Microbial biooceanography articles within Nature Communications

Featured

• Article
  28 March 2024 | Open Access

  Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

  Identifying the metabolic interactions that underlie microbial communities is challenging. Here, the authors combine Tara Oceans -omics data with co-activity networks and genome-scale metabolic models to predict biotic interactions among planktonic prokaryotes in the upper ocean.

  • Nils Giordano
  • , Marinna Gaudin
  •  & Samuel Chaffron

• Article
  07 March 2024 | Open Access

  Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre

  This study shows that a multitrophic community model jointly recapitulates diel rhythms in abundances of Prochlorococcus picocyanobacteria, as well as viral infection, viral abundances and grazer abundances. Model-data integration implies that grazing predominantly controls Prochlorococcus abundances in surface waters of the North Pacific Subtropical Gyre, despite high viral densities.

  • Stephen J. Beckett
  • , David Demory
  •  & Joshua S. Weitz

• Article
  19 February 2024 | Open Access

  Patterns in the temporal complexity of global chlorophyll concentration

  For satellite data, noisy observations can often be ignored in favour of smooth trends and signals. Here, the authors developed a method to quantify the complexity of chlorophyll-α time series on a global scale, which led to the discovery of greater differences among regions than previously recognized.

  • Vitul Agarwal
  • , Jonathan Chávez-Casillas
  •  & Colleen B. Mouw

• Article
  07 November 2023 | Open Access

  Planktonic microbial signatures of sinking particle export in the open ocean’s interior

  Sinking of organic particles to the deep seafloor is fundamental to ocean carbon cycling. Here, the authors investigate prokaryotic communities in sinking and suspended particles, identifying depth-specific signatures of particle export and carbon cycling processes.

  • Fuyan Li
  • , Andrew Burger
  •  & Edward F. DeLong

• Article
  17 August 2023 | Open Access

  Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation

  Nutrient limitation is a key constraint on ocean productivity. Here, by analysing a compilation of field experiments spanning the global ocean, this study shows that increasing the number of different nutrients supplied significantly increases net phytoplankton growth, suggesting multiple nutrients are often approaching co-limiting levels.

  • Thomas J. Browning
  •  & C. Mark Moore

• Comment
  10 May 2023 | Open Access

  Phosphate limitation and ocean acidification co-shape phytoplankton physiology and community structure

  This Comment discusses the complexity of how ocean acidification and phosphate limitation affect phytoplankton physiologies, as well as what future research is needed to address remaining crucial questions.

  • Senjie Lin

• Article
  21 November 2022 | Open Access

  Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers

  Planktonic foraminifera are key to understanding paleoclimate and plankton evolution, but their origins are unclear. Here, the authors use a molecular clock to suggest that benthic foraminifera dispersed in plankton and renew planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction.

  • Raphaël Morard
  • , Christiane Hassenrück
  •  & Michal Kucera

• Article
  11 May 2022 | Open Access

  Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter

  Computational methods to analyse microbial systems rely on reference databases which do not capture their full functional diversity. Here the authors develop a deep learning model and apply it using transfer learning, creating biologically useful models for multiple different tasks.

  • A. Hoarfrost
  • , A. Aptekmann
  •  & Y. Bromberg

• Article
  04 May 2022 | Open Access

  Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

  Coastal upwelling sustains some of the most productive ocean regions. Here, the authors find that spatial patterns and temporal changes in nutrient supply explain marine microbial community structure and diversity in the Southern California Current region.

  • Chase C. James
  • , Andrew D. Barton
  •  & Andrew E. Allen

• Article
  29 March 2022 | Open Access

  Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates

  Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.

  • Trang T. H. Nguyen
  • , Emily J. Zakem
  •  & Naomi M. Levine

• Article
  10 February 2022 | Open Access

  Overlooked and widespread pennate diatom-diazotroph symbioses in the sea

  Nitrogen depletion in the ocean provides a favourable niche for nitrogen-fixing cyanobacteria, which can form symbioses with eukaryotic algae. This study reports the discovery of two distinct marine pennate diatom–diazotroph symbioses, which had previously only been observed in freshwater environments and represent an overlooked but widespread source of bioavailable nitrogen in marine habitats.

  • Christopher R. Schvarcz
  • , Samuel T. Wilson
  •  & Grieg F. Steward

• Article
  10 January 2022 | Open Access

  Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

  Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.

  • Tianjiao Dai
  • , Donghui Wen
  •  & Yunfeng Yang

• Article
  17 November 2021 | Open Access

  Seasonal mixed layer depth shapes phytoplankton physiology, viral production, and accumulation in the North Atlantic

  Phytoplankton are important primary producers. Here the authors investigate phytoplankton physiological changes associated with bloom phases and mixing regimes in the North Atlantic, finding that stratification and deep mixing shape accumulation rates by altering physiology and viral production.

  • Ben P. Diaz
  • , Ben Knowles
  •  & Kay D. Bidle

• Article
  05 November 2021 | Open Access

  Marine phytoplankton functional types exhibit diverse responses to thermal change

  Phytoplankton communities are important players in biogeochemical processes, but are sensitive to global warming. Here, a meta-analysis shows how the varied responses of phytoplankton to rising temperatures could potentially alter growth dynamics and community structure in a future ocean.

  • S. I. Anderson
  • , A. D. Barton
  •  & T. A. Rynearson

• Article
  16 September 2021 | Open Access

  The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

  Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.

  • Kara Martin
  • , Katrin Schmidt
  •  & Thomas Mock

• Article
  10 September 2021 | Open Access

  Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia

  Trends in antimicrobial resistance (AMR) in aquatic food animals are seldom documented, particularly in Asia. Here, Schar et al. review 749 point prevalence surveys, describing AMR trends in Asian aquaculture and fisheries over two decades, and identifying resistance hotspots as well as regions that would benefit most from future surveillance efforts.

  • Daniel Schar
  • , Cheng Zhao
  •  & Thomas P. Van Boeckel

• Article
  06 July 2021 | Open Access

  Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

  Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.

  • Juan José Pierella Karlusich
  • , Eric Pelletier
  •  & Rachel A. Foster

• Article
  09 February 2021 | Open Access

  Manganese co-limitation of phytoplankton growth and major nutrient drawdown in the Southern Ocean

  Southern Ocean productivity is a crucial component of the carbon cycle, but phytoplankton there are thought to be limited by iron. Here the authors conduct trace metal incubation experiments across the Drake Passage, finding that manganese can play an unexpected role in restricting phytoplankton growth.

  • Thomas J. Browning
  • , Eric P. Achterberg
  •  & Edward Mawji

• Article
  22 October 2020 | Open Access

  Marine plankton show threshold extinction response to Neogene climate change

  High-latitude records show large diversity losses of marine plankton, such as radiolarians, with historical climate change. Here, Trubovitz et al. present a low-latitude record spanning the last 10 million years, finding that many high-latitude radiolarians did not shift equatorward but instead went extinct.

  • Sarah Trubovitz
  • , David Lazarus
  •  & Paula J. Noble

• Article
  29 July 2019 | Open Access

  Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming

  Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

  • Melody S. Clark
  • , Leyre Villota Nieva
  •  & Lloyd S. Peck

• Article
  29 April 2019 | Open Access

  Light-dependent grazing can drive formation and deepening of deep chlorophyll maxima

  Previous work on the mechanisms responsible for the formation of deep chlorophyll maxima (DCM) has focused on phytoplankton physiology and behaviour. Here the authors used mathematical models informed by laboratory grazing studies to show that microzooplankton has a mechanism that can reduce phytoplankton biomass but allows accumulation at depth.

  • Holly V. Moeller
  • , Charlotte Laufkötter
  •  & Matthew D. Johnson

• Matters Arising
  30 January 2019 | Open Access

  Caution in inferring viral strategies from abundance correlations in marine metagenomes

  • Hend Alrasheed
  • , Rong Jin
  •  & Joshua S. Weitz

• Matters Arising
  30 January 2019 | Open Access

  Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes

  • F. H. Coutinho
  • , C. B. Silveira
  •  & F. L. Thompson

• Article
  29 May 2018 | Open Access

  High pCO₂-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial

  A Paleoproterozoic carbon isotope anomaly is likely linked to burial of oceanic cyanobacteria, but it is not clear how burial occurred. Here, the authors find that, under Paleoproterozoic pCO₂ conditions, planktonic cyanobacteria increase exopolysaccharide production and mineralization, leading to aggregation and faster sinking.

  • Nina A. Kamennaya
  • , Marcin Zemla
  •  & Christer Jansson

• Article
  30 April 2018 | Open Access

  Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

  The presence and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore oxygen minimum zone waters remains unclear. Here, the authors combine oceanography, molecular, biogeochemical and single-cell techniques to examine their distribution, metabolic capacity, and origins.

  • Cameron M. Callbeck
  • , Gaute Lavik
  •  & Marcel M. M. Kuypers

• Article
  23 March 2018 | Open Access

  Ecological control of nitrite in the upper ocean

  Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.

  • Emily J. Zakem
  • , Alia Al-Haj
  •  & Michael J. Follows

• Article
  19 May 2017 | Open Access

  Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic

  The influence iron exerts over the acquisition of dissolved organic phosphorus in regions of the oceans co-limited by nitrogen and phosphorus is poorly constrained. Here, the authors demonstrate enhanced alkaline phosphatase activity of natural marine microbial communities following iron fertilization.

  • T. J. Browning
  • , E. P. Achterberg
  •  & C. M. Moore

• Article
  27 June 2016 | Open Access

  Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean

  Cyanobacterial nitrogen fixation supplies bioavailable nitrogen to marine ecosystems, but the mechanisms governing iron and phosphorus co-limitation in elevated CO₂remain unknown. Here, the authors show a complex cellular response to co-limitation characterized by changes in growth, cell size, and the proteome.

  • Nathan G. Walworth
  • , Fei-Xue Fu
  •  & David A. Hutchins

• Article
  16 February 2016 | Open Access

  Near-island biological hotspots in barren ocean basins

  The Island Mass Effect (IME), where island proximity enhances phytoplankton biomass, remains a poorly understood phenomenon. Here, the authors show the IME is a common feature among Pacific reefs, driving increased production that creates biological hotspots in otherwise barren ocean basins.

  • Jamison M. Gove
  • , Margaret A. McManus
  •  & Gareth J. Williams

• Article
  17 November 2015 | Open Access

  Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

  The contribution of marine archaea to the ocean's carbon cycle is unclear. Here, Li et al. analyse the genomes and transcriptomes from five deep-sea archaeal groups to reveal their metabolic characteristics, suggesting a crucial role in modulating the carbon cycle in deep oceans.

  • Meng Li
  • , Brett J. Baker
  •  & Gregory J. Dick

• Article | 18 June 2015

  Inefficient microbial production of refractory dissolved organic matter in the ocean

  The extent to which the microbial carbon pump contributes to the generation of marine refractory dissolved organic matter (RDOM) remains a matter of debate. Here, the authors report results from a 3-year mesocosm study, and show that most of the microbial DOM is different from RDOM in the ocean.

  • Helena Osterholz
  • , Jutta Niggemann
  •  & Thorsten Dittmar

• Article
  07 May 2015 | Open Access

  Extreme ¹³C depletion of carbonates formed during oxidation of biogenic methane in fractured granite

  Precipitation of ¹³C-depleted authigenic carbonate is a tracer of sulphate-dependent anaerobic methane oxidation, particularly in marine sediments. Here, the authors present extremely ¹³C-depleted carbonates from deep granitoid rocks suggesting the presence of microbial sulphate reducers and methane oxidisers.

  • Henrik Drake
  • , Mats E. Åström
  •  & Peter Sjövall

• Article
  28 April 2015 | Open Access

  Deep groundwater and potential subsurface habitats beneath an Antarctic dry valley

  Conditions below the active permafrost layer in the McMurdo Dry Valleys, Antarctica, are thought to be ice cemented. Here, the authors use an airborne electromagnetic sensor to image the resistivity beneath the valley floor, which indicates the presence of high-salinity liquids at temperatures well below freezing.

  • J. A. Mikucki
  • , E. Auken
  •  & N. Foley

• Article | 31 March 2015

  Marine sequestration of carbon in bacterial metabolites

  The microbial carbon pump is an important pathway for marine carbon sequestration, yet the chemical complexity and stability of persistent molecules remain enigmatic. Here, the authors use bioassay experiments to investigate the complexity and refractory nature of bacterial dissolved organic matter.

  • Oliver J. Lechtenfeld
  • , Norbert Hertkorn
  •  & Ronald Benner

• Article | 25 March 2015

  A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

  Dimethylsulphide (DMS) is a volatile compound produced by marine microbes through degradation of dimethylsulphoniopropionate (DMSP). Here, Carrión et al.describe an alternative pathway for DMS production from methanethiol that is widespread among bacteria, especially from soil environments.

  • O. Carrión
  • , A. R. J. Curson
  •  & J. D. Todd

• Article | 28 October 2013

  Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

  Oxygen minimum zones in the global ocean have an important role in biogeochemical cycles, yet their response to climate change is poorly understood. Here, the authors show that bacterial community composition is tightly coupled to dissolved oxygen and is likely to fundamentally change as the oceans warm.

  • J. Michael Beman
  •  & Molly T. Carolan