Journal articles: 'Microbial ecology. Aquatic ecology'

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Kemp, Paul F. "Aquatic microbial ecology." Limnology and Oceanography 45, no. 5 (July 2000): 1211. http://dx.doi.org/10.4319/lo.2000.45.5.1211.

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Cognetti, G. "Microbial ecology." Marine Pollution Bulletin 24, no. 5 (May 1992): 273. http://dx.doi.org/10.1016/0025-326x(92)90567-p.

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Cavicchioli, Ricardo. "Microbial ecology of Antarctic aquatic systems." Nature Reviews Microbiology 13, no. 11 (October 12, 2015): 691–706. http://dx.doi.org/10.1038/nrmicro3549.

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Findlay, Stuart. "Stream microbial ecology." Journal of the North American Benthological Society 29, no. 1 (March 2010): 170–81. http://dx.doi.org/10.1899/09-023.1.

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Lewin, Ralph A. "Handbook of Methods in Aquatic Microbial Ecology." Phycologia 33, no. 4 (July 1994): 308. http://dx.doi.org/10.2216/i0031-8884-33-4-308a.1.

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Cavicchioli, Ricardo. "Erratum: Microbial ecology of Antarctic aquatic systems." Nature Reviews Microbiology 13, no. 12 (October 20, 2015): 795. http://dx.doi.org/10.1038/nrmicro3584.

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Grossart, Hans-Peter, and Keilor Rojas-Jimenez. "Aquatic fungi: targeting the forgotten in microbial ecology." Current Opinion in Microbiology 31 (June 2016): 140–45. http://dx.doi.org/10.1016/j.mib.2016.03.016.

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del Giorgio, PA. "Progress and perspectives in aquatic microbial ecology: introduction." Aquatic Microbial Ecology 61, no. 3 (December 30, 2010): 219–20. http://dx.doi.org/10.3354/ame01487.

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Simon, M., HP Grossart, B. Schweitzer, and H. Ploug. "Microbial ecology of organic aggregates in aquatic ecosystems." Aquatic Microbial Ecology 28 (2002): 175–211. http://dx.doi.org/10.3354/ame028175.

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Caron, David A. "Marine microbial ecology in a molecular world: what does the future hold?" Scientia Marina 69, S1 (June 30, 2005): 97–110. http://dx.doi.org/10.3989/scimar.2005.69s197.

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Marxsen, Jürgen, and Karl-Paul Witzel. "Aquatic microbial ecology in the footsteps of Jürgen Overbeck." Fundamental and Applied Limnology / Archiv für Hydrobiologie 182, no. 2 (February 1, 2013): 89–90. http://dx.doi.org/10.1127/1863-9135/2013/0478.

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Psenner, Roland, Albin Alfreider, and Astrid Schwarz. "Aquatic Microbial Ecology: Water Desert, Microcosm, Ecosystem. What's Next?" International Review of Hydrobiology 93, no. 4-5 (October 2008): 606–23. http://dx.doi.org/10.1002/iroh.200711044.

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Kumaresan, Ramasamy, Krishnan Vinitha, and Kattari Kannan. "Bibliometric analysis of Aquatic Microbial Ecology from 2000 – 2014." International Journal of Research in Library Science 3, no. 2 (August 11, 2017): 01. http://dx.doi.org/10.26761/ijrls.3.2.2017.1251.

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Troussellier, Mare, Claude Courties, and André Vaquer. "Recent applications of flow cytometry in aquatic microbial ecology." Biology of the Cell 78, no. 1-2 (1993): 111–21. http://dx.doi.org/10.1016/0248-4900(93)90121-t.

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Kinne, O., F. Rassoulzadegan, and DA Caron. "Ten years 'Aquatic Microbial Ecology': an appreciation by the publisher." Aquatic Microbial Ecology 39 (2005): 1. http://dx.doi.org/10.3354/ame039001.

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GRAHAM, JAMES M. "Symposium Introductory Remarks: A Brief History of Aquatic Microbial Ecology." Journal of Protozoology 38, no. 1 (January 1991): 66–69. http://dx.doi.org/10.1111/j.1550-7408.1991.tb04803.x.

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Yentsch, Charles S., and David A. Phinney. "A bridge between ocean optics and microbial ecology." Limnology and Oceanography 34, no. 8 (December 1989): 1694–705. http://dx.doi.org/10.4319/lo.1989.34.8.1694.

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Saccò, Mattia, Nicole E. White, Matthew Campbell, Sebastian Allard, William F. Humphreys, Paul Pringle, Farid Sepanta, Alex Laini, and Morten E. Allentoft. "Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)." Water 13, no. 14 (July 9, 2021): 1899. http://dx.doi.org/10.3390/w13141899.

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Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.

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Schütt, Christian. "Ecogenetics: A new concept of aquatic microbial ecology at genetical level." SIL Proceedings, 1922-2010 24, no. 4 (September 1991): 2593–96. http://dx.doi.org/10.1080/03680770.1989.11900029.

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Gasol, Josep M., and Carlos M. Duarte. "Comparative analyses in aquatic microbial ecology: how far do they go?" FEMS Microbiology Ecology 31, no. 2 (February 2000): 99–106. http://dx.doi.org/10.1111/j.1574-6941.2000.tb00675.x.

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Kuparinen, J., and H. Galvão. "Microbial ecology: from local to global scales." Aquatic Microbial Ecology 53 (September 18, 2008): 3–11. http://dx.doi.org/10.3354/ame1226.

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Kuparinen, J., and H. Galvão. "Microbial ecology: from local to global scales." Aquatic Microbial Ecology 53, no. 1 (September 18, 2008): 3–11. http://dx.doi.org/10.3354/ame01226.

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Reed, Andrew J., and Randall E. Hicks. "Microbial ecology of Lake SuperiorBacteriaandArchaea: An overview." Aquatic Ecosystem Health & Management 14, no. 4 (October 2011): 386–95. http://dx.doi.org/10.1080/14634988.2011.630282.

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Blanchette, Melanie L., and Mark A. Lund. "Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes." Microorganisms 9, no. 6 (June 3, 2021): 1207. http://dx.doi.org/10.3390/microorganisms9061207.

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Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.

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Höfle, M. G. "RNA chemotaxonomy of aquatic bacteria — solution of a dilemma in microbial ecology?" SIL Proceedings, 1922-2010 24, no. 4 (September 1991): 2591. http://dx.doi.org/10.1080/03680770.1989.11900027.

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Mateus-Barros, Erick, Aylan K. Meneghine, Inessa Lacativa Bagatini, Camila C. Fernandes, Luciano T. Kishi, Armando A. H. Vieira, and Hugo Sarmento. "Comparison of two DNA extraction methods widely used in aquatic microbial ecology." Journal of Microbiological Methods 159 (April 2019): 12–17. http://dx.doi.org/10.1016/j.mimet.2019.02.005.

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Frederick, J. A., D. Jacobs, and W. R. Jones. "Biofilms and biodiversity: an interactive exploration of aquatic microbial biotechnology and ecology." Journal of Industrial Microbiology and Biotechnology 24, no. 5 (May 1, 2000): 334–38. http://dx.doi.org/10.1038/sj.jim.2900827.

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del Giorgio, PA. "Progress, challenges, and perspectives in marine microbial ecology." Aquatic Microbial Ecology 53, no. 1 (September 18, 2008): 1. http://dx.doi.org/10.3354/ame01219.

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Sosedova, Larisa M., Evgeniy A. Titov, Mikhail A. Novikov, Irina A. Shurygina, and Mikhail G. Shurygin. "Impact of metal nanoparticles on the ecology of aquatic biocenosis and microbial communities (Review)." Hygiene and sanitation 100, no. 1 (February 12, 2021): 30–35. http://dx.doi.org/10.47470/0016-9900-2021-100-1-30-35.

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This review contains analysis and generalization of data about aquatic ecotoxicity of metal nanoparticles study. This study showed the effect of their impact on the viability of protozoa, algae, microbial communities. A multi-level approach proves to be important as it considers the main characteristics of the studied materials: solubility, agglomeration, degradation. The transformation in the aquatic environment is important in the study of aquatic ecotoxicity. For assessing the state of environment in ecotoxicological experiments, the Great Daphnia (Daphnia magna) was used as a critical organism of the freshwater ecosystem, due to its high sensitivity to environmental pollution, small body size, and short lifespan. In this regard, numerous studies on the effect of nanoparticles on the state of aquatic ecosystem are carried out on Daphnia magna. The review presents some methodological approaches to test the toxicity of nanoparticles in aquatic environment and assessing their stability. It is proposed to carry out a total assessment of the effect based on the content of pollutants in water with different toxic potentials, given that organisms, including aquatic organisms, are rarely exposed to certain chemicals. A promising approach to the assessment of cytotoxicity is high-throughput screening (HTS), which offers the opportunity to quickly test the effects of nanoparticles on bacteria in parallel in several concentrations. Algae are the most important participants in ecosystem and main components of the food chain. It allows recommending them as a marker when monitoring the environmental pollution by metal nanoparticles. Particular attention is paid to perspectives for further wider use of nanostructured products as adsorbents in wastewater treatment and recultivation processes. Search and selection of sources for review carried out in open databases, including PubMed, Scopus, Google Scholar and RSCI (Russian Science Citation Index) for 2007 - 2018 period.

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Azevedo, Raíza S., Alessandro Del’Duca, Edmo M. Rodrigues, Thiago A. Freato, and Dionéia E. Cesar. "Theory of microbial ecology: Applications in constructing a recirculating aquaculture system." Aquaculture Research 49, no. 12 (October 22, 2018): 3898–908. http://dx.doi.org/10.1111/are.13860.

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Storey, R. G., R. R. Fulthorpe, and D. D. Williams. "Perspectives and predictions on the microbial ecology of the hyporheic zone." Freshwater Biology 41, no. 1 (February 1999): 119–30. http://dx.doi.org/10.1046/j.1365-2427.1999.00377.x.

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Pierce, Melissa L., and J. Evan Ward. "Microbial Ecology of the Bivalvia, with an Emphasis on the Family Ostreidae." Journal of Shellfish Research 37, no. 4 (October 2018): 793–806. http://dx.doi.org/10.2983/035.037.0410.

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Blanchette, Melanie L., Richard Allcock, Jahir Gonzalez, Nina Kresoje, and Mark Lund. "Macroinvertebrates and Microbes (Archaea, Bacteria) Offer Complementary Insights into Mine-Pit Lake Ecology." Mine Water and the Environment 39, no. 3 (November 8, 2019): 589–602. http://dx.doi.org/10.1007/s10230-019-00647-9.

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Abstract The broad objective of this research was to determine the environmental drivers of macroinvertebrate and microbial assemblages in acidic pit lakes. This is important because pit lake ecosystem development is influenced by prevailing environmental characteristics. Three lakes (Stockton, Kepwari, WO5H) within a larger pit-lake district in Collie, Western Australia were surveyed for spatial variability of benthic macroinvertebrate and microbe (Archaea, Bacteria) assemblage composition as well as potential environmental drivers (riparian condition, aquatic habitat, sediments, and aquatic chemistry) of assemblages. With the exception of sediment chemistry, biophysical variables were significantly different across lakes and reflected riparian condition and groundwater chemistry. Microbial assemblages in pit lakes were significantly different across lakes and correlated with water chemistry, particularly metals in Lake WO5H. However, the most abundant microbes were not readily identified beyond class, making it difficult to speculate on their ecological function. Macroinvertebrate assemblage composition and species richness were also significantly different across all lakes, and in Lake WO5H (a lake with low pH and high metal concentrations), taxa were correlated with benthic organic matter as well as water chemistry. Results indicated that despite poor water quality, input of nutrients from terrestrial leaf litter can support or augment pit lake ecosystems. This is a demonstration of the concept that connection of pit lakes to catchments can positively affect aquatic ecosystems, which can inform management actions for remediation.

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López-Archilla, A. I., I. Marin, and R. Amils. "Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain." Microbial Ecology 41, no. 1 (January 2001): 20–35. http://dx.doi.org/10.1007/s002480000044.

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Zablocki, Olivier, Evelien M. Adriaenssens, and Don Cowan. "Diversity and Ecology of Viruses in Hyperarid Desert Soils." Applied and Environmental Microbiology 82, no. 3 (November 20, 2015): 770–77. http://dx.doi.org/10.1128/aem.02651-15.

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ABSTRACTIn recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.

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Duarte, Carlos. "Microbial ecology of Lake Pluβee (J. Overbeck and R. J. CHRóST [ed.])." Limnology and Oceanography 40, no. 4 (June 1995): 841–42. http://dx.doi.org/10.4319/lo.1995.40.4.0841.

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Pedrós-Alió, Carlos. "Microbial ecology of Lake Pluβsee (J. Overbeck and R. J. Chrost [eds.])." Limnology and Oceanography 40, no. 7 (November 1995): 1345. http://dx.doi.org/10.4319/lo.1995.40.7.1345.

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Gignoux-Wolfsohn, SA, WF Precht, EC Peters, BE Gintert, and LS Kaufman. "Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis." Diseases of Aquatic Organisms 137, no. 3 (January 30, 2020): 217–37. http://dx.doi.org/10.3354/dao03441.

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Jacquet, Stéphan, Takeshi Miki, Rachel Noble, Peter Peduzzi, and Steven Wilhelm. "Viruses in aquatic ecosystems: important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology." Advances in Oceanography and Limnology 1, no. 1 (June 1, 2010): 97. http://dx.doi.org/10.4081/aiol.2010.5297.

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Over the last two decades, viruses in aquatic systems have been observed to modify, influence and control aquatic systems. Since the determination decades ago that viruses were abundant in aquatic ecosystems, researchers have demonstrated that viruses are pervasive and dynamic across the expanse and depth of all aquatic systems as well as at the water-sediment interface. There have been a wide range of methodological advancements during this time. To date, aquatic viruses have been suggested to play vital roles in global and small-scale biogeochemical cycling, community structure, algal bloom termination, gene transfer, and evolution of aquatic organisms. Even in harsh and difficult to study environments, aquatic and benthic viruses have been demonstrated to be major players in carbon cycling and recycling of nutrients from organic material. Taxonomic and metagenomic research has shown us that there are major globally-distributed groups, but that their genomes are filled with sequence information that has no similarity to sequences in existing bioinformatic databases. And while the field of viral ecology has expanded exponentially since the late 1980s, there is much that we do not yet understand about virusmediated processes in aquatic systems. Important near-term steps include the combination of advanced metagenomic techniques with studies of function and population control, standardization of methodological approaches to facilitate global data acquisition without concern over methods-based artefacts, understanding of viral life strategies and their triggers, and the role of viruses in the transformation of organic matter. The purpose of this manuscript is to bring the reader a review of the recent advances in aquatic viral ecology in light of new areas of research, applications of viral ecology to real-world problems, and refinement of models of viral interactions on a range of scales.

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Abella, C. A., and L. J. Garcia-Gil. "Microbial ecology of planktonic filamentous phototrophic bacteria in holomictic freshwater lakes." Hydrobiologia 243-244, no. 1 (October 1992): 79–86. http://dx.doi.org/10.1007/bf00007022.

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41

Kent, Angela D., Anthony C. Yannarell, James A. Rusak, Eric W. Triplett, and Katherine D. McMahon. "Synchrony in aquatic microbial community dynamics." ISME Journal 1, no. 1 (May 2007): 38–47. http://dx.doi.org/10.1038/ismej.2007.6.

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Apprill, A., H. Holm, AE Santoro, C. Becker, M. Neave, K. Hughen, A. Richards Donà, et al. "Microbial ecology of coral-dominated reefs in the Federated States of Micronesia." Aquatic Microbial Ecology 86 (April 22, 2021): 115–36. http://dx.doi.org/10.3354/ame01961.

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Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km2. On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features.

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Dolan, JR, F. Rassoulzadegan, and DA Caron. "The first decade of 'Aquatic Microbial Ecology' (1995-2005): evidence for gradualism or punctuated equilibrium?" Aquatic Microbial Ecology 39 (2005): 3–6. http://dx.doi.org/10.3354/ame039003.

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Rochera, Carlos, and Antonio Camacho. "Limnology and Aquatic Microbial Ecology of Byers Peninsula: A Main Freshwater Biodiversity Hotspot in Maritime Antarctica." Diversity 11, no. 10 (October 21, 2019): 201. http://dx.doi.org/10.3390/d11100201.

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Here we present a comprehensive review of the diversity revealed by research in limnology and microbial ecology conducted in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) during the last two decades. The site constitutes one of the largest ice-free areas within the Antarctic Peninsula region. Since it has a high level of environmental protection, it is less human-impacted compared to other sites within the South Shetland archipelago. The main investigations in Byers Peninsula focused on the physical and chemical limnology of the lakes, ponds, rivers, and wetlands, as well as on the structure of their planktonic and benthic microbial communities, and on the functional ecology of the microbial food webs. Lakes and ponds in Byers range along a productivity gradient that extends from the less productive lakes located upland to the eutrophic coastal lakes. Their planktonic assemblages include viruses, bacteria, a metabolically diverse community of protists (i.e., autotrophs, heterotrophs, and mixotrophs), and a few metazooplankton species. Most of the studies conducted in the site demonstrate the strong influence of the physical environment (i.e., temperature, availability of light, and water) and nutrient availability in structuring these microbial communities. However, top-down biotic processes may occur in summer, when predation by zooplankton can exert a strong influence on the abundance of protists, including flagellates and ciliated protozoa. As a consequence, bacterioplankton could be partly released from the grazing pressure exerted by these protists, and proliferates fueled by external nutrient subsidies from the lake’s catchment. As summer temperatures in this region are slightly above the melting point of water, biotic processes, such as those related to the productivity of lakes during ice-free periods, could become even more relevant as warming induced by climate change progresses. The limnological research carried out at the site proves that Byers Peninsula deserves special attention in the framework of the research in extreme environments. Together with nearby sites, such as Signy Island, Byers Peninsula comprises a featuring element of the Maritime Antarctic region that represents a benchmark area relative to the global distribution and diversity of aquatic microorganisms.

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Luef, Birgit, Thomas R. Neu, and Peter Peduzzi. "Imaging and quantifying virus fluorescence signals on aquatic aggregates: a new method and its implication for aquatic microbial ecology." FEMS Microbiology Ecology 68, no. 3 (June 2009): 372–80. http://dx.doi.org/10.1111/j.1574-6941.2009.00675.x.

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Sebastián, Marta, and Josep M. Gasol. "Visualization is crucial for understanding microbial processes in the ocean." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (October 7, 2019): 20190083. http://dx.doi.org/10.1098/rstb.2019.0083.

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Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue ‘Single cell ecology’.

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Sime-Ngando, Télesphore, and Jonathan Colombet. "Virus et prophages dans les écosystèmes aquatiques." Canadian Journal of Microbiology 55, no. 2 (February 2009): 95–109. http://dx.doi.org/10.1139/w08-099.

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In this review, available data on the structure (diversity, abundance, biomass) and functional imprints (bacteriolysis, lysogeny, gene transfers, regulation of prokaryotic diversity) of natural viruses in the context of food webs in aquatic microbial ecology, and the related biogeochemical cycles, are summarized. Viruses are the most abundant, and probably the most diverse, biological entities in aquatic ecosystems and in the biosphere (i.e., viriosphere). Aquatic viruses typically exceed 107particles/mL in mesotrophic conditions, the majority being represented by phages without tails and by tailed-phages such as members of the family Siphoviridae. Both types of phages have a small capsid and a small genome size, which is considered an evolutionary adaptation to planktonic life. Their contribution to microbial mortality is significant. There is strong evidence that phages exert a significant pressure on the community structure and diversity and on the diversification of potential hosts, mainly through two major pathways: biogeochemical catalysis from lysis products and horizontal gene transfers. In turn, phages are sensitive to environmental factors, both in terms of integrity and of infectivity. Some phages contain typical viral genes that code for biological functions of interest, such as photosynthesis. In general, development in viral ecology is a source of new knowledge for the scientific community in the domain of environmental sciences, but also in the context of evolutionary biology of living cellular organisms, the obligatory hosts for viruses. For example, the recent discovery of a giant virus that becomes ill through infection by another virus (i.e., a viriophage) is fuelling debate about whether viruses are alive. Finally, future research directions are identified in the context of general aquatic ecology, including ecological researches on cyanophages and other phytoplanktonic phages as a priority, primarily in freshwater lakes.

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Van Colen, Carl, Graham J. C. Underwood, João Serôdio, and David M. Paterson. "Ecology of intertidal microbial biofilms: Mechanisms, patterns and future research needs." Journal of Sea Research 92 (September 2014): 2–5. http://dx.doi.org/10.1016/j.seares.2014.07.003.

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Du, Wanlin, Yang Liu, Jinhui Sun, Naicheng Wu, Yongzhan Mai, and Chao Wang. "The aquatic microbial community: a bibliometric analysis of global research trends (1991– 2018)." Fundamental and Applied Limnology / Archiv für Hydrobiologie 194, no. 1 (August 31, 2020): 19–32. http://dx.doi.org/10.1127/fal/2020/1305.

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We performed a bibliometric analysis of relevant research trends, based on academic articles about the aquatic microbial community and recorded in the Web of Science during 1991–2018. The number of publications per annum is clearly rising and began to grow rapidly in 2005. Developed countries (e.g.the USA and some European countries) published the most articles, and led international cooperation. International cooperation benefitted from the implementation of the European Union (EU) Water Framework Directive and from the origination and development of molecular biological techniques. A strong correlation existed among such key words as "bacteria", "DGGE" (Denaturing Gradient Gel Electrophoresis), "16S rRNA", "pyrosequencing" and "sediment" as key research directions for many years. Sediment, biofilm and wetland were the main habitats studied; and high-throughput sequencing gradually replaced the traditional DGGE and other technologies, remaining the most popular research method at present. Studies still focus on basic research; interest in microbial community composition, structure, diversity and ecology remains high; and metagenomics and the microbiome have received considerable attention recently. Key words such as "organic matter", "nutrient", "enzyme activity", "nitrification", "denitrification" and "cyanobacteria" indicate current research hotspots, and we suggest this is because increasing attention is paid to environmental protection and management of the water environment by aquatic microorganisms. We predict that future research will promote the ultimate goals of warning about threats to the water environment and restoration by investigating the function of the aquatic microbial community.

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Mayali, Xavier. "NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts." Annual Review of Marine Science 12, no. 1 (January 3, 2020): 449–67. http://dx.doi.org/10.1146/annurev-marine-010419-010714.

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One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future.

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Journal articles on the topic 'Microbial ecology. Aquatic ecology'

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