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Ryckman M, Gantois N, Dominguez RG, Desramaut J, Li LL, Even G, Audebert C, Devos DP, Chabé M, Certad G, Monchy S, Viscogliosi E. Molecular Identification and Subtype Analysis of Blastocystis sp. Isolates from Wild Mussels ( Mytilus edulis) in Northern France. Microorganisms 2024; 12:710. [PMID: 38674653 PMCID: PMC11051716 DOI: 10.3390/microorganisms12040710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Blastocystis sp. is the most common single-celled eukaryote colonizing the human gastrointestinal tract worldwide. Because of the proven zoonotic potential of this protozoan, sustained research is therefore focused on identifying various reservoirs of transmission to humans, and in particular animal sources. Numerous groups of animals are considered to be such reservoirs due to their handling or consumption. However, some of them, including mollusks, remain underexplored. Therefore, a molecular epidemiological survey conducted in wild mussels was carried out in Northern France (Hauts-de-France region) to evaluate the frequency and subtypes (STs) distribution of Blastocystis sp. in these bivalve mollusks. For this purpose, 100 mussels (Mytilus edulis) were randomly collected in two sampling sites (Wimereux and Dannes) located in the vicinity of Boulogne-sur-Mer. The gills and gastrointestinal tract of each mussel were screened for the presence of Blastocystis sp. by real-time polymerase chain reaction (qPCR) assay followed by direct sequencing of positive PCR products and subtyping through phylogenetic analysis. In parallel, sequences of potential representative Blastocystis sp. isolates that were previously obtained from temporal surveys of seawater samples at marine stations offshore of Wimereux were integrated in the present analysis. By taking into account the qPCR results from all mussels, the overall prevalence of the parasite was shown to reach 62.0%. In total, more than 55% of the positive samples presented mixed infections. In the remaining mussel samples with a single sequence, various STs including ST3, ST7, ST14, ST23, ST26 and ST44 were reported with varying frequencies. Such distribution of STs coupled with the absence of a predominant ST specific to these bivalves strongly suggested that mussels might not be natural hosts of Blastocystis sp. and might rather be carriers of parasite isolates from both human and animal (bovid and birds) waste. These data from mussels together with the molecular identification of isolates from marine stations were subsequently discussed along with the local geographical context in order to clarify the circulation of this protozoan in this area. The identification of human and animal STs of Blastocystis sp. in mussels emphasized the active circulation of this protozoan in mollusks and suggested a significant environmental contamination of fecal origin. This study has provided new insights into the host/carrier range and transmission of Blastocystis sp. and emphasized its potential as an effective sentinel species for water quality and environmental contamination.
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Affiliation(s)
- Manon Ryckman
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
- Université du Littoral Côte d’Opale, CNRS, University Lille, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, F-62930 Wimereux, France; (L.-L.L.); (S.M.)
| | - Nausicaa Gantois
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
| | - Ruben Garcia Dominguez
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | - Jeremy Desramaut
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
| | - Luen-Luen Li
- Université du Littoral Côte d’Opale, CNRS, University Lille, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, F-62930 Wimereux, France; (L.-L.L.); (S.M.)
| | - Gaël Even
- GD Biotech—Gènes Diffusion, F-59000 Lille, France; (G.E.); (C.A.)
- PEGASE-Biosciences (Plateforme d’Expertises Génomiques Appliquées aux Sciences Expérimentales), Institut Pasteur de Lille, F-59000 Lille, France
| | - Christophe Audebert
- GD Biotech—Gènes Diffusion, F-59000 Lille, France; (G.E.); (C.A.)
- PEGASE-Biosciences (Plateforme d’Expertises Génomiques Appliquées aux Sciences Expérimentales), Institut Pasteur de Lille, F-59000 Lille, France
| | - Damien Paul Devos
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | - Magali Chabé
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
| | - Gabriela Certad
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
- Délégation à la Recherche Clinique et à l’Innovation, Groupement des Hôpitaux de l’Institut Catholique de Lille, F-59000 Lille, France
| | - Sébastien Monchy
- Université du Littoral Côte d’Opale, CNRS, University Lille, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, F-62930 Wimereux, France; (L.-L.L.); (S.M.)
| | - Eric Viscogliosi
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, F-59000 Lille, France; (M.R.); (N.G.); (J.D.); (D.P.D.); (M.C.); (G.C.)
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Zou S, Lian Q, Ni M, Zhou D, Liu M, Zhang X, Chen G, Yuan J. Spatiotemporal assembly and functional composition of planktonic microeukaryotic communities along productivity gradients in a subtropical lake. Front Microbiol 2024; 15:1351772. [PMID: 38440145 PMCID: PMC10909917 DOI: 10.3389/fmicb.2024.1351772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/16/2024] [Indexed: 03/06/2024] Open
Abstract
Microeukaryotes play crucial roles in the microbial loop of freshwater ecosystems, functioning both as primary producers and bacterivorous consumers. However, understanding the assembly of microeukaryotic communities and their functional composition in freshwater lake ecosystems across diverse environmental gradients remains limited. Here, we utilized amplicon sequencing of 18S rRNA gene and multivariate statistical analyses to examine the spatiotemporal and biogeographical patterns of microeukaryotes in water columns (at depths of 0.5, 5, and 10 m) within a subtropical lake in eastern China, covering a 40 km distance during spring and autumn of 2022. Our results revealed that complex and diverse microeukaryotic communities were dominated by Chlorophyta (mainly Chlorophyceae), Fungi, Alveolata, Stramenopiles, and Cryptophyta lineages. Species richness was higher in autumn than in spring, forming significant hump-shaped relationships with chlorophyll a concentration (Chl-a, an indicator of phytoplankton biomass). Microeukaryotic communities exhibited significant seasonality and distance-decay patterns. By contrast, the effect of vertical depth was negligible. Stochastic processes mainly influenced the assembly of microeukaryotic communities, explaining 63, 67, and 55% of community variation for spring, autumn, and both seasons combined, respectively. Trait-based functional analysis revealed the prevalence of heterotrophic and phototrophic microeukaryotic plankton with a trade-off along N:P ratio, Chl-a, and dissolved oxygen (DO) gradients. Similarly, the mixotrophic proportions were significantly and positively correlated with Chl-a and DO concentrations. Overall, our findings may provide useful insights into the assembly patterns of microeukaryotes in lake ecosystem and how their functions respond to environmental changes.
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Affiliation(s)
- Songbao Zou
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Qingping Lian
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Meng Ni
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Dan Zhou
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Mei Liu
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Xin Zhang
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Guangmei Chen
- Zhejiang Fenghe Fishery Co., Ltd., Lishui, Zhejiang, China
| | - Julin Yuan
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, Zhejiang, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Huzhou, Zhejiang, China
- Huzhou Key Laboratory of Aquatic Product Quality Improvement and Processing Technology, Huzhou, Zhejiang, China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
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Meziti A, Smeti E, Daniilides D, Spatharis S, Tsirtsis G, Kormas KA. Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems. PeerJ 2023; 11:e16655. [PMID: 38144191 PMCID: PMC10740597 DOI: 10.7717/peerj.16655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Background-Aim Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions. Methods Protistan community structure analysis was based on the diversity of the V2-V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis. Results It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage. Conclusion Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.
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Affiliation(s)
- Alexandra Meziti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
| | - Evangelia Smeti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, Greece
| | - Daniil Daniilides
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Athens, Greece
| | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
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Wu P, Liu Y, Li C, Zheng Q, Hong Y, Wu J, Xu S, Lin L, Xiao Y, Wang T, Liu Y. Distribution and co-occurrence networks of the bacterial community in sediment cores from the subtropical Daya Bay, China. MARINE POLLUTION BULLETIN 2023; 196:115580. [PMID: 37801799 DOI: 10.1016/j.marpolbul.2023.115580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/01/2023] [Accepted: 09/21/2023] [Indexed: 10/08/2023]
Abstract
The bacterial community plays an important role in biogeochemical cycles in marine sediment. However, little is known about the vertical profiles and co-occurrence patterns of bacterial community in sediment cores from the marine environment. In this study, five sediment cores were taken from a subtropical bay in China, heavily impacted by anthropogenic activities. The bacterial composition in sediment cores was investigated by using high-throughput sequencing of the 16S rRNA gene. A principal coordinates analysis and an adonis analysis of the operational taxonomic unit (OTU) compositions showed that spatial variation, rather than vertical variation, determined the bacterial structure in sediment cores. The bacterial complexity varied greatly across the five sediment cores, and the rare taxa played an important role in supporting the stability of the bacterial network. This study revealed that sediment properties and anthropogenic activities may induce a shift in the bacterial composition in sediment cores of a subtropical bay.
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Affiliation(s)
- Peng Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
| | - Chunhou Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
| | - Qiushi Zheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Shannan Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Lin Lin
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yayuan Xiao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Teng Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yu Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
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Houliez E, Schmitt FG, Breton E, Skouroliakou DI, Christaki U. On the conditions promoting Pseudo-nitzschia spp. blooms in the eastern English Channel and southern North Sea. HARMFUL ALGAE 2023; 125:102424. [PMID: 37220977 DOI: 10.1016/j.hal.2023.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/18/2023] [Accepted: 03/13/2023] [Indexed: 05/25/2023]
Abstract
This study investigated the drivers of the blooms of Pseudo-nitzschia seriata and Pseudo-nitzschia delicatissima complexes in the eastern English Channel and southern North Sea. Phytoplankton data series acquired from 1992 to 2020 were analyzed with a multivariate statistical approach based on Hutchinson's niche concept. P. seriata and P. delicatissima complexes were found to be typically present year round, but they bloomed at different periods because they occupied different realized ecological niches. P. delicatissima complex occupied a more marginal niche and was less tolerant than P. seriata complex. P. delicatissima complex typically bloomed in April-May at the same time as Phaeocystis globosa while P. seriata complex blooms were more frequently observed in June during the decline of low intensity P. globosa blooms. P. delicatissima and P. seriata complexes were both favored by low-silicate environments and relatively low turbulence but they responded differently to water temperature, light, ammonium, phosphate and nitrite + nitrate conditions. Niche shifts and biotic interactions played important roles in the control of the blooms of P. delicatissima and P. seriata complexes. The two complexes occupied different sub-niches during their respective low abundance and bloom periods. The phytoplankton community structure and the number of other taxa presenting a niche overlapping the niches of P. delicatissima and P. seriata complexes also differed between these periods. P. globosa was the taxa contributing the most to the dissimilarity in community structure. P. globosa interacted positively with P. delicatissima complex and negatively with P. seriata complex.
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Affiliation(s)
- Emilie Houliez
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France.
| | - François G Schmitt
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Elsa Breton
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Dimitra-Ioli Skouroliakou
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Urania Christaki
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
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Skouroliakou DI, Breton E, Irion S, Artigas LF, Christaki U. Stochastic and Deterministic Processes Regulate Phytoplankton Assemblages in a Temperate Coastal Ecosystem. Microbiol Spectr 2022; 10:e0242722. [PMID: 36222680 PMCID: PMC9769578 DOI: 10.1128/spectrum.02427-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 01/06/2023] Open
Abstract
Assessing the relative contributions of the interacting deterministic and stochastic ecological processes for phytoplankton community assembly is crucial in understanding and predicting community organization and succession at different temporal and spatial scales. In this study, we hypothesized that deterministic and stochastic ecological processes regulating phytoplankton, present seasonal and repeating patterns. This hypothesis was explored during a 5-year survey (287 samples) conducted at a small spatial scale (~15km) in a temperate coastal ecosystem (eastern English Channel). Microscopy and flow cytometry quantified phytoplankton abundance and biomass, while metabarcoding data allowed an extended evaluation of diversity and the exploration of the ecological processes regulating phytoplankton using null model analysis. Alpha diversity of phytoplankton was governed by the effect of environmental conditions (environmental filtering). Temporal community turnover (beta diversity) evidenced a consistent interannual pattern that determined the phytoplankton seasonal structure. In winter and early spring (from January to March), determinism (homogeneous selection) was the major process in the phytoplankton community assembly. The overall mean in the year was 38%. Stochastic processes (ecological drift) prevailed during the rest of the year from April to December, where the overall mean for the year was 55%. The maximum values were recorded in late spring and summer, which often presented recurrent and transient monospecific phytoplankton peaks. Overall, the prevalence of stochastic processes rendered less predictable seasonal dynamics of phytoplankton communities to future environmental change. IMPORTANCE While ecological deterministic processes are conducive to modeling, stochastic ones are far less predictable. Understanding the overall assembly processes of phytoplankton is critical in tracking and predicting future changes. The novelty of this study was that it addressed a long-posed question, on a pluriannual scale. Was seasonal phytoplankton succession influenced by deterministic processes (e.g., abiotic environment) or by stochastic ones (e.g., dispersal, or ecological drift)? Our results provided strong support for a seasonal and repeating pattern with stochastic processes (drift) prevailing during most of the year and periods with monospecific phytoplankton peaks.
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Affiliation(s)
| | - Elsa Breton
- University Littoral Côte d’Opale, CNRS, Wimereux, France
| | - Solène Irion
- University Littoral Côte d’Opale, CNRS, Wimereux, France
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Xu D, Kong H, Yang EJ, Wang Y, Li X, Sun P, Jiao N, Lee Y, Jung J, Cho KH. Spatial dynamics of active microeukaryotes along a latitudinal gradient: Diversity, assembly process, and co-occurrence relationships. ENVIRONMENTAL RESEARCH 2022; 212:113234. [PMID: 35390306 DOI: 10.1016/j.envres.2022.113234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Recent global warming is profoundly and increasingly influencing the Arctic ecosystem. Understanding how microeukaryote communities respond to changes in the Arctic Ocean is crucial for understanding their roles in the biogeochemical cycles of nutrients and elements. Between July 22 and August 19, 2016, during cruise ARA07, seawater samples were collected along a latitudinal transect extending from the East Sea of Korea to the central Arctic Ocean. Environmental RNA was extracted and the V4 hypervariable regions of the reverse transcribed SSU rRNA were amplified. The sequences generated by high throughput sequencing were clustered into zero-radius OTUs (ZOTUs), and the taxonomic identities of each ZOTU were assigned using SINTAX against the PR2 database. Thus, the diversity, community composition, and co-occurrence networks of size fractionated microeukaryotes were revealed. The present study found: 1) the alpha diversity of pico- and nano-sized microeukaryotes showed a latitudinal diversity gradient; 2) three distinct communities were identified, i.e., the Leg-A, Leg-B surface, and Leg-B subsurface chlorophyll a maximum (SCM) groups; 3) distinct network structure and composition were found in the three groups; and 4) water temperature was identified as the primary factor driving both the alpha and beta diversities of microeukaryotes. This study conducted a comprehensive and systematic survey of active microeukaryotes along a latitudinal gradient, elucidated the diversity, community composition, co-occurrence relationships, and community assembly processes among major microeukaryote assemblages, and will help shed more light on our understanding of the responses of microeukaryote communities to the changing Arctic Ocean.
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Affiliation(s)
- Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
| | - Hejun Kong
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Xinran Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
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8
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Chen Z, Gu T, Wang X, Wu X, Sun J. Oxygen gradients shape the unique structure of picoeukaryotic communities in the Bay of Bengal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152862. [PMID: 35016938 DOI: 10.1016/j.scitotenv.2021.152862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Picoeukaryotic communities respond rapidly to global climate change and play an important role in marine biological food webs and ecosystems. The formation of oxygen minimum zones (OMZ) is facilitated by the stratification of seawater and higher primary production in the surface layer, and the marine picoeukaryotic community this low-oxygen environment is topic of interest. To better understand the picoeukaryotic community assembly mechanisms in an OMZ, we collected samples from the Bay of Bengal (BOB) in October and November 2020 and used 18S rDNA to study the picoeukaryotic communities and their community assembly mechanisms that they are controlled by in deep-sea and hypoxic zones. The results show that deterministic and stochastic processes combine to shape picoeukaryotic communities in the BOB. We divided the water column into three vertical layers: the upper oxycline (UO), the OMZ, and the lower oxycline (LO), based on dissolved oxygen concentrations (dissolved oxygen: UO > LO > OMZ) at vertical depths (from 5 m to 2000 m). Deterministic processes controlled the picoeukaryotic community in the UO, while the picoeukaryotic communities in the OMZ and LO were dominated by stochastic processes. The OMZ had a stronger diffusional limitation and the habitat niche breadth in the UO was wider than that in OMZ and LO. We classified the picoeukaryotic community into three functional composition types (phototrophic, mixotrophic, and heterotrophic); heterotrophs were most abundant in the surveyed area, and the proportion of decreased significantly with increasing depth and decreasing dissolved oxygen. The picoeukaryotes in the investigated area also correlated with temperature, salinity, and nutrients (phosphate, silicate, nitrate, nitrite, and ammonium). These findings contribute to a better understanding of picoeukaryotic communities in deep-sea and low-oxygen environments, their functional structuring, as well as the effects of environmental changes on their community structure.
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Affiliation(s)
- Zhuo Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Ting Gu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xi Wu
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, Hubei 430074, PR China.
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9
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Fang G, Yu H, Sheng H, Chen C, Tang Y, Liang Z. Seasonal variations and co-occurrence networks of bacterial communities in the water and sediment of artificial habitat in Laoshan Bay, China. PeerJ 2022; 9:e12705. [PMID: 35036171 PMCID: PMC8740510 DOI: 10.7717/peerj.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/07/2021] [Indexed: 12/03/2022] Open
Abstract
Marine bacteria in the seawater and seafloor are essential parts of Earth’s biodiversity, as they are critical participants of the global energy flow and the material cycles. However, their spatial-temporal variations and potential interactions among varied biotopes in artificial habitat are poorly understood. In this study, we profiled the variations of bacterial communities among seasons and areas in the water and sediment of artificial reefs using 16S rRNA gene sequencing, and analyzed the potential interaction patterns among microorganisms. Distinct bacterial community structures in the two biotopes were exhibited. The Shannon diversity and the richness of phyla in the sediment were higher, while the differences among the four seasons were more evident in the water samples. The seasonal variations of bacterial communities in the water were more distinct, while significant variations among four areas were only observed in the sediment. Correlation analysis revealed that nitrite and mud content were the most important factors influencing the abundant OTUs in the water and sediment, respectively. Potential interactions and keystone species were identified based on the three co-occurrence networks. Results showed that the correlations among bacterial communities in the sediment were lower than in the water. Besides, the abundance of the top five abundant species and five keystone species had different changing patterns among four seasons and four areas. These results enriched our understanding of the microbial structures, dynamics, and interactions of microbial communities in artificial habitats, which could provide new insights into planning, constructing and managing these special habitats in the future.
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Affiliation(s)
- Guangjie Fang
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Haolin Yu
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Huaxiang Sheng
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Chuanxi Chen
- College of ocean and earth sciences, Xiamen University, Xiamen, Fujian, China
| | - Yanli Tang
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai, Shandong, China
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10
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Fang G, Yu H, Sheng H, Tang Y, Liang Z. Comparative analysis of microbial communities between water and sediment in Laoshan Bay marine ranching with varied aquaculture activities. MARINE POLLUTION BULLETIN 2021; 173:112990. [PMID: 34634629 DOI: 10.1016/j.marpolbul.2021.112990] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
We profiled and compared the bacterial and protist community compositions and dynamics in the Laoshan Bay marine ranching involving varied aquaculture activities. The dominant species, differential species and community compositions among the five aquaculture areas, two habitats and two periods were significantly different. The relationships between microbial communities and environmental factors were analyzed. We found that microbial communities in the water were more sensitive to the environmental changes than sediment, and the responses of bacterial and protist communities to the disturbances were varied. To meet the challenges of higher aquaculture density, the proportion of the positive correlations among co-occurrence networks in the water increased markedly from July to November; while the positive proportion in the sediment was stable. Potential ecological interactions and keystone taxa between bacteria and protists were studied. These results advanced our understanding of how mariculture stressors affect microbial communities in marine ranching.
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Affiliation(s)
- Guangjie Fang
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Haolin Yu
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Huaxiang Sheng
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Yanli Tang
- Fisheries College, Ocean University of China, Qingdao 266002, China.
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai 264200, China
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11
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Li R, Hu C, Wang J, Sun J, Wang Y, Jiao N, Xu D. Biogeographical Distribution and Community Assembly of Active Protistan Assemblages Along an Estuary to a Basin Transect of the Northern South China Sea. Microorganisms 2021; 9:microorganisms9020351. [PMID: 33578968 PMCID: PMC7916720 DOI: 10.3390/microorganisms9020351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/21/2022] Open
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.
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Affiliation(s)
- Ran Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430000, China;
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
- Correspondence: (N.J.); (D.X.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
- Correspondence: (N.J.); (D.X.)
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12
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Gu R, Sun P, Wang Y, Yu F, Jiao N, Xu D. Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China. Front Microbiol 2020; 11:592489. [PMID: 33424795 PMCID: PMC7785585 DOI: 10.3389/fmicb.2020.592489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/27/2020] [Indexed: 11/28/2022] Open
Abstract
Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.
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Affiliation(s)
- Rong Gu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Fengling Yu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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13
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Wang Y, Li G, Shi F, Dong J, Gentekaki E, Zou S, Zhu P, Zhang X, Gong J. Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans. Front Microbiol 2020; 11:601037. [PMID: 33343542 PMCID: PMC7744618 DOI: 10.3389/fmicb.2020.601037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022] Open
Abstract
Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.
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Affiliation(s)
- Yaping Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Guihao Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Fei Shi
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Jun Dong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Songbao Zou
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Ping Zhu
- School of Life Sciences, Ludong University, Yantai, China
| | - Xiaoli Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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14
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Variability and Community Composition of Marine Unicellular Eukaryote Assemblages in a Eutrophic Mediterranean Urban Coastal Area with Marked Plankton Blooms and Red Tides. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12030114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Thessaloniki Bay is a eutrophic coastal area which has been characterized in recent years by frequent and intense phytoplankton blooms and red tides. The aim of the study was to investigate the underexplored diversity of marine unicellular eukaryotes in four different sampling sites in Thessaloniki Bay during a year of plankton blooms, red tides, and mucilage aggregates. High-Throughput Sequencing (HTS) was applied in extracted DNA from weekly water samples targeting the 18S rRNA gene. In almost all samples, phytoplankton blooms and/or red tides and mucilage aggregates were observed. The metabarcoding analysis has detected the known unicellular eukaryotic groups frequently observed in the Bay, dominated by Bacillariophyta and Dinoflagellata, and revealed taxonomic groups previously undetected in the study area (MALVs, MAST, and Cercozoa). The dominant OTUs were closely related to species known to participate in red tides, harmful blooms, and mucilage aggregates. Other OTUs, present also during the blooms in low abundance (number of reads), were closely related to known harmful species, suggesting the occurrence of rare taxa with potential negative impacts on human health not detectable with classical microscopy. Overall, the unicellular eukaryote assemblages showed temporal patterns rather than small-scale spatial separation responding to the variability of physical and chemical factors.
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15
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Sassenhagen I, Irion S, Jardillier L, Moreira D, Christaki U. Protist Interactions and Community Structure During Early Autumn in the Kerguelen Region (Southern Ocean). Protist 2019; 171:125709. [PMID: 32004979 DOI: 10.1016/j.protis.2019.125709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/22/2019] [Accepted: 12/01/2019] [Indexed: 02/03/2023]
Abstract
This study investigated protist community composition and biotic interactions focusing on microplankton at four distinct sites around the Kerguelen Islands (Southern Ocean) after the summer phytoplankton bloom. Protist diversity in different size fractions, sampled with Niskin bottles and plankton nets, was assessed by sequencing of the V4 18S rDNA region. Combining different approaches, i.e. sequencing of different plankton size fractions, and isolation and sequencing of single cells, provided new insights into microbial interactions in protist communities. The communities displayed high variability, including short-term fluctuations in relative abundance of large protists (>35μm) highlighted by the plankton net samples. Size fractionation of protist communities showed high concentrations of free Syndiniales spores but relatively few Syndiniales associated with microplankton, suggesting low parasitic infection in early autumn. Co-variance network analyses and sequencing of individually isolated single cells highlighted the important role of Rhizaria as consumers of a wide range of different diatom taxa. The data also raised the hypothesis that different Syndiniales clades might be directly or indirectly associated with some diatom genera, thus suggesting a potentially wider host range of these parasites than has been previously reported. These associations and the potential impact on carbon fluxes are discussed.
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Affiliation(s)
- Ingrid Sassenhagen
- Laboratoire d'Océanologie et Géosciences, UMR CNRS 8187, Université du Littoral Côte d'Opale, 32 Avenue du Maréchal Foch, 62930 Wimereux, France.
| | - Solène Irion
- Laboratoire d'Océanologie et Géosciences, UMR CNRS 8187, Université du Littoral Côte d'Opale, 32 Avenue du Maréchal Foch, 62930 Wimereux, France
| | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Rue du doyen A. Guinier bât. 360, 91405 Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Rue du doyen A. Guinier bât. 360, 91405 Orsay Cedex, France
| | - Urania Christaki
- Laboratoire d'Océanologie et Géosciences, UMR CNRS 8187, Université du Littoral Côte d'Opale, 32 Avenue du Maréchal Foch, 62930 Wimereux, France
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16
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Armeli Minicante S, Piredda R, Quero GM, Finotto S, Bernardi Aubry F, Bastianini M, Pugnetti A, Zingone A. Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding. Front Microbiol 2019; 10:2736. [PMID: 32038505 PMCID: PMC6988810 DOI: 10.3389/fmicb.2019.02736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 11/28/2022] Open
Abstract
The Lagoon of Venice (LoV) and the Gulf of Venice (GoV), two adjacent coastal Long Term Ecological Research (LTER) sites in the northern Adriatic Sea, represent a transitional/marine coupled ecosystem under the influence of regional and local factors. In this study, these sites were sampled on four dates from April 2016 to February 2017 for environmental DNA and relevant abiotic variables, aiming to assess the relative importance of habitat heterogeneity and connectivity in structuring the protist community. High Throughput Sequencing of V4-18S rRNA gene from 56 samples collected at seven stations produced ca 6 million reads, grouped into 7,336 Operational Taxonomic Units (OTUs) at 97% similarity, which were affiliated to protists belonging to 34 taxonomic groups. The whole community was dominated by Bacillariophyta, especially in spring-summer in the LoV, and by Dinophyta, mainly in the GoV. Ciliophora, Syndiniales, and Cryptophyceae were the next more abundant groups. The community structure varied across the seasons and was different in the two ecosystems, which shared 96% of the reads but showed a high proportion of OTUs distributed preferentially in one of the two sites (specialists) and a different partitioning of trophic categories. GoV specialists were mainly Dinophyceae (>56%), followed by Syndiniales and Bacillariophyta, while the LoV specialists were distributed among several groups, including Bacillariophyta, Syndiniales, Ciliophora, Cryptophyceae, and Trebouxiophyceae. The main abiotic drivers of the differences between protist communities were salinity and temperature, which however explained a minor part of the variance (17%), pointing at a higher relevance of biotic factors and inter-taxa relationships. This was more evident in the LoV, where the network analysis highlighted a higher number of OTUs’ connections than in the GoV. Overall, the metabarcoding approach allowed to depict the composition of the whole protist community in the lagoon and adjacent coastal waters with high resolution, revealing many taxa so far not reported in the area. In addition, despite no clear barrier to dispersal processes, differences in the relative abundance and temporal variability of local protist communities indicate that environmental heterogeneity, in these adjacent and connected ecosystems, can be strong enough to allow for ecological segregation.
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Affiliation(s)
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grazia Marina Quero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stefania Finotto
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Mauro Bastianini
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Adriana Zingone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
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17
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Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition. Pathogens 2019; 8:pathogens8010037. [PMID: 30893890 PMCID: PMC6471099 DOI: 10.3390/pathogens8010037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023] Open
Abstract
Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.
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18
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Ramond P, Sourisseau M, Simon N, Romac S, Schmitt S, Rigaut-Jalabert F, Henry N, de Vargas C, Siano R. Coupling between taxonomic and functional diversity in protistan coastal communities. Environ Microbiol 2019; 21:730-749. [PMID: 30672084 DOI: 10.1111/1462-2920.14537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/19/2019] [Indexed: 01/11/2023]
Abstract
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the operational taxonomic units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade-offs) in order to build the best functional groups. Based on the annotated OTUs and our functional groups, we demonstrated that the functional diversity of marine protist communities varied in parallel with their taxonomic diversity. The coupling between functional and taxonomic diversity was conserved across different protist size classes. However, the smallest size-fraction was characterized by wider taxonomic and functional groups diversity, corroborating the idea that nanoplankton and picoplankton are part of a more stable ecological background on which larger protists and metazoans might develop.
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Affiliation(s)
- Pierre Ramond
- IFREMER, Dyneco Pelagos, BP 70, 29280 Plouzané, France.,Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | - Sarah Romac
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS - FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France
| | - Nicolas Henry
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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19
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Giner CR, Balagué V, Krabberød AK, Ferrera I, Reñé A, Garcés E, Gasol JM, Logares R, Massana R. Quantifying long‐term recurrence in planktonic microbial eukaryotes. Mol Ecol 2019; 28:923-935. [DOI: 10.1111/mec.14929] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Caterina R. Giner
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Vanessa Balagué
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Anders K. Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene) University of Oslo Oslo Norway
| | - Isabel Ferrera
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Albert Reñé
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Esther Garcés
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Josep M. Gasol
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Ramiro Logares
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene) University of Oslo Oslo Norway
| | - Ramon Massana
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
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20
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Stefanidou N, Genitsaris S, Lopez-Bautista J, Sommer U, Moustaka-Gouni M. Unicellular Eukaryotic Community Response to Temperature and Salinity Variation in Mesocosm Experiments. Front Microbiol 2018; 9:2444. [PMID: 30356732 PMCID: PMC6189394 DOI: 10.3389/fmicb.2018.02444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/24/2018] [Indexed: 12/24/2022] Open
Abstract
Climate change has profound impacts on marine biodiversity and biodiversity changes in turn might affect the community sensitivity to impacts of abiotic changes. We used mesocosm experiments and Next Generation Sequencing to study the response of the natural Baltic and Mediterranean unicellular eukaryotic plankton communities (control and +6°C heat shock) to subsequent salinity changes (-5 psu, +5 psu). The impact on Operational Taxonomic Unit (OTU) richness, taxonomic and functional composition and rRNA:rDNA ratios were examined. Our results showed that heat shock leads to lower OTU richness (21% fewer OTUs in the Baltic and 14% fewer in the Mediterranean) and a shift in composition toward pico- and nanophytoplankton and heterotrophic related OTUs. Heat shock also leads to increased rRNA:rDNA ratios for pico- and micrograzers. Less than 18% of shared OTUs were found among the different salinities indicating the crucial role of salinity in shaping communities. The response of rRNA:rDNA ratios varied highly after salinity changes. In both experiments the diversity decrease brought about by heat shock influenced the sensitivity to salinity changes. The heat shock either decreased or increased the sensitivity of the remaining community, depending on whether it removed the more salinity-sensitive or the salinity-tolerant taxa.
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Affiliation(s)
- Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.,School of Economics, Business Administration and Legal Studies, International Hellenic University, Thermi, Greece
| | - Juan Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States
| | - Ulrich Sommer
- Geomar Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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21
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Hernández-Ruiz M, Barber-Lluch E, Prieto A, Álvarez-Salgado XA, Logares R, Teira E. Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system. Environ Microbiol 2018; 20:2955-2973. [DOI: 10.1111/1462-2920.14313] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/12/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Marta Hernández-Ruiz
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Esther Barber-Lluch
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Antero Prieto
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | | | - Ramiro Logares
- Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC); Barcelona, 08003 Spain
| | - Eva Teira
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
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22
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Rachik S, Christaki U, Li LL, Genitsaris S, Breton E, Monchy S. Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel). PLoS One 2018; 13:e0196987. [PMID: 29746519 PMCID: PMC5944946 DOI: 10.1371/journal.pone.0196987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023] Open
Abstract
The diversity of planktonic eukaryotic microbes was studied at a coastal station of the eastern English Channel (EEC) from March 2011 to July 2015 (77 samples) using high throughput sequencing (454-pyrosequencing and Illumina) of the V2-V3 hypervariable region of the 18S SSU rDNA gene. Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing >1% of the total number of OTUs) were observed with the two methods (Kolmogorov-Smirnov p-value = 0.22). Eight super-groups were identified throughout all samples: Alveolata, Stramenopiles, Opisthokonta, Hacrobia, Archeaplastida, Apusozoa, Rhizaria, and Amoebozoa (ordered by decreasing OTU richness). To gain further insight into microbial activity in the EEC, ribosomal RNA was extracted for samples from 2013–2015 (30 samples). Analysis of 18S rDNA and rRNA sequences led to the detection of 696 and 700 OTUs, respectively. Cluster analysis based on OTUs’ abundance indicated three major seasonal groups that were associated to spring, winter/autumn, and summer conditions. The clusters inferred from rRNA data showed a clearer seasonal representation of the community succession than the one based on rDNA. The rRNA/rDNA ratio was used as a proxy for relative cell activity. When all OTUs were considered, the average rRNA:rDNA ratio showed a linear trend around the 1:1 line, suggesting a linear relation between OTU abundance (rDNA) and activity (rRNA). However, this ratio was highly variable over time when considering individual OTUs. Interestingly, the OTU affiliated with P. globosa displayed rRNA:rDNA ratio that allowed to delimit high vs low abundance and high vs low activity periods. It unveiled quite well the Phaeocystis bloom dynamic regarding cell proliferation and activity, and could even be used as early indicator of an upcoming bloom.
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Affiliation(s)
- Sara Rachik
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Urania Christaki
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Luen Luen Li
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Savvas Genitsaris
- International Hellenic University, School of Economics, Business Administration & Legal Studies, Thessaloniki, Greece
| | - Elsa Breton
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Sébastien Monchy
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
- * E-mail:
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23
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Berdjeb L, Parada A, Needham DM, Fuhrman JA. Short-term dynamics and interactions of marine protist communities during the spring-summer transition. ISME JOURNAL 2018; 12:1907-1917. [PMID: 29599520 DOI: 10.1038/s41396-018-0097-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 02/15/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022]
Abstract
We examined the short-term variability, by daily to weekly sampling, of protist assemblages from March to July in surface water of the San Pedro Ocean Time-series station (eastern North Pacific), by V4 Illumina sequencing of the 18S rRNA gene. The sampling period encompassed a spring bloom followed by progression to summer conditions. Several protistan taxa displayed sharp increases and declines, with whole community Bray-Curtis dissimilarities of adjacent days being 66% in March and 40% in May. High initial abundance of parasitic Cercozoa Cryothecomonas longipes and Protaspis grandis coincided with a precipitous decline of blooming Pseudo-nitzschia diatoms, possibly suggesting their massive infection by these parasites; these cercozoans were hardly detectable afterwards. Canonical correspondence analysis indicated a limited predictability of community variability from environmental factors. This indicates that other factors are relevant in explaining changes in protist community composition at short temporal scales, such as interspecific relationships, stochastic processes, mixing with adjacent water, or advection of patches with different protist communities. Association network analysis revealed that interactions between the many parasitic OTUs and other taxa were overwhelmingly positive and suggest that although sometimes parasites may cause a crash of host populations, they may often follow their hosts and do not regularly cause enough mortality to potentially create negative correlations at the daily to weekly time scales we studied.
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Affiliation(s)
- Lyria Berdjeb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alma Parada
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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24
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Yang W, Zheng Z, Zheng C, Lu K, Ding D, Zhu J. Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:720-727. [PMID: 28866399 DOI: 10.1016/j.scitotenv.2017.08.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics.
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Affiliation(s)
- Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Cheng Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Dewen Ding
- The First Institute of Oceanography, State Oceanic Administration (SOA), Qingdao 266061, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315211, China.
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25
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Piredda R, Tomasino MP, D'Erchia AM, Manzari C, Pesole G, Montresor M, Kooistra WHCF, Sarno D, Zingone A. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site. FEMS Microbiol Ecol 2016; 93:fiw200. [DOI: 10.1093/femsec/fiw200] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2016] [Indexed: 11/13/2022] Open
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