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von Dassow P. Some fall to sleep slowly: cell biophysics and metabolism of quiescence in diatom resting cells. THE NEW PHYTOLOGIST 2024; 243:1284-1286. [PMID: 38650314 DOI: 10.1111/nph.19768] [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] [Indexed: 04/25/2024]
Abstract
This article is a Commentary on Wang et al. (2024), 243: 1347–1360.
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Affiliation(s)
- Peter von Dassow
- Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, 8331150, Chile
- Millennium Institute of Oceanography, Universidad de Concepción, Barrio Universitario S/N, Concepción, Región Biobío, 4070112, Chile
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, 80121, Italy
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2
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Li S, Nilsson E, Seidel L, Ketzer M, Forsman A, Dopson M, Hylander S. Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming. Front Microbiol 2024; 15:1369102. [PMID: 38596378 PMCID: PMC11002985 DOI: 10.3389/fmicb.2024.1369102] [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: 01/11/2024] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then used to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.
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Affiliation(s)
- Songjun Li
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Laura Seidel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marcelo Ketzer
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Samuel Hylander
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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Mailli AA, Jakt LM, Reiss H, Kopp ME, Moum TB. Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes. Mar Genomics 2022; 62:100934. [DOI: 10.1016/j.margen.2022.100934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
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Seidel L, Broman E, Turner S, Ståhle M, Dopson M. Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history. Sci Rep 2021; 11:23384. [PMID: 34862412 PMCID: PMC8642432 DOI: 10.1038/s41598-021-02725-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Coastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood. In this study, we compared 16S rRNA gene amplicon based bacterial communities in coastal sediments of a Baltic Sea basin in November 2013 and 2017 at three sites along a water depth gradient with varying bottom water oxygen histories. The shallow site showed changes of only 1.1% in relative abundance of bacterial populations in 2017 compared to 2013, while the deep oxygen-deficient site showed up to 11% changes in relative abundance including an increase of sulfate-reducing bacteria along with a 36% increase in organic matter content. The data suggested that bacterial communities in shallow sediments were more resilient to seasonal oxygen decline, while bacterial communities in sediments subjected to long-term hypoxia seemed to be sensitive to oxygen changes and were likely to be under hypoxic/anoxic conditions in the future. Our data demonstrate that future climate changes will likely fuel eutrophication related spread of low oxygen zones.
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Affiliation(s)
- Laura Seidel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Magnus Ståhle
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Behrenfeld MJ, Halsey KH, Boss E, Karp‐Boss L, Milligan AJ, Peers G. Thoughts on the evolution and ecological niche of diatoms. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1457] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Michael J. Behrenfeld
- Department of Botany and Plant Pathology Oregon State University 4575 SW Research Way Corvallis Oregon 97333 USA
| | - Kimberly H. Halsey
- Department of Microbiology Oregon State University Nash Hall 226 Corvallis Oregon 97331 USA
| | - Emmanuel Boss
- School of Marine Sciences University of Maine 5706 Aubert Hall Orono Maine 04469‐5706 USA
| | - Lee Karp‐Boss
- School of Marine Sciences University of Maine 5706 Aubert Hall Orono Maine 04469‐5706 USA
| | - Allen J. Milligan
- Department of Botany and Plant Pathology Oregon State University 4575 SW Research Way Corvallis Oregon 97333 USA
| | - Graham Peers
- Department of Biology Colorado State University Biology Building, Room 111, 1878 Campus Delivery Fort Collins Colorado 80523‐1878 USA
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Uritskiy G, Tisza MJ, Gelsinger DR, Munn A, Taylor J, DiRuggiero J. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community. Environ Microbiol 2020; 23:3401-3417. [DOI: 10.1111/1462-2920.15023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/12/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Gherman Uritskiy
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
| | - Michael J. Tisza
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Laboratory of Cellular Oncology NCI, NIH Bethesda MD 20892‐4263 USA
| | | | - Adam Munn
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
| | - James Taylor
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA
| | - Jocelyne DiRuggiero
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Department of Earth and Planetary Sciences Johns Hopkins University Baltimore MD 21218 USA
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Kamp A, Petro C, Røy H, Nielsen S, Carvalho P, Stief P, Schramm A. Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms. FEMS Microbiol Ecol 2018; 94:5040219. [PMID: 29931199 DOI: 10.1093/femsec/fiy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1.6 cm into the sediment. Intracellular nitrate contents were particularly high at stations where chlorophyll contents suggested high settling rates of pelagic primary production. The depth distribution of intracellular nitrate matched that of the diatom-specific photopigment fucoxanthin in the upper 1.6 cm and calculations support that diatoms are the major nitrate-storing microbes in these sediments. In contrast, other known nitrate-storing microbes, such as sulfide-oxidizing bacteria and foraminifers, played only a minor role, if any. Strikingly, 18S rRNA gene sequencing revealed that the majority of the diatoms in the sediment were pelagic species. We conclude that intracellular nitrate stored by pelagic diatoms is transported to the seafloor by settling phytoplankton blooms, implying a so far overlooked 'biological nitrate pump'.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.,Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caitlin Petro
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Susanne Nielsen
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Pedro Carvalho
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Peter Stief
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Broman E, Sachpazidou V, Pinhassi J, Dopson M. Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism. Front Microbiol 2017; 8:2453. [PMID: 29312168 PMCID: PMC5733055 DOI: 10.3389/fmicb.2017.02453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 01/24/2023] Open
Abstract
The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.
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Affiliation(s)
- Elias Broman
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Varvara Sachpazidou
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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