the first time, an A. purpuratus settlement-related biofilm was described by the next generation sequencing tool (NGS) and compared with traditional methodologies.
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Falcioni, Tania, Stefano Papa et Josep M. Gasol. « Evaluating the Flow-Cytometric Nucleic Acid Double-Staining Protocol in Realistic Situations of Planktonic Bacterial Death ». Applied and Environmental Microbiology 74, no 6 (25 janvier 2008) : 1767–79. http://dx.doi.org/10.1128/aem.01668-07.

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ABSTRACT Since heterotrophic prokaryotes play an important biogeochemical role in aquatic ecosystems and have a high capacity to survive in extreme environments, easy-to-perform protocols that probe their physiological states and the effects of environmental variables on those states are highly desired. Some methodologies combine a general nucleic acid stain with a membrane integrity probe. We calibrated one of these, the nucleic acid double-staining (NADS) protocol (G. Grégori, S. Citterio, A. Ghiani, M. Labra, S. Sgorbati, S. Brown, and M. Denis, Appl. Environ. Microbiol. 67:4662-4670, 2001), determining the optimal stain concentrations in seawater and the response to conditions that generate prokaryote death (such as heat) and to conditions that are known to produce death in plankton, such as nutrient limitation or flagellate grazing. The protocol was validated by comparison to two methods used to detect viability: active respiration by 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) and incorporation of tritiated leucine. We show that concentrations in the range of 5 to 20 μg ml−1 of propidium iodide, simultaneous to a 10× concentration of Sybr green I, are best for detecting two separated populations of “live” (green cells) and “dead” (red cells) organisms. During exposure to heat and UVC, we observed that the number of live cells declined concurrently with that of actively respiring cells (CTC positive) and with total leucine incorporation. In seawater mesocosms, the NADS protocol allowed detection of bacterioplankton starvation-related death and flagellate predation. The protocol was also tested in deep profiles in the northwest Atlantic, demonstrating its potential for routine characterization of this fraction of the physiological diversity of marine heterotrophic prokaryotic plankton.
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Boon, PI, P. Virtue et PD Nichols. « Microbial consortia in wetland sediments : a biomarker analysis of the effect of hydrological regime, vegetation and season on benthic microbes ». Marine and Freshwater Research 47, no 1 (1996) : 27. http://dx.doi.org/10.1071/mf9960027.

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Microbial consortia in the sediments from a permanent wetland near Albury-Wodonga in north-eastern Victoria, Australia (Ryans 1 Billabong), and an ephemeral wetland near Shepparton in central Victoria (Raftery's Swamp) were quantified by analyses of phospholipid fatty acid (PLFA), polar lipid ether lipid (PLEL), sterol and alcohol profiles. Prokaryotic organisms dominated the benthic assemblages in both wetlands. Total prokaryotic abundance (i.e. eubacteria plus archaea) was estimated to be (7-17) × 109 cells g-1 sediment (dry weight). Methanogenic archaea were estimated to number (1-5.4) × 109 cells g-1 and to account for 11-36% of the total benthic prokaryotes; these values are apparently among the highest recorded for temperate lake or river environments. PLFAs indicative of specific metabolic groups (e.g. sulfate-reducing bacteria (SRB), methanotrophic bacteria, etc.) were also detected. The PLFA profiles indicated that Type I methanotrophs (abundant in C16 PLFAs) were more abundant than the Type II group, which contain C18 PLFAs. Acetate-utilizing SRB were more abundant than were lactate-utilizing SRB, but neither group was dominant. Ergosterol was not detected, which suggested that fungi were not a significant component of the benthic microbial consortia in spite of both wetlands having abundant inputs from aquatic and fringing vascular plants. Other biomarkers, such as sterols, long-chain alcohols, triterpenoids and phytol, demonstrated inputs from these higher plants. PLFA, PLEL and sterol profiles indicated that benthic microbial consortia were affected by hydrological regime, the presence of aquatic vegetation, and season. Information from this preliminary study may assist in the making of informed management decisions on environmental water allocations for natural ecosystems.
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He, C., S. Xu, Z. Kang, S. Song et C. Li. « Prokaryotic community composition and structure during Phaeocystis globosa blooms in the Beibu Gulf, China ». Aquatic Microbial Ecology 86 (6 mai 2021) : 137–51. http://dx.doi.org/10.3354/ame01962.

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Phaeocystis globosa blooms have become one of the major ecological issues in the Beibu Gulf, China, in recent years, resulting in a series of negative impacts on local fisheries and industry. While prokaryotes play key roles in nutrient cycling and energy flow during algal blooms, information regarding the response of the prokaryotic community during Phaeocystis blooms remains scarce. Thus, a comprehensive field study covering the onset and senescent phase of P. globosa blooms was conducted in the area from December 2016 to February 2017. The community composition was revealed with high-throughput sequencing of the 16S rRNA gene. A total of 7426 operational taxonomic units (OTUs) (97% similarity) were identified from 3132328 effective tags, with Proteobacteria, Cyanobacteria, Thaumarchaeota, Verrucomicrobia, Euryarchaeota, Actinobacteria, and Bacteroidetes being the predominant taxa. The composition and structure of particle-attached (PA) and free-living (FL) prokaryotic communities were significantly different: the PA fraction was more diverse and unstable temporally compared to the FL fraction. Variations in the composition and structure of the prokaryotic community were closely associated with major environmental variables, particularly dissolved oxygen (DO), NH4+, PO43-, and dissolved organic carbon (DOC). The presence of P. globosa may result in differences in the prokaryotic community; members of Rhodobacteraceae, Alteromonadales, Porticoccaceae, Vibrio, Flavobacteriales, and Verrucomicrobiae were the key taxa in the prokaryotic communities during the outbreak and senescent phases of P. globosa blooms. This study provides primary information on the response of prokaryotic communities during P. globosa blooms and will facilitate further study on biogeochemical processes of algal-derived organic matter in the tropical gulf.
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Pomar, Luis, Pamela Hallock, Guillem Mateu-Vicens et Juan I. Baceta. « Why Do Bio-Carbonates Exist ? » Journal of Marine Science and Engineering 10, no 11 (3 novembre 2022) : 1648. http://dx.doi.org/10.3390/jmse10111648.

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Calcium carbonate precipitation associated with biotic activity is first recorded in Archaean rocks. The oldest putative fossils related to hydrothermal vents have been dated at ~3.77 Ga (possibly 4.29 Ga). Stromatolites, the oldest dated at 3.70 Ga, have since occurred through Earth history, despite dramatic changes in physical and chemical conditions in aquatic environments. A key question is: what advantages do photosynthesizing aquatic prokaryotes and algae gain by precipitating carbonates? We propose the Phosphate Extraction Mechanism (PEM) to explain the benefits of biomineralization in warm, oligotrophic, alkaline, euphotic environments. Carbonate precipitation enhances access to otherwise limited carbon dioxide and phosphate in such environments. This mechanism also provides an explanation for prolific production of carbonates during times of elevated atmospheric carbon dioxide at intervals in the Phanerozoic.
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Lefèvre, Christopher T., Fernanda Abreu, Ulysses Lins et Dennis A. Bazylinski. « Nonmagnetotactic Multicellular Prokaryotes from Low-Saline, Nonmarine Aquatic Environments and Their Unusual Negative Phototactic Behavior ». Applied and Environmental Microbiology 76, no 10 (2 avril 2010) : 3220–27. http://dx.doi.org/10.1128/aem.00408-10.

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ABSTRACT Magnetotactic multicellular prokaryotes (MMPs) are unique magnetotactic bacteria of the Deltaproteobacteria class and the first found to biomineralize the magnetic mineral greigite (Fe3S4). Thus far they have been reported only from marine habitats. We questioned whether MMPs exist in low-saline, nonmarine environments. MMPs were observed in samples from shallow springs in the Great Boiling Springs geothermal field and Pyramid Lake, both located in northwestern Nevada. The temperature at all sites was ambient, and salinities ranged from 5 to 11 ppt. These MMPs were not magnetotactic and did not contain magnetosomes (called nMMPs here). nMMPs ranged from 7 to 11 μm in diameter, were composed of about 40 to 60 Gram-negative cells, and were motile by numerous flagella that covered each cell on one side, characteristics similar to those of MMPs. 16S rRNA gene sequences of nMMPs show that they form a separate phylogenetic branch within the MMP group in the Deltaproteobacteria class, probably representing a single species. nMMPs exhibited a negative phototactic behavior to white light and to wavelengths of ≤480 nm (blue). We devised a “light racetrack” to exploit this behavior, which was used to photoconcentrate nMMPs for specific purposes (e.g., DNA extraction) even though their numbers were low in the sample. Our results show that the unique morphology of the MMP is not restricted to marine and magnetotactic prokaryotes. Discovery of nonmagnetotactic forms of the MMP might support the hypothesis that acquisition of the magnetosome genes involves horizontal gene transfer. To our knowledge, this is the first report of phototaxis in bacteria of the Deltaproteobacteria class.
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Suzuki, Marcelino T., Lance T. Taylor et Edward F. DeLong. « Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays ». Applied and Environmental Microbiology 66, no 11 (1 novembre 2000) : 4605–14. http://dx.doi.org/10.1128/aem.66.11.4605-4614.2000.

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ABSTRACT Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5′-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from Synechococcus plusProchlorococcus and marine Archaea and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5′-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5′-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry.
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Villegas-Mendoza, Josué, Ramón Cajal-Medrano et Helmut Maske. « The Chemical Transformation of the Cellular Toxin INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) as an Indicator of Prior Respiratory Activity in Aquatic Bacteria ». International Journal of Molecular Sciences 20, no 3 (12 février 2019) : 782. http://dx.doi.org/10.3390/ijms20030782.

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In the ocean, the prokaryote respiration rates dominate the oxidation of organics, but the measurements may be biased due to pre-incubation size filtration and long incubation times. To overcome these difficulties, proxies for microbial respiration rates have been proposed, such as the in vitro and in vivo estimation of electron transport system rates (ETS) based on the reduction of tetrazolium salts. INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) is the most commonly applied tetrazolium salt, although it is toxic on time scales of less than 1 h for prokaryotes. This toxicity invalidates the interpretation of the rate of in vivo INT reduction to formazan as a proxy for oxygen consumption rates. We found that with aquatic bacteria, the amount of reduced INT (F; µmol/L formazan) showed excellent relation with the respiration rates prior to INT addition (R; O2 µmol/L/hr), using samples of natural marine microbial communities and cultures of bacteria (V. harveyi) in batch and continuous cultures. We are here relating a physiological rate with the reductive potential of the poisoned cell with units of concentration. The respiration rate in cultures is well related to the cellular potential of microbial cells to reduce INT, despite the state of intoxication.
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Dando, P. R., A. J. Southward, E. C. Southward et R. L. Barrett. « Possible energy sources for chemoautotrophic prokaryotes symbiotic with invertebrates from a Norwegian fjord ». Ophelia 26, no 1 (31 décembre 1986) : 135–50. http://dx.doi.org/10.1080/00785326.1986.10421984.

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Bayer, Anne, Regina Drexel, Nina Weber et Christian Griebler. « Quantification of aquatic sediment prokaryotes—A multiple-steps optimization testing sands from pristine and contaminated aquifers ». Limnologica 56 (janvier 2016) : 6–13. http://dx.doi.org/10.1016/j.limno.2015.11.003.

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Deng, Wenchao, Shanlin Wang, Xianhui Wan, Zhenzhen Zheng, Nianzhi Jiao, Shuh‐Ji Kao, Jefferson Keith Moore et Yao Zhang. « Potential competition between marine heterotrophic prokaryotes and autotrophic picoplankton for nitrogen substrates ». Limnology and Oceanography 66, no 9 (30 juin 2021) : 3338–55. http://dx.doi.org/10.1002/lno.11883.

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Karuza, Ana, Serena Fonda Umani et Paola Del Negro. « The (un)coupling between viruses and prokaryotes in the Gulf of Trieste ». Estuarine, Coastal and Shelf Science 115 (décembre 2012) : 87–97. http://dx.doi.org/10.1016/j.ecss.2012.03.030.

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Lavergne, Céline, Hélène Agogué, Aude Leynaert, Mélanie Raimonet, Rutger De Wit, Philippe Pineau, Martine Bréret, Nicolas Lachaussée et Christine Dupuy. « Factors influencing prokaryotes in an intertidal mudflat and the resulting depth gradients ». Estuarine, Coastal and Shelf Science 189 (avril 2017) : 74–83. http://dx.doi.org/10.1016/j.ecss.2017.03.008.

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Lemaire, Olivier N., Vincent Méjean et Chantal Iobbi-Nivol. « The Shewanella genus : ubiquitous organisms sustaining and preserving aquatic ecosystems ». FEMS Microbiology Reviews 44, no 2 (10 janvier 2020) : 155–70. http://dx.doi.org/10.1093/femsre/fuz031.

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ABSTRACT The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ­-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.
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Blifernez-Klassen, Olga, Julia Hassa, Diana L. Reinecke, Tobias Busche, Viktor Klassen et Olaf Kruse. « Microbial Diversity and Community Structure of Wastewater-Driven Microalgal Biofilms ». Microorganisms 11, no 12 (16 décembre 2023) : 2994. http://dx.doi.org/10.3390/microorganisms11122994.

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Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and 16S rRNA gene amplicon sequencing, we profiled the microbial communities of four microbial biofilms from ATS systems operated with municipal wastewater (mWW), diluted cattle and pig manure (CattleM and PigM), and biogas plant effluent supernatant (BGE) in comparison to the initial inocula and the respective wastewater substrates. The wastewater-driven biofilms differed significantly in their biodiversity and structure, exhibiting an inocula-independent but substrate-dependent establishment of the microbial communities. The prokaryotic communities were comparable among themselves and with other microbiomes of aquatic environments and were dominated by metabolically flexible prokaryotes such as nitrifiers, polyphosphate-accumulating and algicide-producing microorganisms, and anoxygenic photoautotrophs. Striking differences occurred in eukaryotic communities: While the mWW biofilm was characterized by high biodiversity and many filamentous (benthic) microalgae, the agricultural wastewater-fed biofilms consisted of less diverse communities with few benthic taxa mainly inhabited by unicellular chlorophytes and saprophytes/parasites. This study advances our understanding of the microbiome structure and function within the ATS-based wastewater treatment process.
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Bettarel, Yvan, Anne Desnues et Emma Rochelle-Newall. « Lytic failure in cross-inoculation assays between phages and prokaryotes from three aquatic sites of contrasting salinity ». FEMS Microbiology Letters 311, no 2 (23 août 2010) : 113–18. http://dx.doi.org/10.1111/j.1574-6968.2010.02074.x.

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Giere, Olav, Reinhard Windoffer et Eve C. Southward. « The Bacterial Endosymbiosis of the Gutless Nematode,Astomonema Southwardorum : Ultrastructural Aspects ». Journal of the Marine Biological Association of the United Kingdom 75, no 1 (février 1995) : 153–64. http://dx.doi.org/10.1017/s0025315400015265.

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The recently described gutlessAstomonema southwardorumAusten, Warwick & Ryan 1993, from North Sea methane seeps lives in symbiosis with oval, extracellular bacteria completely filling the lumen of a modified gut. The bacterial strand is tightly lined by a thin layer representing very long intestinal cells of the host. The bacteria are 5.5–6.0 µm in maximum length and 3.5–4.0 µm in width. In the anterior body the alimentary tract is completely reduced. The structure and size of the symbiotic prokaryotes, as well as their extracellular location in the lumen of a non-functional gut, differ substantially from those inA. jenneri, the single species of this genus thoroughly studied electron-microscopically (Ott et al., 1982). These structural discrepancies suggest a careful reassessment of the genusAstomonema.
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Bae, Hee-Sung, Forrest E. Dierberg et Andrew Ogram. « Syntrophs Dominate Sequences Associated with the Mercury Methylation-Related GenehgcAin the Water Conservation Areas of the Florida Everglades ». Applied and Environmental Microbiology 80, no 20 (8 août 2014) : 6517–26. http://dx.doi.org/10.1128/aem.01666-14.

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ABSTRACTThe mechanisms and rates of mercury methylation in the Florida Everglades are of great concern because of potential adverse impacts on human and wildlife health through mercury accumulation in aquatic food webs. We developed a new PCR primer set targetinghgcA, a gene encoding a corrinoid protein essential for Hg methylation across broad phylogenetic boundaries, and used this primer set to study the distribution ofhgcAsequences in soils collected from three sites along a gradient in sulfate and nutrient concentrations in the northern Everglades. The sequences obtained were distributed in diverse phyla, includingProteobacteria,Chloroflexi,Firmicutes, andMethanomicrobia; however,hgcAclone libraries from all sites were dominated by sequences clustering within the orderSyntrophobacteralesof theDeltaproteobacteria(49 to 65% of total sequences).dsrBmRNA sequences, representing active sulfate-reducing prokaryotes at the time of sampling, obtained from these sites were also dominated bySyntrophobacterales(75 to 89%). Laboratory incubations with soils taken from the site low in sulfate concentrations also suggested that Hg methylation activities were primarily mediated by members of the orderSyntrophobacterales, with some contribution by methanogens,Chloroflexi, iron-reducingGeobacter, and non-sulfate-reducingFirmicutesinhabiting the sites. This suggests that prokaryotes distributed within clades defined by syntrophs are the predominant group controlling methylation of Hg in low-sulfate areas of the Everglades. Any strategy for managing mercury methylation in the Everglades should consider that net mercury methylation is not limited to the action of sulfate reduction.
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Maldonado, Manuel. « Intergenerational transmission of symbiotic bacteria in oviparous and viviparous demosponges, with emphasis on intracytoplasmically-compartmented bacterial types ». Journal of the Marine Biological Association of the United Kingdom 87, no 6 (décembre 2007) : 1701–13. http://dx.doi.org/10.1017/s0025315407058080.

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Recent molecular detection of vast microbial communities exclusively associated with sponges has made evident the need for a better understanding of the mechanisms by which these symbiotic microbes are handled and transferred from one sponge generation to another. This transmission electron microscopy (TEM) study investigated the occurrence of symbiotic bacteria in free-swimming larvae of two viviparous species (Haliclona caerulea and Corticium candelabrum) and spawned gametes of two oviparous species (Chondrilla nucula and Petrosia ficiformis). Complex microbial communities were found in these sponges, which in two cases included bacteria characterized by an intra-cytoplasmic membrane (ICM). When ICM-bearing and ICM-lacking bacteria co-existed, they were transferred following identical pathways. Nevertheless, the mechanism for microbial transference varied substantially between species. In C. nucula, a combination of intercellular symbiotic ICM-bearing and ICM-lacking bacteria, along with cyanobacteria and yeasts, were collected from the mesohyl by amoeboid nurse cells, then transported and transferred to the oocytes. In the case of Corticium candelabrum, intercellular bacteria did not enter the gametes, but spread into the division furrows of early embryos and proliferated in the central cavity of the free-swimming larva. Surprisingly, symbiotic bacteria were not vertically transmitted by P. ficiformis gametes or embryos, but apparently acquired from the environment by the juveniles of each new generation. This study failed to unravel the mechanism by which the intercellular endosymbiotic bacterium found in the central mesohyl of the H. caerulea larva got there. Nevertheless, the ultrastructure of this bacterial rod, which was characterized by a star-shaped cross section with nine radial protrusions, an ICM-bound riboplasm, and a putative membrane-bound acidocalcisome, suggested that it may represent a novel organization grade within the prokaryotes. It combines traits occurring in members of Poribacteria, Planctomycetes and Verrucomicrobia, emerging as one of the most complex prokaryotic architectures known to date.
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Niemi, A., G. Meisterhans et C. Michel. « Response of under-ice prokaryotes to experimental sea-ice DOM enrichment ». Aquatic Microbial Ecology 73, no 1 (15 août 2014) : 17–28. http://dx.doi.org/10.3354/ame01706.

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Sime-Ngando, T., et AS Pradeep Ram. « Grazer effects on prokaryotes and viruses in a freshwater microcosm experiment ». Aquatic Microbial Ecology 41 (2005) : 115–24. http://dx.doi.org/10.3354/ame041115.

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Culley, Alexander I., et Nicholas A. Welschmeyer. « The abundance, distribution, and correlation of viruses, phytoplankton, and prokaryotes along a Pacific Ocean transect ». Limnology and Oceanography 47, no 5 (septembre 2002) : 1508–13. http://dx.doi.org/10.4319/lo.2002.47.5.1508.

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Pohlon, Elisabeth, Nora K. Rütz, Klemens Ekschmitt et Jürgen Marxsen. « Recovery dynamics of prokaryotes and extracellular enzymes during sediment rewetting after desiccation ». Hydrobiologia 820, no 1 (25 mai 2018) : 255–66. http://dx.doi.org/10.1007/s10750-018-3662-4.

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Shimada, Atsuhiro, Noriko Yano, Satoru Kanai, Ralph A. Lewin et Tadashi Maruyama. « Molecular phylogenetic relationship between two symbiotic photo-oxygenic prokaryotes, Prochloron sp. and Synechocystis trididemni ». Phycologia 42, no 2 (mars 2003) : 193–97. http://dx.doi.org/10.2216/i0031-8884-42-2-193.1.

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Vázquez-Domínguez, Evaristo, Josep M. Gasol, Susana Agustí, Carlos M. Duarte et Dolors Vaqué. « Growth and grazing losses of prokaryotes in the central Atlantic Ocean ». Journal of Plankton Research 27, no 10 (1 octobre 2005) : 1055–66. http://dx.doi.org/10.1093/plankt/fbi074.

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Vázquez-Domínguez, E., J. M. Gasol, S. Agustí, C. M. Duarte et D. Vaqué. « Growth and grazing losses of prokaryotes in the central Atlantic Ocean ». Journal of Plankton Research 28, no 9 (1 septembre 2006) : 879. http://dx.doi.org/10.1093/plankt/fbl026.

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Panda, Monalisa, Ushashee Mandal, Saurav Barman et Praveen Boddana. « Morphological study of nitrogen fixers ». INTERNATIONAL JOURNAL OF AGRICULTURAL SCIENCES 17, no 2 (15 juin 2021) : 685–90. http://dx.doi.org/10.15740/has/ijas/17.2/685-690.

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Biological diversity, the common term of biodiversity, in the simplest word means the variation and variety of life forms. The biodiversity being the amalgamation of dual word i.e. ‘Bios’ meaning “Life” and ‘Diversitas’ meaning “Variety” or “Difference”. Nitrogen fixation on one hand and Photosynthesis on the other hand is the foundation of all the living system in this planet. Nitrogen fixation can be defined as a chemical process involving the conversion of atmospheric nitrogen into the nitrogenous compound, either biologically or physically. Biological Nitrogen Fixation (BNF) contributes about 90% of the process and rest 10% is carried out by the physical activities which include lightening, thunder, etc. Each and every year, approximately 17.2x10^7 tons of nitrogen are biologically fixed worldwide. The main contributors in BNF are the microorganisms which falls under two categories i.e. may be aerobic or anaerobic. Majority of the microbes do not have the potentiality to reduce nitrogen. The microorganisms having the potentiality of reducing nitrogen play a vital role in the nitrogen fixation along with nitrogen cycle in the nature. The microbes involved in BNF are usually the prokaryotes which make use of a biocatalyst or enzyme nitrogenise to bring about the catalysis of atmospheric nitrogen (N2) to form ammonia (NH3). These prokaryotes consists of aquatic organisms like blue green algae, free living nitrogen fixers like Azotobacter, Clostridium, symbiotic nitrogen fixers like Rhizobium and associative symbiotic includes Azospirillium. The current review paper delineates with reference to the morphological study of nitrogen fixers.
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GÜnter, Jost, Mikhail V. Zubkov, Evgeniy Yakushev, Matthias Labrenz et Klaus JÜrgens. « High abundance and dark CO2 fixation of chemolithoautotrophic prokaryotes in anoxic waters of the Baltic Sea ». Limnology and Oceanography 53, no 1 (janvier 2008) : 14–22. http://dx.doi.org/10.4319/lo.2008.53.1.0014.

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Jiang, Cuihong, Jiapeng Wu, Jiaqi Ye et Yiguo Hong. « High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay ». Marine Pollution Bulletin 200 (mars 2024) : 116046. http://dx.doi.org/10.1016/j.marpolbul.2024.116046.

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Cabrol, Léa, Mélanie Delleuze, Arthur Szylit, Guillaume Schwob, Marianne Quéméneur et Benjamin Misson. « Assessing the diversity of plankton-associated prokaryotes along a size-fraction gradient : A methodological evaluation ». Marine Pollution Bulletin 197 (décembre 2023) : 115688. http://dx.doi.org/10.1016/j.marpolbul.2023.115688.

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Morana, Cedric, Hugo Sarmento, Jean-Pierre Descy, Josep M. Gasol, Alberto V. Borges, Steven Bouillon et François Darchambeau. « Production of dissolved organic matter by phytoplankton and its uptake by heterotrophic prokaryotes in large tropical lakes ». Limnology and Oceanography 59, no 4 (juillet 2014) : 1364–75. http://dx.doi.org/10.4319/lo.2014.59.4.1364.

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Oliveira, Vanessa, Ana L. Santos, Claúdia Aguiar, Luisa Santos, Ângelo C. Salvador, Newton C. M. Gomes, Helena Silva, Sílvia M. Rocha, Adelaide Almeida et Ângela Cunha. « Prokaryotes in salt marsh sediments of Ria de Aveiro : Effects of halophyte vegetation on abundance and diversity ». Estuarine, Coastal and Shelf Science 110 (septembre 2012) : 61–68. http://dx.doi.org/10.1016/j.ecss.2012.03.013.

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Carreira, C., M. Larsen, RN Glud, CPD Brussaard et M. Middelboe. « Heterogeneous distribution of prokaryotes and viruses at the microscale in a tidal sediment ». Aquatic Microbial Ecology 69, no 3 (14 juin 2013) : 183–92. http://dx.doi.org/10.3354/ame01639.

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Dann, LM, RJ Smith, SS Tobe, JS Paterson, RL Oliver et JG Mitchell. « Microscale distributions of freshwater planktonic viruses and prokaryotes are patchy and taxonomically distinct ». Aquatic Microbial Ecology 77, no 2 (12 août 2016) : 65–77. http://dx.doi.org/10.3354/ame01788.

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Park, JS, H. Kim, DH Choi et BC Cho. « Active flagellates grazing on prokaryotes in high salinity waters of a solar saltern ». Aquatic Microbial Ecology 33 (2003) : 173–79. http://dx.doi.org/10.3354/ame033173.

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Niemczyk, Emilia, Jerzy Pogrzeba, Agnieszka Adamczyk-Woźniak et Jacek Lipok. « Boronic Acids of Pharmaceutical Importance Affect the Growth and Photosynthetic Apparatus of Cyanobacteria in a Dose-Dependent Manner ». Toxins 12, no 12 (13 décembre 2020) : 793. http://dx.doi.org/10.3390/toxins12120793.

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The dynamic increase in the commercial application of antimicrobial derivatives of boronic acids, and potential impact of their presence in aquatic systems, supports the necessity to study the toxicity of these substances towards microorganisms of crucial meaning in the environment. One example of the mentioned derivatives is tavaborole (5-fluoro-substituted benzoxaborole), a pharmaceutical agent with antifungal activity. Cyanobacteria were used as model organisms, which are photoautotrophic prokaryotes, as representative aquatic bacteria and photoautotrophs associated with the plant kingdom. To the best of our knowledge, we investigated this issue for the first time. In order to recognize the under-stress response of those microorganisms, the concentration of photopigments—a key factor in the activity of photosynthetic apparatus—was measured spectrophotometrically. We found that the 3-piperazine bis(benzoxaborole) significantly suppressed the growth of halophilic and freshwater cyanobacteria, at a concentration 3.0 mM and 0.3 mM, respectively. Our results also showed that the tested substances at micromolar concentrations stimulated the growth of cyanobacteria, particularly in the freshwater strain Chroococcidiopsis thermalis. The tested substances acted with various strengths, depending on their structure and concentration; nevertheless, they had a greater influence on the synthesis of phycobiliproteins (e.g., lowered their concentration) than on the formation of chlorophyll and carotenoids.
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Steward, Grieg F., Laura B. Fandino, James T. Hollibaugh, Terry E. Whitledge et Farooq Azam. « Microbial biomass and viral infections of heterotrophic prokaryotes in the sub-surface layer of the central Arctic Ocean ». Deep Sea Research Part I : Oceanographic Research Papers 54, no 10 (octobre 2007) : 1744–57. http://dx.doi.org/10.1016/j.dsr.2007.04.019.

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