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Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 20960

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Dr. Ulrich (Uli) Stingl

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Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Florida Research and Education Center, Davie, FL 32611, USA
Interests: marine microbiology; microbial ecology; microbiome; holobiont; marine bacteria; SAR11; microbes and climate change; microbial community structure; aquatic microbiology; bacterial cultivation
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Dear Colleagues,

The transition from rivers or coastal wetlands to marine estuaries and bays involves steep gradients in salinity and nutrient concentrations, which are usually accompanied with abrupt changes in microbial community composition and function. While there is an increased focus on toxic bloom-forming organisms in coastal areas around the world, environmental conditions that lead to the blooms of specific organisms, as well as microbial interactions and heterotrophic activities associated with blooms, are heavily understudied. Increased research into microbial community structure and heterotrophic activities before, during, and after blooms is pivotal to understand bloom formation and improve predictive models.

In this Special Issue, we want to highlight studies on planktonic coastal microbial communities, both on the freshwater end as well as in brackish and coastal marine waters. We are interested in community composition related to environmental parameters, seasonal variations, and functional attributes of both prokaryotic and eukaryotic microbes. Studies analyzing energy and/or nutrient transfer from heterotrophic bacteria to higher trophic levels in coastal waters as well as cultivation-based studies or manuscripts related to blooms of phototrophic (or heterotrophic) organisms are also welcome.

Dr. Ulrich (Uli) Stingl
Guest Editor

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Published Papers (7 papers)

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18 pages, 2284 KiB

Open AccessArticle

Water Column Microbial Communities Vary along Salinity Gradients in the Florida Coastal Everglades Wetlands

by Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski and Ulrich Stingl

Microorganisms 2022, 10(2), 215; https://doi.org/10.3390/microorganisms10020215 - 20 Jan 2022

Cited by 5 | Viewed by 2943

Abstract

Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This study provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) together with nutrient concentrations and environmental parameters at 14 sites along two transects covering two distinctly different drainages: the peat-based Shark River Slough (SRS) and marl-based Taylor Slough/Panhandle (TS/Ph). Both bacterial as well as eukaryotic community structures varied significantly along the salinity gradient. Although freshwater communities were relatively similar in both transects, bacterioplankton community composition at the ecotone (where freshwater and marine water mix) differed significantly. The most abundant taxa in the freshwater marshes include heterotrophic Polynucleobacter sp. and potentially phagotrophic cryptomonads of the genus Chilomonas, both of which could be key players in the transfer of detritus-based biomass to higher trophic levels. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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13 pages, 2339 KiB

Open AccessArticle

Photosynthetic Characteristics of Smaller and Larger Cell Size-Fractioned Phytoplankton Assemblies in the Daya Bay, Northern South China Sea

by Guangming Mai, Xingyu Song, Xiaomin Xia, Zengling Ma, Yehui Tan and Gang Li

Microorganisms 2022, 10(1), 16; https://doi.org/10.3390/microorganisms10010016 - 23 Dec 2021

Cited by 4 | Viewed by 2265

Abstract

Cell size of phytoplankton is known to influence their physiologies and, consequently, marine primary production. To characterize the cell size-dependent photophysiology of phytoplankton, we comparably explored the photosynthetic characteristics of piconano- (<20 µm) and micro-phytoplankton cell assemblies (>20 µm) in the Daya Bay, northern South China Sea, using a 36-h in situ high-temporal-resolution experiment. During the experimental periods, the phytoplankton biomass (Chl a) in the surface water ranged from 0.92 to 5.13 μg L⁻¹, which was lower than that in bottom layer (i.e., 1.83–6.84 μg L⁻¹). Piconano-Chl a accounted for 72% (mean value) of the total Chl a, with no significant difference between the surface and bottom layers. The maximum photochemical quantum yield (F_V/F_M) of Photosystem II (PS II) and functional absorption cross-section of PS II photochemistry (σ_{PS II}) of both piconano- and micro-cells assemblies varied inversely with solar radiation, but this occurred to a lesser extent in the former than in the latter ones. The σ_{PS II} of piconano- and micro-cell assemblies showed a similar change pattern to the F_V/F_M in daytime, but not in nighttime. Moreover, the fluorescence light curve (FLC)-derived light utilization efficiency (α) displayed the same daily change pattern as the F_V/F_M, and the saturation irradiance (E_K) and maximal rETR (rETR_max) mirrored the change in the solar radiation. The F_V/F_M and σ_{PS II} of the piconano-cells were higher than their micro-counterparts under high solar light; while the E_K and rETR_max were lower, no matter in what light regimes. In addition, our results indicate that the F_V/F_M of the micro-cell assembly varied quicker in regard to Chl a change than that of the piconano-cell assembly, indicating the larger phytoplankton cells are more suitable to grow than the smaller ones in the Daya Bay through timely modulating the PS II activity. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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13 pages, 2700 KiB

Open AccessArticle

Lowering pO₂ Interacts with Photoperiod to Alter Physiological Performance of the Coastal Diatom Thalassiosira pseudonana

by Bokun Chen, Jihua Liu, Ge Xu and Gang Li

Microorganisms 2021, 9(12), 2541; https://doi.org/10.3390/microorganisms9122541 - 09 Dec 2021

Cited by 7 | Viewed by 2244

Abstract

Exacerbating deoxygenation is extensively affecting marine organisms, with no exception for phytoplankton. To probe these effects, we comparably explored the growth, cell compositions, photosynthesis, and transcriptome of a diatom Thalassiosira pseudonana under a matrix of pO₂ levels and Light:Dark cycles at an optimal growth light. The growth rate (μ) of T. pseudonana under a 8:16 L:D cycle was enhanced by 34% by low pO₂ but reduced by 22% by hypoxia. Under a 16:8 L:D cycle, however, the μ decreased with decreasing pO₂ level. The cellular Chl a content decreased with decreasing pO₂ under a 8:16 L:D cycle, whereas the protein content decreased under a 16:8 L:D cycle. The prolonged photoperiod reduced the Chl a but enhanced the protein contents. The lowered pO₂ reduced the maximal PSII photochemical quantum yield (F_V/F_M), photosynthetic oxygen evolution rate (Pn), and respiration rate (Rd) under the 8:16 or 16:8 L:D cycles. Cellular malondialdehyde (MDA) content and superoxide dismutase (SOD) activity were higher under low pO₂ than ambient pO₂ or hypoxia. Moreover, the prolonged photoperiod reduced the F_V/F_M and Pn among all three pO₂ levels but enhanced the Rd, MDA, and SOD activity. Transcriptome data showed that most of 26 differentially expressed genes (DEGs) that mainly relate to photosynthesis, respiration, and metabolism were down-regulated by hypoxia, with varying expression degrees between the 8:16 and 16:8 L:D cycles. In addition, our results demonstrated that the positive or negative effect of lowering pO₂ upon the growth of diatoms depends on the pO₂ level and is mediated by the photoperiod. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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16 pages, 2646 KiB

Open AccessArticle

Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea

by Ruba Abdulrahman Ashy, Curtis A. Suttle and Susana Agustí

Microorganisms 2021, 9(6), 1269; https://doi.org/10.3390/microorganisms9061269 - 11 Jun 2021

Cited by 7 | Viewed by 3287

Abstract

Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 10⁶ viruses mL⁻¹ and 1.9 to 3.2 × 10⁵ bacteria mL⁻¹, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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15 pages, 4160 KiB

Open AccessArticle

Composition of Prokaryotic and Eukaryotic Microbial Communities in Waters around the Florida Reef Tract

by Peeter Laas, Kelly Ugarelli, Michael Absten, Breege Boyer, Henry Briceño and Ulrich Stingl

Microorganisms 2021, 9(6), 1120; https://doi.org/10.3390/microorganisms9061120 - 21 May 2021

Cited by 10 | Viewed by 2727

Abstract

The Florida Keys, a delicate archipelago of sub-tropical islands extending from the south-eastern tip of Florida, host the vast majority of the only coral barrier reef in the continental United States. Abiotic as well as microbial components of the surrounding waters are pivotal for the health of reef habitats, and thus could play an important role in understanding the development and transmission of coral diseases in Florida. In this study, we analyzed microbial community structure and abiotic factors in waters around the Florida Reef Tract. Both bacterial and eukaryotic community structure were significantly linked with variations in temperature, dissolved oxygen, and total organic carbon values. High abundances of copiotrophic bacteria as well as several potentially harmful microbes, including coral pathogens, fish parasites and taxa that have been previously associated with Red Tide and shellfish poisoning were present in our datasets and may have a pivotal impact on reef health in this ecosystem. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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20 pages, 3686 KiB

Open AccessArticle

Biogeographical Distribution and Community Assembly of Active Protistan Assemblages along an Estuary to a Basin Transect of the Northern South China Sea

by Ran Li, Chen Hu, Jianning Wang, Jun Sun, Ying Wang, Nianzhi Jiao and Dapeng Xu

Microorganisms 2021, 9(2), 351; https://doi.org/10.3390/microorganisms9020351 - 10 Feb 2021

Cited by 7 | Viewed by 3530

Abstract

Marine protists are essential for globally critical biological processes, including the biogeochemical cycles of matter and energy. However, compared with their prokaryotic counterpart, it remains largely unclear how environmental factors determine the diversity and distribution of the active protistan communities on the regional scale. In the present study, the biodiversity, community composition, and potential drivers of the total, abundant, and rare protistan groups were studied using high throughput sequencing on the V9 hyper-variable regions of the small subunit ribosomal RNA (SSU rRNA) along an estuary to basin transect in the northern South China Sea. Overall, Bacillariophyta and Cercozoa were abundant in the surface water; heterotrophic protists including Spirotrichea and marine stramenopiles 3 (MAST-3) were more abundant in the subsurface waters near the heavily urbanized Pearl River estuary; Chlorophyta and Pelagophyceae were abundant at the deep chlorophyll maximum depth, while Hacrobia, Radiolaria, and Excavata were the abundant groups in the deep water. Salinity, followed by water depth, temperature, and other biological factors, were the primary factors controlling the distinct vertical and horizontal distribution of the total and abundant protists. Rare taxa were driven by water depth, followed by temperature, salinity, and the concentrations of PO₄³⁻. The active protistan communities were mainly driven by dispersal limitation, followed by drift and other ecological processes. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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Other

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15 pages, 3498 KiB

Open AccessBrief Report

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

by Xiao-Peng Du, Zhong-Hua Cai, Ping Zuo, Fan-Xu Meng, Jian-Ming Zhu and Jin Zhou

Microorganisms 2020, 8(1), 107; https://doi.org/10.3390/microorganisms8010107 - 12 Jan 2020

Cited by 10 | Viewed by 3159

Abstract

Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions. Full article

(This article belongs to the Special Issue Planktonic Coastal Microbial Communities – Composition, Seasonal Variation, Genomics, and Physiology)

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