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Diversity
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Ecology of Microbes in Marine and Estuarine Ecosystems
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Ecology of Microbes in Marine and Estuarine Ecosystems

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (10 February 2023) | Viewed by 11522

Special Issue Editor

Dr. Angia Sriram Pradeep Ram

E-Mail Website
Guest Editor
Laboratoire Microorganismes, Génome et Environnement, Université Clermont-Auvergne, 63178 Aubière CEDEX, France
Interests: aquatic microbial ecology; microbial food-web; viruses; prokaryotes; viral life strategies; virus-prokaryote interaction

Special Issue Information

Dear Colleagues,

The marine environment, which constitutes a large fraction of the Earth’s surface, is teeming with a vast array of microbes such as bacteria, archaea, viruses, fungi, and protists that are genetically, physiologically, and ecologically diverse. Invisible to the naked eye, these life forms that encompass a taxonomically and functionally different lineage represent unfathomable levels of marine diversity. Marine microbes, which dominate the living biomass, are known to exist rationally in any environment and garner energy from a variety of sources, ranging from solar radiation to chemosynthesis. Through their numerous and novel metabolic strategies, they contribute significantly to all global biogeochemical cycles of matter and energy. The staggering presence of unprecedented microbial diversity flourishing in the marine environment as revealed through ‘omics’ approaches has dramatically changed our understanding of the distribution of genes and organisms as well as the selective forces that structure microbial community composition and distribution across space and time. The combined effect of countless and complex interactions occurring among different microbial taxa underpins community stability and functioning of marine ecosystems. A great deal of research on the biogeography of marine microorganisms has been carried out, but many unknowns persist, and more work is needed to elucidate and understand their complexity.

The Special Issue is devoted to advancing the study on the ecology of microbes across different marine environments (coastal zone, estuaries, oceanic and polar systems) focusing on a broad spectrum of topics pertaining to their distribution, activity, physiology, metabolism, and identification of diversity of bacteria, archaea, viruses, fungi, and protists in the water column and sediments. 

Dr. Angia Sriram Pradeep Ram
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  •  marine microbial biogeography
  • microbial mediated nutrient cycling
  • microbial physiology and metabolism
  • viral life strategies
  • phage–host interaction
  • top-down and bottom-up mechanisms
  • marine microbial diversity
  • laboratory microcosms
  • marine mesocosms

Published Papers (5 papers)

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Research

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14 pages, 2794 KiB  
Article
Microbiome Profile of the Mediterranean Mussel (Mytilus galloprovincialis) from Northern Aegean Sea (Greece) Culture Areas, Based on a 16S rRNA Next Generation Sequencing Approach
by Konstantinos Schoinas, Vasiliki Konstantou, Emmanouela Bompou, George Floros, Dimitrios Chatziplis, Anastasia Imsiridou and Dimitrios Loukovitis
Diversity 2023, 15(3), 463; https://doi.org/10.3390/d15030463 - 21 Mar 2023
Cited by 1 | Viewed by 2030
Abstract
Mediterranean mussels (Mytilus galloprovincialis), due to their nutritional mechanisms which involve filtering huge amounts of water, are affected by seawater pollution and can host microbial diversity of environmental origin, as well as pathogenic bacteria that must be constantly monitored. Herein, we [...] Read more.
Mediterranean mussels (Mytilus galloprovincialis), due to their nutritional mechanisms which involve filtering huge amounts of water, are affected by seawater pollution and can host microbial diversity of environmental origin, as well as pathogenic bacteria that must be constantly monitored. Herein, we applied a Next Generation Sequencing (NGS) metabarcoding approach in order to study the M. galloprovincialis microbiota. Collection of samples was conducted during winter and summer months from various mussel farm zones located in specific farm regions in the Thermaikos gulf, the northern Aegean Sea, Greece. A microbiological test was performed for the enumeration of Escherichia coli and the presence of Salmonella sp. DNA extraction and amplification of the whole bacterial 16S rRNA gene, followed by NGS amplicon sequencing and taxonomic classification, were carried out. Statistically significant differences (p < 0.05) in the abundance of the most dominant bacterial phyla, families and genera between winter and summer time periods, regions, as well as zones within each region of sampling, were evaluated with z-score computation. According to the obtained results, the most prevalent taxa at the genus level were Mycoplasma (12.2%), Anaplasma (5.8%), Ruegeria (5.2%) and Mariniblastus (2.1%). Significant differences in the abundance of the most dominant genera were found at all levels of comparison (seasons, regions and zones within each region), highlighting the dynamic character of microorganisms, which might be affected by microenvironmental, temporal and spatial changes. The present research contributes to the characterization of M. galloprovincialis microbiome in areas that have not been studied previously, setting the baseline for future, more thorough investigations of the specific bivalve species and its bacterial profile in the above geographic regions. Full article
(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)
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24 pages, 5861 KiB  
Article
Taxonomic Composition of Protist Communities in the Coastal Stratified Lake Kislo-Sladkoe (Kandalaksha Bay, White Sea) Revealed by Microscopy
by Yulia V. Mindolina, Elena A. Selivanova, Marina E. Ignatenko, Elena D. Krasnova, Dmitry A. Voronov and Andrey O. Plotnikov
Diversity 2023, 15(1), 44; https://doi.org/10.3390/d15010044 - 29 Dec 2022
Cited by 1 | Viewed by 1846
Abstract
Lake Kislo-Sladkoe is a stratified water body partly isolated from the White Sea. Perennial meromixis in the lake irregularly alternates with mixing events. Taking into account that the protists of Arctic coastal stratified water bodies are understudied, we evaluated for the first time [...] Read more.
Lake Kislo-Sladkoe is a stratified water body partly isolated from the White Sea. Perennial meromixis in the lake irregularly alternates with mixing events. Taking into account that the protists of Arctic coastal stratified water bodies are understudied, we evaluated for the first time the vertical structure, species richness, and diversity of protists assigned to different taxonomic groups in Lake Kislo-Sladkoe using light, luminescent, and scanning electron microscopy. To test the research hypothesis that a mixing event affects the vertical stratification and species composition of protists in a stratified lake, we compared the protist communities of Lake Kislo-Sladkoe in two extremely different states: strong meromixis vs. full vertical mixing. A total of 97 morphologically distinct phototrophic, heterotrophic, and mixotrophic protists were revealed with the most diverse supertaxa SAR (59), Obazoa (9), and Excavates (14). The hidden diversity of protists (43 species) was a bit less than the active diversity (54 species). A taxonomic list and micrographs of cells for the observed protists are provided. The majority of species revealed are cosmopolitan or widespread in the northern sea waters. The vertical patterns of protist communities were absolutely different in 2018 and 2021. In July 2018, clearly distinct protist communities inhabited different layers of the lake. Bloom of cryptophyte Rhodomonas cf. baltica was detected in chemocline, whereas the maximum density of its grazers was observed in adjacent layers, mainly dinoflagellates Gymnodinium sp. and Scrippsiella trochoidea, as well as a ciliate Prorodon sp. In 2021 due to the recent mixing of lake and seawater, there were no distinct communities in the water column except the superficial 0–1 m layer of fresh water. Full article
(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)
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10 pages, 1576 KiB  
Article
Insights into Virus–Prokaryote Relationships in a Subtropical Danshui River Estuary of Northern Taiwan in Summer
by An-Yi Tsai, Gwo-Ching Gong, Vladimir Mukhanov and Patrichka Wei-Yi Chen
Diversity 2022, 14(4), 237; https://doi.org/10.3390/d14040237 - 24 Mar 2022
Viewed by 1724
Abstract
In spite of the fact that the interactions between environmental parameters and prokaryotic and viral abundance have been explored in various aquatic environments, only a few independent estimates of viral production and decay in the estuarine region have been explored. In this study, [...] Read more.
In spite of the fact that the interactions between environmental parameters and prokaryotic and viral abundance have been explored in various aquatic environments, only a few independent estimates of viral production and decay in the estuarine region have been explored. In this study, data were analyzed for viral and prokaryotic abundance, viral production, and viral decay in a subtropical Danshui estuary in summer 2021. Prokaryotic abundance varied from 2.4 ± 0.6 × 105 to 12 ± 2.3 × 105 cells mL−1, and viral abundance ranged from 2.3 ± 0.9 × 105 to 6.9 ± 1.3 × 105 viruses mL−1 during the study period. Viral abundance was significantly correlated with prokaryotic abundance and chlorophyll a concentration. Furthermore, studies of changes in viral to prokaryotic abundance ratio (VPR) ranged from 0.42 ± 0.11 to 2.0 ± 0.25. Viral decay values were 2.1 ± 0.5 and 2.1 ± 0.3 × 104 virus mL−1h−1, and non-significant differences were observed between the inner estuary and coastal water region. Viral decay almost balanced gross viral production in this study. The dilution experiments revealed non-significant net viral production in July; thus, a lower VPR might be explained in this estuarine environment. Full article
(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)
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16 pages, 6504 KiB  
Article
Contrasting Impact of Viral Activity on Prokaryotic Populations in the Coastal and Offshore Regions of the Eastern Arabian Sea
by PK Shruthi, Ammini Parvathi, Angia Sriram Pradeep Ram, Shyla Hafza, Jose K. Albin, Erathodi Rajagopalan Vignesh, Jaleel Abdul and Telesphore Sime-Ngando
Diversity 2022, 14(3), 230; https://doi.org/10.3390/d14030230 - 21 Mar 2022
Cited by 1 | Viewed by 2303
Abstract
Viral processes in the coastal and offshore regions of the Eastern Arabian Sea (west coast of India) and their contribution of viral lysis to the organic carbon and nitrogen pool was examined. Water samples were collected during the southwest monsoon season at different [...] Read more.
Viral processes in the coastal and offshore regions of the Eastern Arabian Sea (west coast of India) and their contribution of viral lysis to the organic carbon and nitrogen pool was examined. Water samples were collected during the southwest monsoon season at different depths (up to 1000 m) from four transects, with each transect consisting of two sampling points (S1–S8). Abundances of viruses and prokaryotes together with viral mediated prokaryotic mortality (up to 49.7%) were significantly (p < 0.001) higher in eutrophic coastal stations, whereas high percent lysogeny (up to 93%) was observed in the offshore regions. High viral-mediated carbon (Mean ± SD = 67.47 ± 2.0 μM C L−1 d−1) and nitrogen (Mean ± SD = 13.49 ± 14.0 μM N L−1 d−1) release was evident in the surface coastal waters compared to offshore regions. The percentage contributions of carbon and nitrogen released by viral lysis to the total dissolved organic carbon and nitrogen pool were estimated to be 7.4% and 3.9%, respectively, in the coastal surface waters. Our findings suggest that the contribution of viral lysis to DOM production through viral shunt could be crucial for the cycling of major biogeochemical elements and functioning of the studied tropical ecosystem. Full article
(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)
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14 pages, 1026 KiB  
Review
Mechanisms Generating Dichotomies in the Life Strategies of Heterotrophic Marine Prokaryotes
by Tron Frede Thingstad, Lise Øvreås and Olav Vadstein
Diversity 2022, 14(3), 217; https://doi.org/10.3390/d14030217 - 16 Mar 2022
Cited by 5 | Viewed by 2611
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Ecology of Microbes in Marine and Estuarine Ecosystems)
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