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Stenow R, Robertson EK, Kourtchenko O, Whitehouse MJ, Pinder MIM, Benvenuto G, Töpel M, Godhe A, Ploug H. Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions. Environ Microbiol 2024; 26:e16625. [PMID: 38653479 DOI: 10.1111/1462-2920.16625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Diatoms can survive long periods in dark, anoxic sediments by forming resting spores or resting cells. These have been considered dormant until recently when resting cells of Skeletonema marinoi were shown to assimilate nitrate and ammonium from the ambient environment in dark, anoxic conditions. Here, we show that resting cells of S. marinoi can also perform dissimilatory nitrate reduction to ammonium (DNRA), in dark, anoxic conditions. Transmission electron microscope analyses showed that chloroplasts were compacted, and few large mitochondria had visible cristae within resting cells. Using secondary ion mass spectrometry and isotope ratio mass spectrometry combined with stable isotopic tracers, we measured assimilatory and dissimilatory processes carried out by resting cells of S. marinoi under dark, anoxic conditions. Nitrate was both respired by DNRA and assimilated into biomass by resting cells. Cells assimilated nitrogen from urea and carbon from acetate, both of which are sources of dissolved organic matter produced in sediments. Carbon and nitrogen assimilation rates corresponded to turnover rates of cellular carbon and nitrogen content ranging between 469 and 10,000 years. Hence, diatom resting cells can sustain their cells in dark, anoxic sediments by slowly assimilating and respiring substrates from the ambient environment.
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Affiliation(s)
- Rickard Stenow
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Matthew I M Pinder
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
- IVL-Swedish Environmental Research Institute, Gothenburg, SE, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
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Stenow R, Robertson EK, Whitehouse MJ, Ploug H. Single cell dynamics and nitrogen transformations in the chain forming diatom Chaetoceros affinis. THE ISME JOURNAL 2023; 17:2070-2078. [PMID: 37723340 PMCID: PMC10579250 DOI: 10.1038/s41396-023-01511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
Colony formation in phytoplankton is often considered a disadvantage during nutrient limitation in aquatic systems. Using stable isotopic tracers combined with secondary ion mass spectrometry (SIMS), we unravel cell-specific activities of a chain-forming diatom and interactions with attached bacteria. The uptake of 13C-bicarbonate and15N-nitrate or 15N-ammonium was studied in Chaetoceros affinis during the stationary growth phase. Low cell-to-cell variance of 13C-bicarbonate and 15N-nitrate assimilation within diatom chains prevailed during the early stationary phase. Up to 5% of freshly assimilated 13C and 15N was detected in attached bacteria within 12 h and supported bacterial C- and N-growth rates up to 0.026 h-1. During the mid-stationary phase, diatom chain-length decreased and 13C and 15N-nitrate assimilation was significantly higher in solitary cells as compared to that in chain cells. During the late stationary phase, nitrate assimilation ceased and ammonium assimilation balanced C fixation. At this stage, we observed highly active cells neighboring inactive cells within the same chain. In N-limited regimes, bacterial remineralization of N and the short diffusion distance between neighbors in chains may support surviving cells. This combination of "microbial gardening" and nutrient transfer within diatom chains represents a strategy which challenges current paradigms of nutrient fluxes in plankton communities.
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Affiliation(s)
- Rickard Stenow
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden.
| | - Elizabeth K Robertson
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden
| | - Martin J Whitehouse
- Swedish Museum of Natural History, Box 50 007, SE, 104 05, Stockholm, Sweden
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden
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Cruz QSD, Cutrim MVJ, Santos TP, Sá AKDDS, Cavalcanti-Lima LF. Environmental heterogeneity of a tropical river-to-sea continuum and its relationship with structure and phytoplankton dynamics - Lençóis Maranhenses National Park. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105950. [PMID: 36934510 DOI: 10.1016/j.marenvres.2023.105950] [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: 01/02/2023] [Revised: 02/26/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
β-diversity and functional traits of phytoplankton indicators associated with environmental heterogeneity were investigated as environmental quality descriptors in coastal (CS), estuarine (ES), and limnetic (LS) sectors in a tropical river-to-sea ecosystem. Results showed that environmental heterogeneity was marked by spatial differences, contributing to biological heterogeneity. Sporadic and recurrent blooms were associated with environmental spatiotemporal variations and reflected a reduction in ES α-diversity. Salinity acted as an environmental filter that governed the structure and dynamics of the community. The spatial heterogeneity and high turnover of phytoplankton resulted in reliable bioindicators selection. Colonial, bloom-forming and harmful species were associated with highly suspended particulate matter (SPM) because these species are better adapted to these conditions. Species small in size were associated with high concentrations of silicate and chlorophyll-a in the ES because of the occurrence of diatom recurrent blooms. Most flagellates indicators genera have bloom-forming potential. Integrating morphofunctional with taxonomic approaches enabled detailed observations of environmental filters, supporting the selection of priority species and areas for introducing biodiversity monitoring programs and conservation in tropical ecosystems.
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Affiliation(s)
- Quedyane Silva da Cruz
- Federal University of Maranhão, Cidade Universitária Dom Delgado, Portugueses Road, N°1966, 65080-805, São Luís, Maranhão, Brazil
| | - Marco Valério Jansen Cutrim
- Federal University of Maranhão, Cidade Universitária Dom Delgado, Portugueses Road, N°1966, 65080-805, São Luís, Maranhão, Brazil.
| | - Taiza Pimentel Santos
- Federal University of Maranhão, Cidade Universitária Dom Delgado, Portugueses Road, N°1966, 65080-805, São Luís, Maranhão, Brazil
| | - Ana Karoline Duarte Dos Santos Sá
- Federal Institute of Education, Science and Technology of Maranhão (IFMA), Rosário Campus, BR 402, Km 3, Sapucaia District, 65150-000, Rosário, Maranhão, Brazil
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Liu S, Wang Y, Xu Q, Zhang M, Chen N. Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation. BMC Genomics 2021; 22:746. [PMID: 34654361 PMCID: PMC8520197 DOI: 10.1186/s12864-021-07999-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07999-z.
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Affiliation(s)
- Shuya Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yichao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Qing Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjia Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Nansheng Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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