Journal articles on the topic 'Marine prokaryotes'
To see the other types of publications on this topic, follow the link: Marine prokaryotes.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Marine prokaryotes.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Ochi Agostini, Vanessa, Letícia Terres Rodrigues, Alexandre José Macedo, and Erik Muxagata. "Comparison of techniques for counting prokaryotes in marine planktonic and biofilm samples." Scientia Marina 85, no. 3 (September 2, 2021): 211–20. http://dx.doi.org/10.3989/scimar.05117.019.
Full textAbstract:
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.
2
Zubkov, M. V. "Photoheterotrophy in marine prokaryotes." Journal of Plankton Research 31, no. 9 (June 18, 2009): 933–38. http://dx.doi.org/10.1093/plankt/fbp043.
Full text
3
WEINER, R. "Biopolymers from marine prokaryotes." Trends in Biotechnology 15, no. 10 (October 1997): 390–94. http://dx.doi.org/10.1016/s0167-7799(97)01099-8.
Full text
4
Joglar, Vanessa, Antero Prieto, Esther Barber-Lluch, Marta Hernández-Ruiz, Emilio Fernández, and Eva Teira. "Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system." Biogeosciences 17, no. 10 (May 26, 2020): 2807–23. http://dx.doi.org/10.5194/bg-17-2807-2020.
Full textAbstract:
Abstract. We experimentally evaluated the temporal (interday and interseason) and spatial variability in microbial plankton responses to vitamin B12 and/or B1 supply (solely or in combination with inorganic nutrients) in coastal and oceanic waters of the northeast Atlantic Ocean. Phytoplankton and, to a lesser extent, prokaryotes were strongly limited by inorganic nutrients. Interday variability in microbial plankton responses to B vitamins was limited compared to interseason variability, suggesting that B-vitamin availability might be partially controlled by factors operating at seasonal scale. Chlorophyll a (Chl a) concentration and prokaryote biomass (PB) significantly increased after B-vitamin amendments in 13 % and 21 %, respectively, of the 216 cases (36 experiments × 6 treatments). Most of these positive responses were produced by treatments containing either B12 solely or B12 combined with B1 in oceanic waters, which was consistent with the significantly lower average vitamin-B12 ambient concentrations compared to that in the coastal station. Negative responses, implying a decrease in Chl a or PB, represented 21 % for phytoplankton and 26 % for prokaryotes. Growth stimulation by B1 addition was more frequent on prokaryotes than in phytoplankton, suggesting that B1 auxotrophy in the sampling area could be more widespread in prokaryotes than in phytoplankton. Negative responses to B vitamins were generalized in coastal surface waters in summer and were associated with a high contribution of Flavobacteriales to the prokaryote community. This observation suggests that the external supply of B12 and/or B1 may promote negative interactions between microbial components when B-vitamin auxotrophs are abundant. The microbial response patterns to B12 and/or B1 amendments were significantly correlated with changes in the prokaryotic community composition, highlighting the pivotal role of prokaryotes in B-vitamin cycling in marine ecosystems.
5
Bianchelli, Silvia, Daniele Nizzoli, Marco Bartoli, Pierluigi Viaroli, Eugenio Rastelli, and Antonio Pusceddu. "Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient." Diversity 12, no. 5 (May 12, 2020): 189. http://dx.doi.org/10.3390/d12050189.
Full textAbstract:
In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities are influenced by multiple environmental variables, which can vary across different habitats. However, analyses of these relationships have mostly been conducted by considering the different habitats separately, even though freshwater, transitional, and marine ecosystems, physically linked to each other, are not worlds apart. Here, we investigated the quantity and nutritional quality of sedimentary OM, along with the prokaryotic and meiofauna abundance, biomass, and biodiversity, in two sampling periods, corresponding to high vs. low freshwater inputs to the sea, along a river-to-sea transect. The highest values of sedimentary organic loads and their nutritional quality, prokaryotic and meiofaunal abundance, and biomass were consistently observed in lagoon systems. Differences in the prokaryotic Operational Taxonomic Units (OTUs) and meiofaunal taxonomic composition, rather than changes in the richness of taxa, were observed among the three habitats and, in each habitat, between sampling periods. Such differences were driven by either physical or trophic variables, though with differences between seasons. Overall, our results indicate that the apparent positive relationship between sedimentary OM, prokaryote and meiofaunal abundance, and biomass across the river-lagoon-sea transect under scrutiny is more the result of a pattern of specifically adapted prokaryotic and meiofaunal communities to different habitats, rather than an actually positive ‘response’ to OM enrichment. We conclude that the synoptic analysis of prokaryotes and meiofauna can provide useful information on the relative effect of organic enrichment and environmental settings across gradients of environmental continuums, including rivers, lagoons, and marine coastal ecosystems.
6
Deppeler, Stacy, Kai G. Schulz, Alyce Hancock, Penelope Pascoe, John McKinlay, and Andrew Davidson. "Ocean acidification reduces growth and grazing impact of Antarctic heterotrophic nanoflagellates." Biogeosciences 17, no. 16 (August 18, 2020): 4153–71. http://dx.doi.org/10.5194/bg-17-4153-2020.
Full textAbstract:
Abstract. High-latitude oceans have been identified as particularly vulnerable to ocean acidification if anthropogenic CO2 emissions continue. Marine microbes are an essential part of the marine food web and are a critical link in biogeochemical processes in the ocean, such as the cycling of nutrients and carbon. Despite this, the response of Antarctic marine microbial communities to ocean acidification is poorly understood. We investigated the effect of increasing fCO2 on the growth of heterotrophic nanoflagellates (HNFs), nano- and picophytoplankton, and prokaryotes (heterotrophic Bacteria and Archaea) in a natural coastal Antarctic marine microbial community from Prydz Bay, East Antarctica. At CO2 levels ≥634 µatm, HNF abundance was reduced, coinciding with increased abundance of picophytoplankton and prokaryotes. This increase in picophytoplankton and prokaryote abundance was likely due to a reduction in top-down control of grazing HNFs. Nanophytoplankton abundance was elevated in the 634 µatm treatment, suggesting that moderate increases in CO2 may stimulate growth. The taxonomic and morphological differences in CO2 tolerance we observed are likely to favour dominance of microbial communities by prokaryotes, nanophytoplankton, and picophytoplankton. Such changes in predator–prey interactions with ocean acidification could have a significant effect on the food web and biogeochemistry in the Southern Ocean, intensifying organic-matter recycling in surface waters; reducing vertical carbon flux; and reducing the quality, quantity, and availability of food for higher trophic levels.
7
Lannes, Romain, Karen Olsson-Francis, Philippe Lopez, and Eric Bapteste. "Carbon Fixation by Marine Ultrasmall Prokaryotes." Genome Biology and Evolution 11, no. 4 (March 23, 2019): 1166–77. http://dx.doi.org/10.1093/gbe/evz050.
Full text
8
Thingstad, Tron Frede, Lise Øvreås, and Olav Vadstein. "Mechanisms Generating Dichotomies in the Life Strategies of Heterotrophic Marine Prokaryotes." Diversity 14, no. 3 (March 16, 2022): 217. http://dx.doi.org/10.3390/d14030217.
Full textAbstract:
Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes consists of organisms with two main types of life strategies. We illustrate this dichotomy by SAR11 and Vibrio spp. as typical representatives of the two strategies. A theory for life strategy dichotomy exists in classical r/K-selection. We here discuss an additional dichotomy introduced by what we term S/L-selection (for Small and Large, respectively). While r/K-selection focuses on the role of environmental disturbances, steady-state models suggest that high abundance at species level should be closely related to a low trade-off between competition and defense. We summarize literature indicating that the high availability of organic C is an essential environmental factor favoring Vibrio spp. and suggest that the essence of the generalized L-strategy is to reduce the competition-predator defense trade-off by using non-limiting organic C to increase size. The “streamlining” theory that has been suggested for the S-strategist SAR11 proposes the opposite: that low trade-off is achieved by a reduction in size. We show how this apparent contradiction disappears when the basic assumptions of diffusion-limited uptake are considered. We propose a classification scheme that combines S/L and r/K-selection using the two dimensions of organic C availability and environmental disturbance. As organic C in terrestrial runoff and size of the oligotrophic oceanic gyres are both changing, habitat size for both S- and L-strategists are affected by global change. A theory capturing the main aspects of prokaryote life strategies is therefore crucial for predicting responses of the marine microbial food web to climate change and other anthropogenic influences.
9
Lipps, Jere H. "Prokaryotes and Protists." Notes for a Short Course: Studies in Geology 18 (1987): 1–19. http://dx.doi.org/10.1017/s0271164800001470.
Full textAbstract:
Perhaps two of the most important groups of fossils are the prokaryotes and protists, both single-celled organisms. They are not spectacular fossils and so may be less interesting to students than the more complicated metazoans and metaphytes, yet these two groups not only dominate life on Earth today, but they contribute enormously to our understanding of Earth and life history. Prokaryotes dominated the fossil record of Earth from 3.5 to nearly .5 billion years ago (Knoll, 1985). For the last 1.5 billion years, protists have been an important element in marine and probably other ecosystems.
10
Hiraoka, Satoshi, Tomomi Sumida, Miho Hirai, Atsushi Toyoda, Shinsuke Kawagucci, Taichi Yokokawa, and Takuro Nunoura. "Diverse DNA modification in marine prokaryotic and viral communities." Nucleic Acids Research 50, no. 3 (January 21, 2022): 1531–50. http://dx.doi.org/10.1093/nar/gkab1292.
Full textAbstract:
Abstract DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent ‘metaepigenomic’ analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
11
Kientz, Betty, Peter Vukusic, Stephen Luke, and Eric Rosenfeld. "Iridescence of a Marine Bacterium and Classification of Prokaryotic Structural Colors." Applied and Environmental Microbiology 78, no. 7 (January 20, 2012): 2092–99. http://dx.doi.org/10.1128/aem.07339-11.
Full textAbstract:
ABSTRACTIridescence is a property of structural color that is occasionally encountered in higher eukaryotes but that has been poorly documented in the prokaryotic kingdom. In the present work, we describe a marine bacterium, identified asCellulophaga lytica, isolated from the surface of an anemone, that exhibits bright green iridescent colonies under direct epi-illumination. This phenomenon has not previously been investigated in detail. In this study, color changes ofC. lyticacolonies were observed at various angles of direct illumination or observation. Its iridescent green appearance was dominant on various growth media. Red and violet colors were also discerned on colony edges. RemarkableC. lyticabacterial iridescence was revealed and characterized using high-resolution optical spectrometry. In addition to this, by culturing other bacterial strains to which various forms of faintly iridescent traits have previously been attributed, we identify four principal appearance characteristics of structural color in prokaryotes. A new general classification of bacterial iridescence is therefore proposed in this study. Furthermore, a specific separate class is described for iridescentC. lyticastrains because they exhibit what is so far a unique intense glitter-like iridescence in reflection.C. lyticais the first prokaryote discovered to produce the same sort of intense iridescence under direct illumination as that associated with higher eukaryotes, like some insects and birds. Due to the nature of bacterial biology, cultivation, and ubiquity, this discovery may be of significant interest for both ecological and nanoscience endeavors.
12
Garuglieri, Elisa, Jenny Marie Booth, Marco Fusi, Xinyuan Yang, Ramona Marasco, Tumeka Mbobo, Emanuela Clementi, Luciano Sacchi, and 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 (April 14, 2022): e0266977. http://dx.doi.org/10.1371/journal.pone.0266977.
Full textAbstract:
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.
13
Rahav, Eyal, Natalia Belkin, Adina Paytan, and Barak Herut. "The Relationship between Air-Mass Trajectories and the Abundance of Dust-Borne Prokaryotes at the SE Mediterranean Sea." Atmosphere 10, no. 5 (May 20, 2019): 280. http://dx.doi.org/10.3390/atmos10050280.
Full textAbstract:
Airborne prokaryotes are transported along with dust/aerosols, yet very little attention is given to their temporal variability above the oceans and the factors that govern their abundance. We analyzed the abundance of autotrophic (cyanobacteria) and heterotopic airborne microbes in 34 sampling events between 2015–2018 at a coastal site in the SE Mediterranean Sea. We show that airborne autotrophic (0.2–7.6 cells × 103 m−3) and heterotrophic (0.2–30.6 cells × 103 m−3) abundances were affected by the origin and air mass trajectory, and the concentration of dust/aerosols in the air, while seasonality was not coherent. The averaged ratio between heterotrophic and autotrophic prokaryotes in marine-dominated trajectories was ~1.7 ± 0.6, significantly lower than for terrestrial routes (6.8 ± 6.1). Airborne prokaryotic abundances were linearly and positively correlated to the concentrations of total aerosol, while negatively correlated with the aerosol’s anthropogenic fraction (using Pb/Al or Cu/Al ratios as proxies). While aerosols may play a major role in dispersing terrestrial and marine airborne microbes in the SE Mediterranean Sea, the mechanisms involved in the dispersal and diversity of airborne microorganisms remain to be studied and should include standardization in collection and analysis protocols.
14
Caruso, Gabriella, Maurizio Azzaro, Carmela Caroppo, Franco Decembrini, Luis Salvador Monticelli, Marcella Leonardi, Giovanna Maimone, Renata Zaccone, and Rosabruna La Ferla. "Microbial community and its potential as descriptor of environmental status." ICES Journal of Marine Science 73, no. 9 (June 19, 2016): 2174–77. http://dx.doi.org/10.1093/icesjms/fsw101.
Full textAbstract:
Abstract Planktonic communities hold a relevant role within the EU Marine Strategy Framework Directive (MSFD). In view of reaching the Good Environmental Status of marine ecosystems, within this Directive the phyto- and zooplanktonic communities have received great attention, while Prokaryotes (Bacteria, Archaea, and Cyanobacteria) have been neglected. Indeed, the relevance of microbes (particularly of the faecal pollution indicators) as water quality indicators, the role that microorganisms play within the biogeochemical fluxes and in the whole ecosystem functioning, are all important features that deserve to be focused within the MSFD. The present study aims at reviewing the main issues where prokaryotic variables find useful application as descriptors of environmental status, trying to develop a panel of prokaryotic indicators suitable for the environmental quality assessment. From a survey of scientific literature and on field datasets, prokaryotic abundance and activities (enzymatic hydrolysis, prokaryotic production, and respiratory rates) are here chosen as early warning sentinels to detect changes in environmental quality, using an integrated approach with trophic (chlorophyll-a, particulate and dissolved organic matter) measurements.
15
Malmstrom, Rex R., Ronald P. Kiene, Matthew T. Cottrell, and David L. Kirchman. "Contribution of SAR11 Bacteria to Dissolved Dimethylsulfoniopropionate and Amino Acid Uptake in the North Atlantic Ocean." Applied and Environmental Microbiology 70, no. 7 (July 2004): 4129–35. http://dx.doi.org/10.1128/aem.70.7.4129-4135.2004.
Full textAbstract:
ABSTRACT SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of 3H-amino acids and [35S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.
16
Lipps, Jere H., and Stephen J. Culver. "The Trophic Role of Marine Microorganisms Through Time." Paleontological Society Papers 8 (October 2002): 69–92. http://dx.doi.org/10.1017/s1089332600001066.
Full textAbstract:
Microorganisms (prokaryotes and protists) seldom fossilize, but they form much of the trophic structure in marine pelagic and benthic environments, chiefly as primary producers and secondary consumers. The fossil record of unskeletonized groups is meager or non-existent. Skeletonized groups have excellent records but represent a small portion of the total microbial diversity.The evolution of trophic structures and roles of microorganisms can be reconstructed broadly for most of geologic history. When life first evolved, it had a trophic structure. The first microbial fossils appear to be benthic mats; these are abundant in the Precambrian but sparse later; body fossils are very rare. The Archean saw pelagic and benthic prokaryotes and possibly protists later on. Proterozoic trophic structures became increasingly complex as protists entered pelagic environments. Benthic assemblages likewise became complex, as prokaryotes and protists formed mats and stromatolites in many environments. At the end of the eon, animals appeared; microbial primary producers and predation on microorganisms and among animals fueled these assemblages. The fundamental trophic structures that developed then persisted with modification into modern times. Phanerozoic ecosystems became very complex as skeletonized animals and protists evolved. Among the important trophic developments in the Phanerozoic history of microorganisms were the early diversification of phytoplankton and siliceous micro-zooplankton (Cambrian), algal endosymbiosis with benthic metazoans (Cambrian to Recent) and rock-forming foraminifera (late Paleozoic to Recent), the radiation of pelagic skeletal primary producers and micro-zooplankton (mid-Mesozoic), and radiations in the deep sea, reefs, and shallow areas (Mesozoic and Cenozoic). Each evolutionary change increased trophic complexity by adding more species at each level, while episodic mass extinctions decreased species diversity and trophic complexity.Marine trophic structures evolved over immense intervals of geologic time, growing complex and then suffering destruction at major extinction events. The effects of human impact on these structures should be examined, for without them, Earth may change dramatically.
17
Sergeev, Vladimir N., and J. William Schopf. "Taxonomy, paleoecology and biostratigraphy of the late Neoproterozoic Chichkan microbiota of South Kazakhstan: the marine biosphere on the eve of metazoan radiation." Journal of Paleontology 84, no. 3 (May 2010): 363–401. http://dx.doi.org/10.1666/09-133.1.
Full textAbstract:
Carbonaceous bedded cherts of the late Neoproterozoic (Cryogenian) ∼800 to 750 Ma old Chichkan Formation of South Kazakhstan contain an abundant, diverse assemblage of exquisitely preserved microorganisms. Like many Proterozoic microbiotas, the Chichkan assemblage is dominated by prokaryotic cyanobacteria, both filamentous (oscillatorialeans and nostocaleans, represented primarily by cellular trichomes and empty sheaths) and coccoidal (chroococcaleans and pleurocapsaleans, including solitary, colonial, and stalk-forming specimens). However, unlike Proterozoic microbiotas reported from peritidal settings, the Chichkan fossils, permineralized in cherts deposited in the open shelf facies of the formation, include diverse microscopic eukaryotes: vase-shaped testate amoebae, spiny (acanthomorphic) phytoplanktonic unicells, large (up to ∼1 mm diameter) megasphaeromorphic acritarchs, and sausage-shaped vaucheriacean green alga-like filaments.Given the composition of this biota and the presence in it and similarly aged assemblages of numerous taxa typical of late Neoproterozoic deposits (e.g., Cerebrosphaera, Jacutianema, Melanocyrillium, Stictosphaeridium, Trachyhystrichosphaera, and Vandalosphaeridium), the Chichkan Lagerstätte appears representative of the Cryogenian biota as now known, thereby documenting the status of the marine biosphere at a time closely preceding the radiation of the Metazoa. As such, we interpret this and other coeval mixed assemblages of prokaryotic and eukaryotic microfossils as representing an evolutionary stage transitional between the predominantly prokaryote-dominated Precambrian and the eukaryote-dominated Phanerozoic biospheres.As reported here, the Chichkan assemblage is composed of 39 taxa (of which two forms are described informally) that are assigned to 23 genera of microscopic prokaryotes and eukaryotes and that include two new species: Polybessurus crassus n. sp. and Vandalosphaeridium koksuicum n. sp.
18
Tsai, An-Yi, Gwo-Ching Gong, and Vladimir Mukhanov. "Experimental Warming Effects on Prokaryotic Growth and Viral Production in Coastal Waters of the Northwest Pacific during the Cold Season." Diversity 13, no. 9 (August 27, 2021): 409. http://dx.doi.org/10.3390/d13090409.
Full textAbstract:
Climate warming can directly affect biological processes in marine environments. Here, we investigated if warming (+2 °C) can change dynamics in viral and prokaryotic populations in the cold seasons in natural seawaters. We monitored the changes in viral production and prokaryotic growth rate. The prokaryotic average gross growth rates were 0.08 and 0.34 h−1 in November and 0.06 and 0.41 h−1 in December in the in situ and warming experiments, respectively. We found that warming water temperature resulted in a significant increase in prokaryotic growth rates. In warming experiments, the overall viral production rate was about 0.77–14.4 × 105 viruses mL−1 h−1, and a rough estimate of prokaryotic mortality was about 5.6–6.8 × 104 cells mL−1 h−1. Based on our estimation, burst sizes of about 21 and 14 viruses prokaryotes−1 were measured under the experimental warming period. Moreover, the results found that an increased water temperature in the subtropical western Pacific coastal waters increases prokaryotic growth rates, enhances viral production, and changes the carbon fluxes in the trophic interactions of microbes.
19
Matsumoto, Kaoru, Tomoko Sakami, Tsuyoshi Watanabe, Yukiko Taniuchi, Akira Kuwata, Shigeho Kakehi, Tan Engkong, et al. "Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters." PLOS ONE 16, no. 10 (October 12, 2021): e0257862. http://dx.doi.org/10.1371/journal.pone.0257862.
Full textAbstract:
The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.
20
Franzmann, P. D., and S. J. Dobson. "The phylogeny of bacteria from a modern Antarctic refuge." Antarctic Science 5, no. 3 (September 1993): 267–70. http://dx.doi.org/10.1017/s0954102093000355.
Full textAbstract:
The 16S rRNAs of nine new species of prokaryotes, that had been isolated from four lakes of the Vestfold Hills, have been sequenced. These sequences were compared with those of their closest taxonomic relatives available from publicly available databases. The Antarctic species were of wide diversity with representatives from the domains Archaea and Bacteria (sensu Woese). Generally, they were most closely related to organisms from marine environments. The sequence dissimilarity between the rRNA sequences of the Antarctic strains and their nearest known relatives suggest they diverged from each other much earlier than the establishment of their modern Antarctic habitat. The conserved nature of the 16S rRNA molecule suggests it may not be as useful for detecting evolutionary change in Antarctic prokaryotes as distinct from non-Antarctic prokaryotes. Although the optimal temperature for growth of each species is well above the temperature of its environment, each has a reduced optimal temperature for growth when compared with its taxonomic counterpart from non-Antarctic environments. The vast majority of Antarctic prokaryotes remains to be described.
21
Garcia-Martinez, J., and F. Rodriguez-Valera. "Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I." Molecular Ecology 9, no. 7 (July 2000): 935–48. http://dx.doi.org/10.1046/j.1365-294x.2000.00953.x.
Full text
22
Lajnef, Rim, Marianne Quéméneur, Moufida Abdennadher, Lamia Dammak Walha, Asma Hamza, Malika Belhassen, and Amel Bellaaj Zouari. "Prokaryotic Diversity and Dynamics during Dinoflagellate Bloom Decays in Coastal Tunisian Waters." Diversity 15, no. 2 (February 14, 2023): 273. http://dx.doi.org/10.3390/d15020273.
Full textAbstract:
(1) Background: Harmful algal blooms (HABs) can negatively impact marine ecosystems, but few studies have evaluated the microbial diversity associated with HABs and its potential role in the fates of these proliferations. (2) Methods: Marine prokaryotic diversity was investigated using high-throughput sequencing of the 16S rRNA gene during the bloom declines of two dinoflagellates detected in the summer of 2019 along the northern and southern Tunisian coasts (South Mediterranean Sea). The species Gymnodinium impudicum (Carthage, Tunis Gulf) and Alexandrium minutum (Sfax, Gabes Gulf) were identified using microscopy and molecular methods and were related to physicochemical factors and prokaryotic compositions. (3) Results: The abundance of G. impudicum decreased over time with decreasing phosphate concentrations. During the G. impudicum bloom decay, prokaryotes were predominated by the archaeal MGII group (Thalassarchaeaceae), Pelagibacterales (SAR11), Rhodobacterales, and Flavobacteriales. At Sfax, the abundance of A. minutum declined with decreasing phosphate concentrations and increasing pH. At the A. minutum peak, prokaryotic communities were largely dominated by anoxygenic phototrophic sulfur-oxidizing Chromatiaceae (Gammaproteobacteria) before decreasing at the end of the survey. Both the ubiquitous archaeal MGII group and Pelagibacterales were found in low proportions during the A. minutum decay. Contrary to the photosynthetic Cyanobacteria, the photo-autotrophic and -heterotrophic Rhodobacterales and Flavobacteriales contents remained stable during the dinoflagellate bloom decays. (4) Conclusions: These results indicated changes in prokaryotic community diversity during dinoflagellate bloom decays, suggesting different bacterial adaptations to environmental conditions, with stable core populations that were potentially able to degrade HABs.
23
Otero-Ferrer, Jose Luis, Pedro Cermeño, Antonio Bode, Bieito Fernández-Castro, Josep M. Gasol, Xosé Anxelu G. Morán, Emilio Marañon, et al. "Factors controlling the community structure of picoplankton in contrasting marine environments." Biogeosciences 15, no. 20 (October 26, 2018): 6199–220. http://dx.doi.org/10.5194/bg-15-6199-2018.
Full textAbstract:
Abstract. The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and low-nucleic-acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters (>20 ∘C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communities.
24
Yoshida-Takashima, Yukari, Takuro Nunoura, Hiromi Kazama, Takuroh Noguchi, Kazuhiro Inoue, Hironori Akashi, Toshiro Yamanaka, et al. "Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments." Applied and Environmental Microbiology 78, no. 5 (December 30, 2011): 1311–20. http://dx.doi.org/10.1128/aem.06491-11.
Full textAbstract:
ABSTRACTViruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments.
25
Pearman, John K., Nigel B. Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson-Laing, Laura Biessy, Javier Atalah, and Xavier Pochon. "Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture." PeerJ 8 (October 27, 2020): e10231. http://dx.doi.org/10.7717/peerj.10231.
Full textAbstract:
Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between “distance” from the farm and “kit” in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
26
Boeuf, D., F. Humily, and C. Jeanthon. "Diversity of Arctic Pelagic Prokaryotes with an emphasis on photoheterotrophic bacteria: a review." Biogeosciences Discussions 11, no. 2 (February 12, 2014): 2419–55. http://dx.doi.org/10.5194/bgd-11-2419-2014.
Full textAbstract:
Abstract. The Arctic Ocean is a unique marine environment with respect to seasonality of light, temperature, perennial ice cover and strong stratification. Other important distinctive features are the influence of extensive continental shelves and its interactions with Atlantic and Pacific water masses and freshwater from sea ice melt and rivers. These characteristics have major influence on the biological and biogeochemical processes occurring in this complex natural system. Heterotrophic bacteria are crucial components of marine food webs and have key roles in controlling carbon fluxes in the oceans. Although it was previously thought that these organisms relied on the organic carbon in seawater for all of their energy needs, several recent discoveries now suggest that pelagic bacteria can depart from a strictly heterotrophic lifestyle by obtaining energy through unconventional mechanisms that are linked to the penetration of sunlight into surface waters. These photoheterotrophic mechanisms may play a significant role in the energy budget in the euphotic zone of marine environments. We can suspect that this role could be of greater importance in the Arctic Ocean where environmental changes triggered by climate change could favor the photoheterotrophic lifestyle. Here we review advances in our knowledge of the diversity of marine photoheterotrophic bacteria and discuss their significance in the Arctic Ocean gained in the framework of the Malina cruise.
27
Parada, Verónica, Gerhard J. Herndl, and 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 (April 10, 2006): 613–21. http://dx.doi.org/10.1017/s002531540601352x.
Full textAbstract:
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.
28
Schleper, Christa, Edward F. DeLong, Christina M. Preston, Robert A. Feldman, Ke-Ying Wu, and Ronald V. Swanson. "Genomic Analysis Reveals Chromosomal Variation in Natural Populations of the Uncultured Psychrophilic ArchaeonCenarchaeum symbiosum." Journal of Bacteriology 180, no. 19 (October 1, 1998): 5003–9. http://dx.doi.org/10.1128/jb.180.19.5003-5009.1998.
Full textAbstract:
ABSTRACT Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial and marine environments. To date these organisms have resisted isolation in pure culture, and so their phenotypic and genotypic characteristics remain largely unknown. To characterize these archaea, and to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeoteCenarchaeum symbiosum found living in association with a marine sponge, Axinella mexicana. Complex DNA libraries derived from the host-symbiont population yielded several large clones containing the ribosomal operon from C. symbiosum. Unexpectedly, cloning and sequence analysis revealed the presence of two closely related variants that were consistently found in the majority of host individuals analyzed. Homologous regions from the two variants were sequenced and compared in detail. The variants exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping region. Our study not only indicates the potential for characterizing uncultivated prokaryotes by genome sequencing but also identifies the primary complication inherent in the approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic populations.
29
Deng, Wenchao, Shanlin Wang, Xianhui Wan, Zhenzhen Zheng, Nianzhi Jiao, Shuh‐Ji Kao, Jefferson Keith Moore, and Yao Zhang. "Potential competition between marine heterotrophic prokaryotes and autotrophic picoplankton for nitrogen substrates." Limnology and Oceanography 66, no. 9 (June 30, 2021): 3338–55. http://dx.doi.org/10.1002/lno.11883.
Full text
30
Bettarel, Yvan, Chiaki Motegi, Markus G. Weinbauer, and Xavier Mari. "Colonization and release processes of viruses and prokaryotes on artificial marine macroaggregates." FEMS Microbiology Letters 363, no. 1 (November 13, 2015): fnv216. http://dx.doi.org/10.1093/femsle/fnv216.
Full text
31
Rontani, Jean-François, and Patricia Bonin. "Production of pristane and phytane in the marine environment: role of prokaryotes." Research in Microbiology 162, no. 9 (November 2011): 923–33. http://dx.doi.org/10.1016/j.resmic.2011.01.012.
Full text
32
Azúa, Iñigo, Itziar Goiriena, Zuriñe Baña, Juan Iriberri, and Marian Unanue. "Release and Consumption of d-Amino Acids During Growth of Marine Prokaryotes." Microbial Ecology 67, no. 1 (September 22, 2013): 1–12. http://dx.doi.org/10.1007/s00248-013-0294-0.
Full text
33
Prieur, D. "20.3. Marine prokaryotes living under elevated hydrostatic pressure: history, diversity and adaptations." Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 148 (August 2007): S91—S92. http://dx.doi.org/10.1016/j.cbpa.2007.06.237.
Full text
34
Vezzulli, Luigi, Chiara Grande, Philip C. Reid, Pierre Hélaouët, Martin Edwards, Manfred G. Höfle, Ingrid Brettar, Rita R. Colwell, and Carla Pruzzo. "Climate influence onVibrioand associated human diseases during the past half-century in the coastal North Atlantic." Proceedings of the National Academy of Sciences 113, no. 34 (August 8, 2016): E5062—E5071. http://dx.doi.org/10.1073/pnas.1609157113.
Full textAbstract:
Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958–2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase inVibrioabundance is promoted by increasing sea surface temperatures (up to ∼1.5 °C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P< 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquiredVibrioinfections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.
35
Paliaga, Paolo, Igor Felja, Andrea Budiša, and Ingrid Ivančić. "The Impact of a Fish Cannery Wastewater Discharge on the Bacterial Community Structure and Sanitary Conditions of Marine Coastal Sediments." Water 11, no. 12 (December 5, 2019): 2566. http://dx.doi.org/10.3390/w11122566.
Full textAbstract:
The effects of fish cannery discharge (FCD) on bacteria in marine coastal sediments were investigated. Redox potentials were measured, and granulometry was determined by wet ASTM sieving, and with the Sedigraph method. Prokaryotic abundance (PA) was determined by epifluorescence microscopy (DAPI staining), and faecal indicator bacteria (FIB) enumerated with the multiple test tube and most probable number method. Total lipids were determined gravimetrically, and sterols analysed by GC/MSD. Bacterial community composition was determined after total DNA isolation, Illumina MiSeq amplification, and SILVAngs processing pipeline. The FCD was rich in lipids, heterotrophic prokaryotes and FIB. The bacterial community of the FCD was dominated by Firmicutes and Gammaproteobacteria and many potentially pathogenic bacteria. Highly porosusgravelly sands clogged with fish remains transitioned to less permeable sandy muds away from the FCD. All sediments were anoxic with extremely negative potentials around the outfall. High surface PA and FIB spread 300 m from the outfall. Gammaproteobacteria and Deltaproteobacteria appeared in all sediments. Sulfurovum and Anaerolineaceae characterized the most polluted locations where gammaproteobacterial Woeseiaceae/JTB255 marine benthic group declined. Gammaproteobacteria and Bacteroidetes characterized surface sediments, while Chloroflexi and Deltaproteobacteria prevailed in deeper layers. The FCD enriched sediments in lipids and allochthonous bacteria degrading sanitary quality, lowering the permeability, redox potential, and bacterial diversity.
36
Bai, Shijie, Jian Zhang, Xiaoxue Qi, Juntao Zeng, Shijun Wu, and Xiaotong Peng. "Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period." Microorganisms 11, no. 2 (February 20, 2023): 536. http://dx.doi.org/10.3390/microorganisms11020536.
Full textAbstract:
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical–chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea.
37
Nichols, David S. "Prokaryotes and the input of polyunsaturated fatty acids to the marine food web." FEMS Microbiology Letters 219, no. 1 (February 2003): 1–7. http://dx.doi.org/10.1016/s0378-1097(02)01200-4.
Full text
38
McDonald, Allison E., and Greg C. Vanlerberghe. "Alternative oxidase and plastoquinol terminal oxidase in marine prokaryotes of the Sargasso Sea." Gene 349 (April 2005): 15–24. http://dx.doi.org/10.1016/j.gene.2004.12.049.
Full text
39
Zhang, Fang, Fenglin Lv, and Mianrun Chen. "Biodiversity and Structure of Microbial Community in Glacial Melts and Soil in the High Arctic Ny-Ålesund, Svalbard." Microorganisms 10, no. 10 (September 29, 2022): 1941. http://dx.doi.org/10.3390/microorganisms10101941.
Full textAbstract:
Ny-Ålesund in Svalbard is a complex area with both continental and tidal glaciers. There are a lot of studies on prokaryotic and eukaryotic communities in coastal water and soil, but without studies in glacial-related waters. We make a distinctive and consolidated study on the structure of the prokaryotic and eukaryotic communities of pure glacial meltwater, glacial melting lake, glacial meltwater flowing via different types of soil at various elevations, estuarine glacial water and marine water. Moreover, we analyze the environmental–microbial relationships of the prokaryotic and eukaryotic communities via a canonical correspondence analysis and redundant analysis compared by a Pearson analysis. We found that there were distinct microbes in different environments. Altitude had significant correlations with prokaryotic and eukaryotic species in the 12 water samples (ppro = 0.001, npro = 1010, and peuk = 0.012, npro = 1651) (Pearson analysis). Altitude, temperature and salinity, respectively, accounted for 28.27%, 10.86% and 8.24% in the prokaryotic community structure and 25.77%, 17.72% and 3.46% in the eukaryotic, respectively, in water. Nitrogen, silicate and pH accounted for 38.15%, 6.15% and 2.48% in the prokaryotic community structure in soil and 26.65%, 12.78% and 8.66% in the eukaryotic. Eukaryotes were more stable than prokaryotes in changing environments. Cyanobacteria and dinoflagellates better adapt to a warming environment. Gammaproteobacteria and Chrysophysceae were most abundant in soil. Alphaproteobacteria, Bacteroidia, Mamiellophyceae and Prasinophytae were most abundant in water. Within these microbes, Bacilli and Chlorophyceae were only found in glaciers; Actinobacteria, KD94-96, Thermleophilia, Embryophyta, Trebouxiophyceae and Sordariomycetes were unique to soil.
40
Pierella Karlusich, Juan José, Federico M. Ibarbalz, and Chris Bowler. "Phytoplankton in the Tara Ocean." Annual Review of Marine Science 12, no. 1 (January 3, 2020): 233–65. http://dx.doi.org/10.1146/annurev-marine-010419-010706.
Full textAbstract:
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
41
Tchesunov, Alexei V., Jeroen Ingels, and Ekaterina V. Popova. "Marine free-living nematodes associated with symbiotic bacteria in deep-sea canyons of north-east Atlantic Ocean." Journal of the Marine Biological Association of the United Kingdom 92, no. 6 (February 6, 2012): 1257–71. http://dx.doi.org/10.1017/s0025315411002116.
Full textAbstract:
Two nematode species living in association with chemoautotrophic prokaryotes were found in two deep-sea canyon/channel systems, the Whittard Canyon and Gollum Channels, north-east Atlantic. Parabostrichus bathyalis gen. nov. sp. nov. (Desmodorida: Desmodoridae: Stilbonematinae) relates to Eubostrichus Greeff 1869 but differs in having well-developed paired dorso-caudal apophyses of the gubernaculum, small pre- and postcloacal latero-ventral papillae with short apical setae, elongate tail with slender posterior portion, and the absence of thorn-like setae (porids) in males. Body of P. bathyalis is loosely covered with elongate cells of prokaryote ectosymbionts. Astomonema southwardorum Austen et al. 1993, originally found at a methane seep pockmark in the North Sea, constitutes a significant portion of nematode communities in certain areas of the deep-sea canyon/channel systems. Taxonomic difficulties within Astomonematinae are discussed in light of the character state of paired male gonads discovered in A. southwardorum. Canyon populations of A. southwardorum are characterized by frequent loss of part of the hind body and wound healing posterior to the vulva in females. Both species tend to occur in deeper subsurface layers of the bottom sediment. Abundance of the nematode species associated with aggregations of ectosymbiotic (Parabostrichus) and endosymbiotic (Astomonema) chemoautotrophic bacteria may indicate reduced conditions at sites in these deep-sea canyons/channels and suggests a potentially substantial ecological role for chemolitotrophic fauna there.
42
Kieft, Thomas L., and Karen A. Simmons. "Allometry of animal–microbe interactions and global census of animal-associated microbes." Proceedings of the Royal Society B: Biological Sciences 282, no. 1810 (July 7, 2015): 20150702. http://dx.doi.org/10.1098/rspb.2015.0702.
Full textAbstract:
Animals live in close association with microorganisms, mostly prokaryotes, living in or on them as commensals, mutualists or parasites, and profoundly affecting host fitness. Most animal–microbe studies focus on microbial community structure; for this project, allometry (scaling of animal attributes with animal size) was applied to animal–microbe relationships across a range of species spanning 12 orders of magnitude in animal mass, from nematodes to whales. Microbial abundances per individual animal were gleaned from published literature and also microscopically counted in three species. Abundance of prokaryotes/individual versus animal mass scales as a nearly linear power function (exponent = 1.07, R 2 = 0.94). Combining this power function with allometry of animal abundance indicates that macrofauna have an outsized share of animal-associated microorganisms. The total number of animal-associated prokaryotes in Earth's land animals was calculated to be 1.3–1.4 × 10 25 cells and the total of marine animal-associated microbes was calculated to be 8.6–9.0 × 10 24 cells. Animal-associated microbes thus total 2.1–2.3 × 10 25 of the approximately 10 30 prokaryotes on the Earth. Microbes associated with humans comprise 3.3–3.5% of Earth's animal-associated microbes, and domestic animals harbour 14–20% of all animal-associated microbes, adding a new dimension to the scale of human impact on the biosphere. This novel allometric power function may reflect underlying mechanisms involving the transfer of energy and materials between microorganisms and their animal hosts. Microbial diversity indices of animal gut communities and gut microbial species richness for 60 mammals did not indicate significant scaling relationships with animal body mass; however, further research in this area is warranted.
43
Caroppo, Carmela, Maurizio Azzaro, Ombretta Dell’Acqua, Filippo Azzaro, Giovanna Maimone, Alessandro Ciro Rappazzo, Francesco Raffa, and Gabriella Caruso. "Microbial Biofilms Colonizing Plastic Substrates in the Ross Sea (Antarctica)." Journal of Marine Science and Engineering 10, no. 11 (November 10, 2022): 1714. http://dx.doi.org/10.3390/jmse10111714.
Full textAbstract:
Very few studies have investigated marine microbial colonization in polar regions, but climate-changing scenarios stress the importance of these investigations to protect life in such extremely vulnerable ecosystems. In two different coastal sites of the Ross Sea (Road and Tethys Bays, Antarctica) exposed to different stressors, the microbial biofilm colonizing the surface of plastic (polyvinyl chloride, PVC, and polyethylene, PE) panels left submerged in two experiments at different timescales (“short-term”: 3 months, and “long-term”: 9 and 12 months) was studied. The abundance and metabolic enzymatic activities [leucine aminopeptidase (LAP), beta-glucosidase (GLU) and alkaline phosphatase (AP)] of the prokaryotes and the microalgal abundance and species composition were analyzed, in parallel with the main environmental parameters. The prokaryotic community showed higher abundance and metabolic activities on PVC than on PE as opposed to microalgae. A peak in the microfouling prokaryotic abundance and metabolic functions was frequently recorded after 3 months of immersion, corresponding to the late austral summer period. LAP and AP were the most active enzymes, suggesting that microbial metabolic profiles were modulated by labile organic substrates. Our results suggest that the composition and function of microbial biofilm could be considered as sentinels of natural or anthropic-related disturbances.
44
Detmers, Jan, Volker Brüchert, Kirsten S. Habicht, and Jan Kuever. "Diversity of Sulfur Isotope Fractionations by Sulfate-Reducing Prokaryotes." Applied and Environmental Microbiology 67, no. 2 (February 1, 2001): 888–94. http://dx.doi.org/10.1128/aem.67.2.888-894.2001.
Full textAbstract:
ABSTRACT Batch culture experiments were performed with 32 different sulfate-reducing prokaryotes to explore the diversity in sulfur isotope fractionation during dissimilatory sulfate reduction by pure cultures. The selected strains reflect the phylogenetic and physiologic diversity of presently known sulfate reducers and cover a broad range of natural marine and freshwater habitats. Experimental conditions were designed to achieve optimum growth conditions with respect to electron donors, salinity, temperature, and pH. Under these optimized conditions, experimental fractionation factors ranged from 2.0 to 42.0‰. Salinity, incubation temperature, pH, and phylogeny had no systematic effect on the sulfur isotope fractionation. There was no correlation between isotope fractionation and sulfate reduction rate. The type of dissimilatory bisulfite reductase also had no effect on fractionation. Sulfate reducers that oxidized the carbon source completely to CO2 showed greater fractionations than sulfate reducers that released acetate as the final product of carbon oxidation. Different metabolic pathways and variable regulation of sulfate transport across the cell membrane all potentially affect isotope fractionation. Previous models that explained fractionation only in terms of sulfate reduction rates appear to be oversimplified. The species-specific physiology of each sulfate reducer thus needs to be taken into account to understand the regulation of sulfur isotope fractionation during dissimilatory sulfate reduction.
45
Falcioni, Tania, Stefano Papa, and 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 (January 25, 2008): 1767–79. http://dx.doi.org/10.1128/aem.01668-07.
Full textAbstract:
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.
46
Winter, Christian, Marie-Emmanuelle Kerros, and Markus G. Weinbauer. "Effects of Sodium Azide on the Abundance of Prokaryotes and Viruses in Marine Samples." PLoS ONE 7, no. 5 (May 18, 2012): e37597. http://dx.doi.org/10.1371/journal.pone.0037597.
Full text
47
Talarmin, A., F. Van Wambeke, P. Catala, C. Courties, and P. Lebaron. "Flow cytometric assessment of specific leucine incorporation in the open Mediterranean." Biogeosciences 8, no. 2 (February 7, 2011): 253–65. http://dx.doi.org/10.5194/bg-8-253-2011.
Full textAbstract:
Abstract. The surface of the Mediterranean Sea is a low-phosphate-low-chlorophyll marine area where marine heterotrophic prokaryotes significantly contribute to the biogeochemical cycles of all biogenic elements such as carbon, notably through the mineralization of dissolved organic compounds. Cell-specific leucine incorporation rates were determined in early summer in the open stratified Mediterranean Sea. The bulk leucine incorporation rate was on average 5 ± 4 pmol leu l−1 h−1 (n=30). Cell-specific 3H-leucine incorporation rates were assayed using flow cytometry coupled to cell sorting. Heterotrophic prokaryotes (Hprok) were divided into cytometric groups according to their side scatter and green fluorescence properties: high nucleic acid containing cells (HNA) with high scatter (HNA-hs) and low scatter (HNA-ls) and low nucleic acid containing cells (LNA). Cell-specific leucine incorporation rates of these cytometric groups ranged from 2 to 54, 0.9 to 11, and 1 to 12 × 10-21 mol cell−1 h−1, respectively. LNA cells represented 45 to 63% of the Hprok abundance, and significantly contributed to the bulk leucine incorporation rates, from 12 to 43%. HNA/LNA ratios of cell-specific leucine incorporation were on average 2.0 ± 0.7 (n=30). In surface layers (from 0 m down to the deep chlorophyll depth, DCM), cell-specific rates of HNA-hs were elevated (7 and 13 times greater than LNA and HNA-ls, respectively). Nevertheless, on average HNA-hs (26%) and LNA (27%) equally contributed to the bulk leucine incorporation in these layers. Prochlorococcus cells were easily sorted near the DCM and displayed cell-specific leucine incorporation rates ranging from 3 to 55 × 10-21 mol leu cell−1 h−1, i.e. as high as HNA-hs'. These sorted groups could therefore be defined as key-players in the process of leucine incorporation into proteins. The mixotrophic features of certain photosynthetic prokaryotes and the high contribution of LNA cells to leucine incorporation within the microbial communities of the Mediterranean could be reinforced.
48
Uzair, Bushra, Sobia Tabassum, Madiha Rasheed, and Saima Firdous Rehman. "Exploring Marine Cyanobacteria for Lead Compounds of Pharmaceutical Importance." Scientific World Journal 2012 (2012): 1–10. http://dx.doi.org/10.1100/2012/179782.
Full textAbstract:
The Ocean, which is called the “mother of origin of life,” is also the source of structurally unique natural products that are mainly accumulated in living organisms. Cyanobacteria are photosynthetic prokaryotes used as food by humans. They are excellent source of vitamins and proteins vital for life. Several of these compounds show pharmacological activities and are helpful for the invention and discovery of bioactive compounds, primarily for deadly diseases like cancer, acquired immunodeficiency syndrome (AIDS), arthritis, and so forth, while other compounds have been developed as analgesics or to treat inflammation, and so forth. They produce a large variety of bioactive compounds, including substances with anticancer and antiviral activity, UV protectants, specific inhibitors of enzymes, and potent hepatotoxins and neurotoxins. Many cyanobacteria produce compounds with potent biological activities. This paper aims to showcase the structural diversity of marine cyanobacterial secondary metabolites with a comprehensive coverage of alkaloids and other applications of cyanobacteria.
49
Glaubitz, Sabine, Katrin Kießlich, Christian Meeske, Matthias Labrenz, and Klaus Jürgens. "SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas." Applied and Environmental Microbiology 79, no. 8 (February 15, 2013): 2767–76. http://dx.doi.org/10.1128/aem.03777-12.
Full textAbstract:
ABSTRACTGammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, thein situabundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescencein situhybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. ThecbbMtranscripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.
50
Mestre, Mireia, Clara Ruiz-González, Ramiro Logares, Carlos M. Duarte, Josep M. Gasol, and M. Montserrat Sala. "Sinking particles promote vertical connectivity in the ocean microbiome." Proceedings of the National Academy of Sciences 115, no. 29 (July 2, 2018): E6799—E6807. http://dx.doi.org/10.1073/pnas.1802470115.
Full textAbstract:
The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean communities.