Articles | Volume 18, issue 1
https://doi.org/10.5194/bg-18-113-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-18-113-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
08 Jan 2021
Research article |
| 08 Jan 2021
| 08 Jan 2021
Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea
Jiangtao Li
State Key Laboratory of Marine Geology, Tongji University, Shanghai
200092, China
Lingyuan Gu
State Key Laboratory of Marine Geology, Tongji University, Shanghai
200092, China
Shijie Bai
Institute of Deep-Sea Science and Engineering, Chinese Academy of
Sciences, Sanya 572000, China
Jie Wang
College of Marine Science, Shanghai Ocean University, Shanghai 201306,
China
Lei Su
State Key Laboratory of Marine Geology, Tongji University, Shanghai
200092, China
Bingbing Wei
State Key Laboratory of Marine Geology, Tongji University, Shanghai
200092, China
Li Zhang
School of Earth Sciences, China University of Geosciences, Wuhan 430074,
China
Jiasong Fang
CORRESPONDING AUTHOR
The Shanghai Engineering Research Center of Hadal Science and
Technology, Shanghai Ocean University, Shanghai 201306, China
Laboratory for Marine Biology and Biotechnology, Qingdao National
Laboratory for Marine Science and Technology, Qingdao 266237, China
Department of Natural Sciences, Hawaii Pacific University, Kaneohe, HI
96744, USA
Related authors
Yong Wang, Tie Gang Li, Meng Ying Wang, Qi Liang Lai, Jiang Tao Li, Zhao Ming Gao, Zong Ze Shao, and Pei-Yuan Qian
Biogeosciences, 13, 6405–6417, https://doi.org/10.5194/bg-13-6405-2016, https://doi.org/10.5194/bg-13-6405-2016, 2016
Short summary
Short summary
Mild eruption of hydrothermal solutions on deep-sea benthic floor can produce anhydrite crystal layers, where microbes are trapped and preserved for a long period of time. These embedded original inhabitants will be biomarkers for the environment when the hydrothermal eruption occurred. This study discovered a thick anhydrite layer in a deep-sea brine pool in the Red Sea. Oil-degrading bacteria were revealed in the crystals with genomic and microscopic evidence.
Shijie Bai and Xiaotong Peng
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-406, https://doi.org/10.5194/bg-2019-406, 2019
Preprint withdrawn
Hengchao Xu, Xiaotong Peng, Shijie Bai, Kaiwen Ta, Shouye Yang, Shuangquan Liu, Ho Bin Jang, and Zixiao Guo
Biogeosciences, 16, 949–960, https://doi.org/10.5194/bg-16-949-2019, https://doi.org/10.5194/bg-16-949-2019, 2019
Short summary
Short summary
Viruses have been acknowledged as important components of the marine system for the past 2 decades, but understanding of their role in the functioning of the geochemical cycle remains poor. Results show viral lysis of cyanobacteria can influence the carbonate equilibrium system remarkably and promotes the formation and precipitation of carbonate minerals. Amorphous calcium carbonate (ACC) and aragonite are evident in the lysate, implying that different precipitation processes have occurred.
Yong Wang, Tie Gang Li, Meng Ying Wang, Qi Liang Lai, Jiang Tao Li, Zhao Ming Gao, Zong Ze Shao, and Pei-Yuan Qian
Biogeosciences, 13, 6405–6417, https://doi.org/10.5194/bg-13-6405-2016, https://doi.org/10.5194/bg-13-6405-2016, 2016
Short summary
Short summary
Mild eruption of hydrothermal solutions on deep-sea benthic floor can produce anhydrite crystal layers, where microbes are trapped and preserved for a long period of time. These embedded original inhabitants will be biomarkers for the environment when the hydrothermal eruption occurred. This study discovered a thick anhydrite layer in a deep-sea brine pool in the Red Sea. Oil-degrading bacteria were revealed in the crystals with genomic and microscopic evidence.
Related subject area
Biodiversity and Ecosystem Function: Marine
Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Composite calcite and opal test in Foraminifera (Rhizaria)
Influence of oxygen minimum zone on macrobenthic community structure in the northern Benguela Upwelling System: a macro-nematode perspective
Simulated terrestrial runoff shifts the metabolic balance of a coastal Mediterranean plankton community towards heterotrophy
Contrasting carbon cycling in the benthic food webs between a river-fed, high-energy canyon and an upper continental slope
A critical trade-off between nitrogen quota and growth allows Coccolithus braarudii life cycle phases to exploit varying environment
Structural complexity and benthic metabolism: resolving the links between carbon cycling and biodiversity in restored seagrass meadows
Planktic foraminifera assemblage composition and flux dynamics inferred from an annual sediment trap record in the Central Mediterranean Sea
Building your own mountain: the effects, limits, and drawbacks of cold-water coral ecosystem engineering
Viability of coastal fish larvae under ocean alkalinity enhancement: from organisms to communities
Phytoplankton response to increased nickel in the context of ocean alkalinity enhancement
Diversity and density relationships between lebensspuren and tracemaking organisms: a study case from abyssal northwest Pacific
Technical note: An autonomous flow-through salinity and temperature perturbation mesocosm system for multi-stressor experiments
Reviews and syntheses: The clam before the storm – a meta-analysis showing the effect of combined climate change stressors on bivalves
A step towards measuring connectivity in the deep sea: elemental fingerprints of mollusk larval shells discriminate hydrothermal vent sites
Spawner weight and ocean temperature drive Allee effect dynamics in Atlantic cod, Gadus morhua: inherent and emergent density regulation
Bacterioplankton dark CO2 fixation in oligotrophic waters
The bottom mixed layer depth as an indicator of subsurface Chlorophyll a distribution
Ideas and perspectives: The fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles – the aquatic oxyscape
Impact of deoxygenation and warming on global marine species in the 21st century
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Unique benthic foraminiferal communities (stained) in diverse environments of sub-Antarctic fjords, South Georgia
Upwelled plankton community modulates surface bloom succession and nutrient availability in a natural plankton assemblage
First phytoplankton community assessment of the Kong Håkon VII Hav, Southern Ocean, during austral autumn
Early life stages of a Mediterranean coral are vulnerable to ocean warming and acidification
Mediterranean seagrasses as carbon sinks: methodological and regional differences
Contrasting vertical distributions of recent planktic foraminifera off Indonesia during the southeast monsoon: implications for paleoceanographic reconstructions
The onset of the spring phytoplankton bloom in the coastal North Sea supports the Disturbance Recovery Hypothesis
Species richness and functional attributes of fish assemblages across a large-scale salinity gradient in shallow coastal areas
Modeling the growth and sporulation dynamics of the macroalga Ulva in mixed-age populations in cultivation and the formation of green tides
Spatial changes in community composition and food web structure of mesozooplankton across the Adriatic basin (Mediterranean Sea)
Predicting mangrove forest dynamics across a soil salinity gradient using an individual-based vegetation model linked with plant hydraulics
Will daytime community calcification reflect reef accretion on future, degraded coral reefs?
Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits
Quantifying functional consequences of habitat degradation on a Caribbean coral reef
Enhanced chlorophyll-a concentration in the wake of Sable Island, eastern Canada, revealed by two decades of satellite observations: a response to grey seal population dynamics?
Population dynamics and reproduction strategies of planktonic foraminifera in the open ocean
The Bouraké semi-enclosed lagoon (New Caledonia) – a natural laboratory to study the lifelong adaptation of a coral reef ecosystem to extreme environmental conditions
Atypical, high-diversity assemblages of foraminifera in a mangrove estuary in northern Brazil
Permanent ectoplasmic structures in deep-sea Cibicides and Cibicidoides taxa – long-term observations at in situ pressure
Ideas and perspectives: Ushering the Indian Ocean into the UN Decade of Ocean Science for Sustainable Development (UNDOSSD) through marine ecosystem research and operational services – an early career's take
Persistent effects of sand extraction on habitats and associated benthic communities in the German Bight
Spatial patterns of ectoenzymatic kinetics in relation to biogeochemical properties in the Mediterranean Sea and the concentration of the fluorogenic substrate used
A 2-decade (1988–2009) record of diatom fluxes in the Mauritanian coastal upwelling: impact of low-frequency forcing and a two-step shift in the species composition
Review and syntheses: Impacts of turbidity flows on deep-sea benthic communities
Ideas and perspectives: When ocean acidification experiments are not the same, repeatability is not tested
The effect of the salinity, light regime and food source on carbon and nitrogen uptake in a benthic foraminifer
Changes in population depth distribution and oxygen stratification are involved in the current low condition of the eastern Baltic Sea cod (Gadus morhua)
Effects of spatial variability on the exposure of fish to hypoxia: a modeling analysis for the Gulf of Mexico
Plant genotype determines biomass response to flooding frequency in tidal wetlands
Skye Yunshu Tian, Martin Langer, Moriaki Yasuhara, and Chih-Lin Wei
Biogeosciences, 21, 3523–3536, https://doi.org/10.5194/bg-21-3523-2024, https://doi.org/10.5194/bg-21-3523-2024, 2024
Short summary
Short summary
Through the first large-scale study of meiobenthic ostracods from the diverse and productive reef ecosystem in the Zanzibar Archipelago, Tanzania, we found that the diversity and composition of ostracod assemblages as controlled by benthic habitats and human impacts were indicative of overall reef health, and we highlighted the usefulness of ostracods as a model proxy to monitor and understand the degradation of reef ecosystems from the coral-dominated phase to the algae-dominated phase.
Julien Richirt, Satoshi Okada, Yoshiyuki Ishitani, Katsuyuki Uematsu, Akihiro Tame, Kaya Oda, Noriyuki Isobe, Toyoho Ishimura, Masashi Tsuchiya, and Hidetaka Nomaki
Biogeosciences, 21, 3271–3288, https://doi.org/10.5194/bg-21-3271-2024, https://doi.org/10.5194/bg-21-3271-2024, 2024
Short summary
Short summary
We report the first benthic foraminifera with a composite test (i.e. shell) made of opal, which coats the inner part of the calcitic layer. Using comprehensive techniques, we describe the morphology and the composition of this novel opal layer and provide evidence that the opal is precipitated by the foraminifera itself. We explore the potential precipitation process and function(s) of this composite test and further discuss the possible implications for palaeoceanographic reconstructions.
Said Mohamed Hashim, Beth Wangui Waweru, and Agnes Muthumbi
Biogeosciences, 21, 2995–3006, https://doi.org/10.5194/bg-21-2995-2024, https://doi.org/10.5194/bg-21-2995-2024, 2024
Short summary
Short summary
The study investigates the impact of decreasing oxygen in the ocean on macrofaunal communities using the BUS as an example. It identifies distinct shifts in community composition and feeding guilds across oxygen zones, with nematodes dominating dysoxic areas. These findings underscore the complex responses of benthic organisms to oxygen gradients, crucial for understanding ecosystem dynamics in hypoxic environments and their implications for marine biodiversity and sustainability.
Tanguy Soulié, Francesca Vidussi, Justine Courboulès, Marie Heydon, Sébastien Mas, Florian Voron, Carolina Cantoni, Fabien Joux, and Behzad Mostajir
Biogeosciences, 21, 1887–1902, https://doi.org/10.5194/bg-21-1887-2024, https://doi.org/10.5194/bg-21-1887-2024, 2024
Short summary
Short summary
Due to climate change, it is projected that extreme rainfall events, which bring terrestrial matter into coastal seas, will occur more frequently in the Mediterranean region. To test the effects of runoffs of terrestrial matter on plankton communities from Mediterranean coastal waters, an in situ mesocosm experiment was conducted. The simulated runoff affected key processes mediated by plankton, such as primary production and respiration, suggesting major consequences of such events.
Chueh-Chen Tung, Yu-Shih Lin, Jian-Xiang Liao, Tzu-Hsuan Tu, James T. Liu, Li-Hung Lin, Pei-Ling Wang, and Chih-Lin Wei
Biogeosciences, 21, 1729–1756, https://doi.org/10.5194/bg-21-1729-2024, https://doi.org/10.5194/bg-21-1729-2024, 2024
Short summary
Short summary
This study contrasts seabed food webs between a river-fed, high-energy canyon and the nearby slope. We show higher organic carbon (OC) flows through the canyon than the slope. Bacteria dominated the canyon, while seabed fauna contributed more to the slope food web. Due to frequent perturbation, the canyon had a lower faunal stock and OC recycling. Only 4 % of the seabed OC flux enters the canyon food web, suggesting a significant role of the river-fed canyon in transporting OC to the deep sea.
Joost de Vries, Fanny Monteiro, Gerald Langer, Colin Brownlee, and Glen Wheeler
Biogeosciences, 21, 1707–1727, https://doi.org/10.5194/bg-21-1707-2024, https://doi.org/10.5194/bg-21-1707-2024, 2024
Short summary
Short summary
Calcifying phytoplankton (coccolithophores) utilize a life cycle in which they can grow and divide into two different phases. These two phases (HET and HOL) vary in terms of their physiology and distributions, with many unknowns about what the key differences are. Using a combination of lab experiments and model simulations, we find that nutrient storage is a critical difference between the two phases and that this difference allows them to inhabit different nitrogen input regimes.
Theodor Kindeberg, Karl Michael Attard, Jana Hüller, Julia Müller, Cintia Organo Quintana, and Eduardo Infantes
Biogeosciences, 21, 1685–1705, https://doi.org/10.5194/bg-21-1685-2024, https://doi.org/10.5194/bg-21-1685-2024, 2024
Short summary
Short summary
Seagrass meadows are hotspots for biodiversity and productivity, and planting seagrass is proposed as a tool for mitigating biodiversity loss and climate change. We assessed seagrass planted in different years and found that benthic oxygen and carbon fluxes increased as the seabed developed from bare sediments to a mature seagrass meadow. This increase was partly linked to the diversity of colonizing algae which increased the light-use efficiency of the seagrass meadow community.
Thibauld M. Béjard, Andrés S. Rigual-Hernández, Javier P. Tarruella, José A. Flores, Anna Sanchez Vidal, Irene Llamas Cano, and Francisco J. Sierro
EGUsphere, https://doi.org/10.5194/egusphere-2023-3101, https://doi.org/10.5194/egusphere-2023-3101, 2024
Short summary
Short summary
The Mediterranean Sea is considered a climate change hotspot. Documenting planktic foraminifera population is crucial. In the Sicily Strait, fluxes are higher during winter and positively linked with chlorophyll-a concentration and cool temperatures. A comparison with other Mediterranean sites shows the transitional aspect of the studied zone. Finally, modern populations significantly differ from those in the sediment, highlighting a possible effect of environmental change.
Anna-Selma van der Kaaden, Sandra R. Maier, Siluo Chen, Laurence H. De Clippele, Evert de Froe, Theo Gerkema, Johan van de Koppel, Furu Mienis, Christian Mohn, Max Rietkerk, Karline Soetaert, and Dick van Oevelen
Biogeosciences, 21, 973–992, https://doi.org/10.5194/bg-21-973-2024, https://doi.org/10.5194/bg-21-973-2024, 2024
Short summary
Short summary
Combining hydrodynamic simulations and annotated videos, we separated which hydrodynamic variables that determine reef cover are engineered by cold-water corals and which are not. Around coral mounds, hydrodynamic zones seem to create a typical reef zonation, restricting corals from moving deeper (the expected response to climate warming). But non-engineered downward velocities in winter (e.g. deep winter mixing) seem more important for coral reef growth than coral engineering.
Silvan Urs Goldenberg, Ulf Riebesell, Daniel Brüggemann, Gregor Börner, Michael Sswat, Arild Folkvord, Maria Couret, Synne Spjelkavik, Nicolás Sánchez, Cornelia Jaspers, and Marta Moyano
EGUsphere, https://doi.org/10.5194/egusphere-2024-286, https://doi.org/10.5194/egusphere-2024-286, 2024
Short summary
Short summary
Ocean alkalinity enhancement (OAE) is being evaluated as carbon dioxide removal technology for climate change mitigation. With experiments on single species and species communities, we show that fish larvae can be resilient to the resulting perturbation of seawater. Larvae may hence recruit successfully and continue to support fisheries production in regions of OAE. Our findings for fish and marine food webs help to establish an environmentally safe operating space for this ocean-based solution.
Xiaoke Xin, Giulia Faucher, and Ulf Riebesell
Biogeosciences, 21, 761–772, https://doi.org/10.5194/bg-21-761-2024, https://doi.org/10.5194/bg-21-761-2024, 2024
Short summary
Short summary
Ocean alkalinity enhancement (OAE) is a promising approach to remove CO2 by accelerating natural rock weathering. However, some of the alkaline substances contain trace metals which could be toxic to marine life. By exposing three representative phytoplankton species to Ni released from alkaline materials, we observed varying responses of phytoplankton to nickel concentrations, suggesting caution should be taken and toxic thresholds should be avoided in OAE with Ni-rich materials.
Olmo Miguez-Salas, Angelika Brandt, Henry Knauber, and Torben Riehl
Biogeosciences, 21, 641–655, https://doi.org/10.5194/bg-21-641-2024, https://doi.org/10.5194/bg-21-641-2024, 2024
Short summary
Short summary
In the deep sea, the interaction between benthic fauna (tracemakers) and substrate can be preserved as traces (i.e. lebensspuren), which are common features of seafloor landscapes, rendering them promising proxies for inferring biodiversity from marine images. No general correlation was observed between traces and benthic fauna. However, a local correlation was observed between specific stations depending on unknown tracemakers, tracemaker behaviour, and lebensspuren morphotypes.
Cale A. Miller, Pierre Urrutti, Jean-Pierre Gattuso, Steeve Comeau, Anaïs Lebrun, Samir Alliouane, Robert W. Schlegel, and Frédéric Gazeau
Biogeosciences, 21, 315–333, https://doi.org/10.5194/bg-21-315-2024, https://doi.org/10.5194/bg-21-315-2024, 2024
Short summary
Short summary
This work describes an experimental system that can replicate and manipulate environmental conditions in marine or aquatic systems. Here, we show how the temperature and salinity of seawater delivered from a fjord is manipulated to experimental tanks on land. By constantly monitoring temperature and salinity in each tank via a computer program, the system continuously adjusts automated flow valves to ensure the seawater in each tank matches the targeted experimental conditions.
Rachel A. Kruft Welton, George Hoppit, Daniela N. Schmidt, James D. Witts, and Benjamin C. Moon
Biogeosciences, 21, 223–239, https://doi.org/10.5194/bg-21-223-2024, https://doi.org/10.5194/bg-21-223-2024, 2024
Short summary
Short summary
We conducted a meta-analysis of known experimental literature examining how marine bivalve growth rates respond to climate change. Growth is usually negatively impacted by climate change. Bivalve eggs/larva are generally more vulnerable than either juveniles or adults. Available data on the bivalve response to climate stressors are biased towards early growth stages (commercially important in the Global North), and many families have only single experiments examining climate change impacts.
Vincent Mouchi, Christophe Pecheyran, Fanny Claverie, Cécile Cathalot, Marjolaine Matabos, Yoan Germain, Olivier Rouxel, Didier Jollivet, Thomas Broquet, and Thierry Comtet
Biogeosciences, 21, 145–160, https://doi.org/10.5194/bg-21-145-2024, https://doi.org/10.5194/bg-21-145-2024, 2024
Short summary
Short summary
The impact of deep-sea mining will depend critically on the ability of larval dispersal of hydrothermal mollusks to connect and replenish natural populations. However, assessing connectivity is extremely challenging, especially in the deep sea. Here, we investigate the potential of using the chemical composition of larval shells to discriminate larval origins between multiple hydrothermal sites in the southwest Pacific. Our results confirm that this method can be applied with high accuracy.
Anna-Marie Winter, Nadezda Vasilyeva, and Artem Vladimirov
Biogeosciences, 20, 3683–3716, https://doi.org/10.5194/bg-20-3683-2023, https://doi.org/10.5194/bg-20-3683-2023, 2023
Short summary
Short summary
There is an increasing number of fish in poor state, and many do not recover, even when fishing pressure is ceased. An Allee effect can hinder population recovery because it suppresses the fish's productivity at low abundance. With a model fitted to 17 Atlantic cod stocks, we find that ocean warming and fishing can cause an Allee effect. If present, the Allee effect hinders fish recovery. This shows that Allee effects are dynamic, not uncommon, and calls for precautionary management measures.
Afrah Alothman, Daffne López-Sandoval, Carlos M. Duarte, and Susana Agustí
Biogeosciences, 20, 3613–3624, https://doi.org/10.5194/bg-20-3613-2023, https://doi.org/10.5194/bg-20-3613-2023, 2023
Short summary
Short summary
This study investigates bacterial dissolved inorganic carbon (DIC) fixation in the Red Sea, an oligotrophic ecosystem, using stable-isotope labeling and spectroscopy. The research reveals that bacterial DIC fixation significantly contributes to total DIC fixation, in the surface and deep water. The study demonstrates that as primary production decreases, the role of bacterial DIC fixation increases, emphasizing its importance with photosynthesis in estimating oceanic carbon dioxide production.
Arianna Zampollo, Thomas Cornulier, Rory O'Hara Murray, Jacqueline Fiona Tweddle, James Dunning, and Beth E. Scott
Biogeosciences, 20, 3593–3611, https://doi.org/10.5194/bg-20-3593-2023, https://doi.org/10.5194/bg-20-3593-2023, 2023
Short summary
Short summary
This paper highlights the use of the bottom mixed layer depth (BMLD: depth between the end of the pycnocline and the mixed layer below) to investigate subsurface Chlorophyll a (a proxy of primary production) in temperate stratified shelf waters. The strict correlation between subsurface Chl a and BMLD becomes relevant in shelf-productive waters where multiple stressors (e.g. offshore infrastructure) will change the stratification--mixing balance and related carbon fluxes.
Marco Fusi, Sylvain Rigaud, Giovanna Guadagnin, Alberto Barausse, Ramona Marasco, Daniele Daffonchio, Julie Régis, Louison Huchet, Capucine Camin, Laura Pettit, Cristina Vina-Herbon, and Folco Giomi
Biogeosciences, 20, 3509–3521, https://doi.org/10.5194/bg-20-3509-2023, https://doi.org/10.5194/bg-20-3509-2023, 2023
Short summary
Short summary
Oxygen availability in marine water and freshwater is very variable at daily and seasonal scales. The dynamic nature of oxygen fluctuations has important consequences for animal and microbe physiology and ecology, yet it is not fully understood. In this paper, we showed the heterogeneous nature of the aquatic oxygen landscape, which we defined here as the
oxyscape, and we addressed the importance of considering the oxyscape in the modelling and managing of aquatic ecosystems.
Anne L. Morée, Tayler M. Clarke, William W. L. Cheung, and Thomas L. Frölicher
Biogeosciences, 20, 2425–2454, https://doi.org/10.5194/bg-20-2425-2023, https://doi.org/10.5194/bg-20-2425-2023, 2023
Short summary
Short summary
Ocean temperature and oxygen shape marine habitats together with species’ characteristics. We calculated the impacts of projected 21st-century warming and oxygen loss on the contemporary habitat volume of 47 marine species and described the drivers of these impacts. Most species lose less than 5 % of their habitat at 2 °C of global warming, but some species incur losses 2–3 times greater than that. We also calculate which species may be most vulnerable to climate change and why this is the case.
Markus A. Min, David M. Needham, Sebastian Sudek, Nathan Kobun Truelove, Kathleen J. Pitz, Gabriela M. Chavez, Camille Poirier, Bente Gardeler, Elisabeth von der Esch, Andrea Ludwig, Ulf Riebesell, Alexandra Z. Worden, and Francisco P. Chavez
Biogeosciences, 20, 1277–1298, https://doi.org/10.5194/bg-20-1277-2023, https://doi.org/10.5194/bg-20-1277-2023, 2023
Short summary
Short summary
Emerging molecular methods provide new ways of understanding how marine communities respond to changes in ocean conditions. Here, environmental DNA was used to track the temporal evolution of biological communities in the Peruvian coastal upwelling system and in an adjacent enclosure where upwelling was simulated. We found that the two communities quickly diverged, with the open ocean being one found during upwelling and the enclosure evolving to one found under stratified conditions.
Wojciech Majewski, Witold Szczuciński, and Andrew J. Gooday
Biogeosciences, 20, 523–544, https://doi.org/10.5194/bg-20-523-2023, https://doi.org/10.5194/bg-20-523-2023, 2023
Short summary
Short summary
We studied foraminifera living in the fjords of South Georgia, a sub-Antarctic island sensitive to climate change. As conditions in water and on the seafloor vary, different associations of these microorganisms dominate far inside, in the middle, and near fjord openings. Assemblages in inner and middle parts of fjords are specific to South Georgia, but they may become widespread with anticipated warming. These results are important for interpretating fossil records and monitoring future change.
Allanah Joy Paul, Lennart Thomas Bach, Javier Arístegui, Elisabeth von der Esch, Nauzet Hernández-Hernández, Jonna Piiparinen, Laura Ramajo, Kristian Spilling, and Ulf Riebesell
Biogeosciences, 19, 5911–5926, https://doi.org/10.5194/bg-19-5911-2022, https://doi.org/10.5194/bg-19-5911-2022, 2022
Short summary
Short summary
We investigated how different deep water chemistry and biology modulate the response of surface phytoplankton communities to upwelling in the Peruvian coastal zone. Our results show that the most influential drivers were the ratio of inorganic nutrients (N : P) and the microbial community present in upwelling source water. These led to unexpected and variable development in the phytoplankton assemblage that could not be predicted by the amount of inorganic nutrients alone.
Hanna M. Kauko, Philipp Assmy, Ilka Peeken, Magdalena Różańska-Pluta, Józef M. Wiktor, Gunnar Bratbak, Asmita Singh, Thomas J. Ryan-Keogh, and Sebastien Moreau
Biogeosciences, 19, 5449–5482, https://doi.org/10.5194/bg-19-5449-2022, https://doi.org/10.5194/bg-19-5449-2022, 2022
Short summary
Short summary
This article studies phytoplankton (microscopic
plantsin the ocean capable of photosynthesis) in Kong Håkon VII Hav in the Southern Ocean. Different species play different roles in the ecosystem, and it is therefore important to assess the species composition. We observed that phytoplankton blooms in this area are formed by large diatoms with strong silica armors, which can lead to high silica (and sometimes carbon) export to depth and be important prey for krill.
Chloe Carbonne, Steeve Comeau, Phoebe T. W. Chan, Keyla Plichon, Jean-Pierre Gattuso, and Núria Teixidó
Biogeosciences, 19, 4767–4777, https://doi.org/10.5194/bg-19-4767-2022, https://doi.org/10.5194/bg-19-4767-2022, 2022
Short summary
Short summary
For the first time, our study highlights the synergistic effects of a 9-month warming and acidification combined stress on the early life stages of a Mediterranean azooxanthellate coral, Astroides calycularis. Our results predict a decrease in dispersion, settlement, post-settlement linear extention, budding and survival under future global change and that larvae and recruits of A. calycularis are stages of interest for this Mediterranean coral resistance, resilience and conservation.
Iris E. Hendriks, Anna Escolano-Moltó, Susana Flecha, Raquel Vaquer-Sunyer, Marlene Wesselmann, and Núria Marbà
Biogeosciences, 19, 4619–4637, https://doi.org/10.5194/bg-19-4619-2022, https://doi.org/10.5194/bg-19-4619-2022, 2022
Short summary
Short summary
Seagrasses are marine plants with the capacity to act as carbon sinks due to their high primary productivity, using carbon for growth. This capacity can play a key role in climate change mitigation. We compiled and published data showing that two Mediterranean seagrass species have different metabolic rates, while the study method influences the rates of the measurements. Most communities act as carbon sinks, while the western basin might be more productive than the eastern Mediterranean.
Raúl Tapia, Sze Ling Ho, Hui-Yu Wang, Jeroen Groeneveld, and Mahyar Mohtadi
Biogeosciences, 19, 3185–3208, https://doi.org/10.5194/bg-19-3185-2022, https://doi.org/10.5194/bg-19-3185-2022, 2022
Short summary
Short summary
We report census counts of planktic foraminifera in depth-stratified plankton net samples off Indonesia. Our results show that the vertical distribution of foraminifera species routinely used in paleoceanographic reconstructions varies in hydrographically distinct regions, likely in response to food availability. Consequently, the thermal gradient based on mixed layer and thermocline dwellers also differs for these regions, suggesting potential implications for paleoceanographic reconstructions.
Ricardo González-Gil, Neil S. Banas, Eileen Bresnan, and Michael R. Heath
Biogeosciences, 19, 2417–2426, https://doi.org/10.5194/bg-19-2417-2022, https://doi.org/10.5194/bg-19-2417-2022, 2022
Short summary
Short summary
In oceanic waters, the accumulation of phytoplankton biomass in winter, when light still limits growth, is attributed to a decrease in grazing as the mixed layer deepens. However, in coastal areas, it is not clear whether winter biomass can accumulate without this deepening. Using 21 years of weekly data, we found that in the Scottish coastal North Sea, the seasonal increase in light availability triggers the accumulation of phytoplankton biomass in winter, when light limitation is strongest.
Birgit Koehler, Mårten Erlandsson, Martin Karlsson, and Lena Bergström
Biogeosciences, 19, 2295–2312, https://doi.org/10.5194/bg-19-2295-2022, https://doi.org/10.5194/bg-19-2295-2022, 2022
Short summary
Short summary
Understanding species richness patterns remains a challenge for biodiversity management. We estimated fish species richness over a coastal salinity gradient (3–32) with a method that allowed comparing data from various sources. Species richness was 3-fold higher at high vs. low salinity, and salinity influenced species’ habitat preference, mobility and feeding type. If climate change causes upper-layer freshening of the Baltic Sea, further shifts along the identified patterns may be expected.
Uri Obolski, Thomas Wichard, Alvaro Israel, Alexander Golberg, and Alexander Liberzon
Biogeosciences, 19, 2263–2271, https://doi.org/10.5194/bg-19-2263-2022, https://doi.org/10.5194/bg-19-2263-2022, 2022
Short summary
Short summary
The algal genus Ulva plays a major role in coastal ecosystems worldwide and is a promising prospect as an seagriculture crop. A substantial hindrance to cultivating Ulva arises from sudden sporulation, leading to biomass loss. This process is not yet well understood. Here, we characterize the dynamics of Ulva growth, considering the potential impact of sporulation inhibitors, using a mathematical model. Our findings are an essential step towards understanding the dynamics of Ulva growth.
Emanuela Fanelli, Samuele Menicucci, Sara Malavolti, Andrea De Felice, and Iole Leonori
Biogeosciences, 19, 1833–1851, https://doi.org/10.5194/bg-19-1833-2022, https://doi.org/10.5194/bg-19-1833-2022, 2022
Short summary
Short summary
Zooplankton play a key role in marine ecosystems, forming the base of the marine food web and a link between primary producers and higher-order consumers, such as fish. This aspect is crucial in the Adriatic basin, one of the most productive and overexploited areas of the Mediterranean Sea. A better understanding of community and food web structure and their response to water mass changes is essential under a global warming scenario, as zooplankton are sensitive to climate change.
Masaya Yoshikai, Takashi Nakamura, Rempei Suwa, Sahadev Sharma, Rene Rollon, Jun Yasuoka, Ryohei Egawa, and Kazuo Nadaoka
Biogeosciences, 19, 1813–1832, https://doi.org/10.5194/bg-19-1813-2022, https://doi.org/10.5194/bg-19-1813-2022, 2022
Short summary
Short summary
This study presents a new individual-based vegetation model to investigate salinity control on mangrove productivity. The model incorporates plant hydraulics and tree competition and predicts unique and complex patterns of mangrove forest structures that vary across soil salinity gradients. The presented model does not hold an empirical expression of salinity influence on productivity and thus may provide a better understanding of mangrove forest dynamics in future climate change.
Coulson A. Lantz, William Leggat, Jessica L. Bergman, Alexander Fordyce, Charlotte Page, Thomas Mesaglio, and Tracy D. Ainsworth
Biogeosciences, 19, 891–906, https://doi.org/10.5194/bg-19-891-2022, https://doi.org/10.5194/bg-19-891-2022, 2022
Short summary
Short summary
Coral bleaching events continue to drive the degradation of coral reefs worldwide. In this study we measured rates of daytime coral reef community calcification and photosynthesis during a reef-wide bleaching event. Despite a measured decline in coral health across several taxa, there was no change in overall daytime community calcification and photosynthesis. These findings highlight potential limitations of these community-level metrics to reflect actual changes in coral health.
Hyewon Heather Kim, Jeff S. Bowman, Ya-Wei Luo, Hugh W. Ducklow, Oscar M. Schofield, Deborah K. Steinberg, and Scott C. Doney
Biogeosciences, 19, 117–136, https://doi.org/10.5194/bg-19-117-2022, https://doi.org/10.5194/bg-19-117-2022, 2022
Short summary
Short summary
Heterotrophic marine bacteria are tiny organisms responsible for taking up organic matter in the ocean. Using a modeling approach, this study shows that characteristics (taxonomy and physiology) of bacteria are associated with a subset of ecological processes in the coastal West Antarctic Peninsula region, a system susceptible to global climate change. This study also suggests that bacteria will become more active, in particular large-sized cells, in response to changing climates in the region.
Alice E. Webb, Didier M. de Bakker, Karline Soetaert, Tamara da Costa, Steven M. A. C. van Heuven, Fleur C. van Duyl, Gert-Jan Reichart, and Lennart J. de Nooijer
Biogeosciences, 18, 6501–6516, https://doi.org/10.5194/bg-18-6501-2021, https://doi.org/10.5194/bg-18-6501-2021, 2021
Short summary
Short summary
The biogeochemical behaviour of shallow reef communities is quantified to better understand the impact of habitat degradation and species composition shifts on reef functioning. The reef communities investigated barely support reef functions that are usually ascribed to conventional coral reefs, and the overall biogeochemical behaviour is found to be similar regardless of substrate type. This suggests a decrease in functional diversity which may therefore limit services provided by this reef.
Emmanuel Devred, Andrea Hilborn, and Cornelia Elizabeth den Heyer
Biogeosciences, 18, 6115–6132, https://doi.org/10.5194/bg-18-6115-2021, https://doi.org/10.5194/bg-18-6115-2021, 2021
Short summary
Short summary
A theoretical model of grey seal seasonal abundance on Sable Island (SI) coupled with chlorophyll-a concentration [chl-a] measured by satellite revealed the impact of seal nitrogen fertilization on the surrounding waters of SI, Canada. The increase in seals from about 100 000 in 2003 to about 360 000 in 2018 during the breeding season is consistent with an increase in [chl-a] leeward of SI. The increase in seal abundance explains 8 % of the [chl-a] increase.
Julie Meilland, Michael Siccha, Maike Kaffenberger, Jelle Bijma, and Michal Kucera
Biogeosciences, 18, 5789–5809, https://doi.org/10.5194/bg-18-5789-2021, https://doi.org/10.5194/bg-18-5789-2021, 2021
Short summary
Short summary
Planktonic foraminifera population dynamics has long been assumed to be controlled by synchronous reproduction and ontogenetic vertical migration (OVM). Due to contradictory observations, this concept became controversial. We here test it in the Atlantic ocean for four species of foraminifera representing the main clades. Our observations support the existence of synchronised reproduction and OVM but show that more than half of the population does not follow the canonical trajectory.
Federica Maggioni, Mireille Pujo-Pay, Jérome Aucan, Carlo Cerrano, Barbara Calcinai, Claude Payri, Francesca Benzoni, Yves Letourneur, and Riccardo Rodolfo-Metalpa
Biogeosciences, 18, 5117–5140, https://doi.org/10.5194/bg-18-5117-2021, https://doi.org/10.5194/bg-18-5117-2021, 2021
Short summary
Short summary
Based on current experimental evidence, climate change will affect up to 90 % of coral reefs worldwide. The originality of this study arises from our recent discovery of an exceptional study site where environmental conditions (temperature, pH, and oxygen) are even worse than those forecasted for the future.
While these conditions are generally recognized as unfavorable for marine life, we found a rich and abundant coral reef thriving under such extreme environmental conditions.
Nisan Sariaslan and Martin R. Langer
Biogeosciences, 18, 4073–4090, https://doi.org/10.5194/bg-18-4073-2021, https://doi.org/10.5194/bg-18-4073-2021, 2021
Short summary
Short summary
Analyses of foraminiferal assemblages from the Mamanguape mangrove estuary (northern Brazil) revealed highly diverse, species-rich, and structurally complex biotas. The atypical fauna resembles shallow-water offshore assemblages and are interpreted to be the result of highly saline ocean waters penetrating deep into the estuary. The findings contrast with previous studies, have implications for the fossil record, and provide novel perspectives for reconstructing mangrove environments.
Jutta E. Wollenburg, Jelle Bijma, Charlotte Cremer, Ulf Bickmeyer, and Zora Mila Colomba Zittier
Biogeosciences, 18, 3903–3915, https://doi.org/10.5194/bg-18-3903-2021, https://doi.org/10.5194/bg-18-3903-2021, 2021
Short summary
Short summary
Cultured at in situ high-pressure conditions Cibicides and Cibicidoides taxa develop lasting ectoplasmic structures that cannot be retracted or resorbed. An ectoplasmic envelope surrounds their test and may protect the shell, e.g. versus carbonate aggressive bottom water conditions. Ectoplasmic roots likely anchor the specimens in areas of strong bottom water currents, trees enable them to elevate themselves above ground, and twigs stabilize and guide the retractable pseudopodial network.
Kumar Nimit
Biogeosciences, 18, 3631–3635, https://doi.org/10.5194/bg-18-3631-2021, https://doi.org/10.5194/bg-18-3631-2021, 2021
Short summary
Short summary
The Indian Ocean Rim hosts many of the underdeveloped and emerging economies that depend on ocean resources for the livelihood of millions. Operational ocean information services cater to the requirements of resource managers and end-users to efficiently harness resources, mitigate threats and ensure safety. This paper outlines existing tools and explores the ongoing research that has the potential to convert the findings into operational services in the near- to midterm.
Finn Mielck, Rune Michaelis, H. Christian Hass, Sarah Hertel, Caroline Ganal, and Werner Armonies
Biogeosciences, 18, 3565–3577, https://doi.org/10.5194/bg-18-3565-2021, https://doi.org/10.5194/bg-18-3565-2021, 2021
Short summary
Short summary
Marine sand mining is becoming more and more important to nourish fragile coastlines that face global change. We investigated the largest sand extraction site in the German Bight. The study reveals that after more than 35 years of mining, the excavation pits are still detectable on the seafloor while the sediment composition has largely changed. The organic communities living in and on the seafloor were strongly decimated, and no recovery is observable towards previous conditions.
France Van Wambeke, Elvira Pulido, Philippe Catala, Julie Dinasquet, Kahina Djaoudi, Anja Engel, Marc Garel, Sophie Guasco, Barbara Marie, Sandra Nunige, Vincent Taillandier, Birthe Zäncker, and Christian Tamburini
Biogeosciences, 18, 2301–2323, https://doi.org/10.5194/bg-18-2301-2021, https://doi.org/10.5194/bg-18-2301-2021, 2021
Short summary
Short summary
Michaelis–Menten kinetics were determined for alkaline phosphatase, aminopeptidase and β-glucosidase in the Mediterranean Sea. Although the ectoenzymatic-hydrolysis contribution to heterotrophic prokaryotic needs was high in terms of N, it was low in terms of C. This study points out the biases in interpretation of the relative differences in activities among the three tested enzymes in regard to the choice of added concentrations of fluorogenic substrates.
Oscar E. Romero, Simon Ramondenc, and Gerhard Fischer
Biogeosciences, 18, 1873–1891, https://doi.org/10.5194/bg-18-1873-2021, https://doi.org/10.5194/bg-18-1873-2021, 2021
Short summary
Short summary
Upwelling intensity along NW Africa varies on the interannual to decadal timescale. Understanding its changes is key for the prediction of future changes of CO2 sequestration in the northeastern Atlantic. Based on a multiyear (1988–2009) sediment trap experiment at the site CBmeso, fluxes and the species composition of the diatom assemblage are presented. Our data help in establishing the scientific basis for forecasting and modeling future states of this ecosystem and its decadal changes.
Katharine T. Bigham, Ashley A. Rowden, Daniel Leduc, and David A. Bowden
Biogeosciences, 18, 1893–1908, https://doi.org/10.5194/bg-18-1893-2021, https://doi.org/10.5194/bg-18-1893-2021, 2021
Short summary
Short summary
Turbidity flows – underwater avalanches – are large-scale physical disturbances believed to have profound impacts on productivity and diversity of benthic communities in the deep sea. We reviewed published studies and found that current evidence for changes in productivity is ambiguous at best, but the influence on regional and local diversity is clearer. We suggest study design criteria that may lead to a better understanding of large-scale disturbance effects on deep-sea benthos.
Phillip Williamson, Hans-Otto Pörtner, Steve Widdicombe, and Jean-Pierre Gattuso
Biogeosciences, 18, 1787–1792, https://doi.org/10.5194/bg-18-1787-2021, https://doi.org/10.5194/bg-18-1787-2021, 2021
Short summary
Short summary
The reliability of ocean acidification research was challenged in early 2020 when a high-profile paper failed to corroborate previously observed impacts of high CO2 on the behaviour of coral reef fish. We now know the reason why: the
replicatedstudies differed in many ways. Open-minded and collaborative assessment of all research results, both negative and positive, remains the best way to develop process-based understanding of the impacts of ocean acidification on marine organisms.
Michael Lintner, Bianca Lintner, Wolfgang Wanek, Nina Keul, and Petra Heinz
Biogeosciences, 18, 1395–1406, https://doi.org/10.5194/bg-18-1395-2021, https://doi.org/10.5194/bg-18-1395-2021, 2021
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changes in salinity immediately influence the foraminiferal activity. Also the light regime has a significant impact on carbon or nitrogen processing in foraminifera which contain no kleptoplasts.
Michele Casini, Martin Hansson, Alessandro Orio, and Karin Limburg
Biogeosciences, 18, 1321–1331, https://doi.org/10.5194/bg-18-1321-2021, https://doi.org/10.5194/bg-18-1321-2021, 2021
Short summary
Short summary
In the past 20 years the condition of the eastern Baltic cod has dropped, with large implications for the fishery. Our results show that simultaneously the cod population has moved deeper while low-oxygenated waters detrimental for cod growth have become shallower. Cod have thus dwelled more in detrimental waters, explaining the drop in its condition. This study, using long-term fish and hydrological monitoring data, evidences the impact of deoxygenation on fish biology and fishing.
Elizabeth D. LaBone, Kenneth A. Rose, Dubravko Justic, Haosheng Huang, and Lixia Wang
Biogeosciences, 18, 487–507, https://doi.org/10.5194/bg-18-487-2021, https://doi.org/10.5194/bg-18-487-2021, 2021
Short summary
Short summary
The hypoxic zone is an area of low dissolved oxygen (DO) in the Gulf of Mexico. Fish can be killed by exposure to hypoxia and can be negatively impacted by exposure to low, nonlethal DO concentrations (sublethal DO). We found that high sublethal area resulted in higher exposure and DO variability had a small effect on exposure. There was a large variation in exposure among individuals, which when combined with spatial variability of DO, can result in an underestimation of exposure when averaged.
Svenja Reents, Peter Mueller, Hao Tang, Kai Jensen, and Stefanie Nolte
Biogeosciences, 18, 403–411, https://doi.org/10.5194/bg-18-403-2021, https://doi.org/10.5194/bg-18-403-2021, 2021
Short summary
Short summary
By conducting a flooding experiment with two genotypes of the salt-marsh grass Elymus athericus, we show considerable differences in biomass response to flooding within the same species. As biomass production plays a major role in sedimentation processes and thereby salt-marsh accretion, we emphasise the importance of taking intraspecific differences into account when evaluating ecosystem resilience to accelerated sea level rise.
Cited articles
Acinas, S. G., Rodríguez-Valera, F., and Pedrós-Alió, C.: Spatial
and temporal variation in marine bacterioplankton diversity as shown by RFLP
fingerprinting of PCR amplified 16S rDNA, FEMS Microbiol. Ecol., 24, 27–40,
1997.
Alldredge, A. L., Cole, J. J., and Caron, D. A.: Production of heterotrophic
bacteria inhabiting macroscopic organic aggregates (marine snow) from
surface waters, Limnol. Oceanogr., 31, 68–78, 1986.
Alonso-Sáez, L., Waller, A. S., Mende, D. R., Bakker, K., Farnelid, H.,
Yager, P. L., Lovejoy, C., Tremblay, J.-É., Potvin, M., Heinrich, F.,
Estrada, M., Riemann, L., Bork, P., Pedrós-Alió, C., and Bertilsson,
S.: Role for urea in nitrification by polar marine Archaea, P. Natl.
Acad. Sci. USA, 109, 17989–17994, https://doi.org/10.1073/pnas.1201914109, 2012.
Apprill, A., McNally, S., Parsons, R., and Weber, L.: Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton, Aquat. Microb. Ecol., 75, 129–137, https://doi.org/10.3354/ame01753, 2015.
Arístegui, J., Gasol, J. M., Duarte, C. M., and Herndl, G. J.: Microbial
oceanography of the dark ocean's pelagic realm, Limnol.Oceanogr.,
54, 1501–529, 2009.
Azam, F. and Malfatti, F.: Microbial structuring of marine ecosystems,
Nat. Rev. Microbiol., 5, 782–791, 2007.
Baker, B. J., Sheik, C. S., Taylor, C. A., Jain, S., Bhasi, A., Cavalcoli,
J. D., and Dick, G. J.: Community transcriptomic assembly reveals microbes that
contribute to deep-sea carbon and nitrogen cycling, ISME J., 7, 1962–973,
https://doi.org/10.1038/ismej.2013.85, 2013.
Bano, N. and Hollibaugh, J. T.: Phylogenetic composition of bacterioplankton
assemblages from the Arctic Ocean, Appl. Environ. Microbiol., 68, 505–518,
2002.
Bano, N., Ruffin, S., Ransom, B., and Hollibaugh, J. T.: Phylogenetic
composition of Arctic Ocean archaeal assemblages and comparison with
antarctic assemblages, Appl. Environ. Microbiol., 70, 781–789, 2004.
Bauer, M., Kube, M., Teeling, H., Richter, M., Lombardot, T., Allers, E.,
Wurdemann, C. A., Quast, C., Kuhl, H., Knaust, F., Woebken, D., Bischof, K.,
Mussmann, M., Choudhuri, J. V., Meyer, F., Reinhardt, R., Amann, R. I., and
Glockner, F. O.: Whole genome analysis of the marine Bacteroidetes “Gramella forsetii” reveals
adaptations to degradation of polymeric organic matter, Environ. Microbiol.,
8, 2201–2213, 2006.
Cammen, L. M. and Walker, J. A.: Distribution and activity of attached and
free-living suspended bacteria in the bay of fundy, Can. J.
Fish. Aquat. Sci., 39, 1655–1663, 1982.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R.: QIIME allows analysis of high-throughput community sequencing data, Nat. Methods., 7, 335–336, https://doi.org/10.1038/nmeth.f.303, 2010.
Caron, D. A., Davis, P. G., Madon, L. P., and Sieburth, J. M.: Heterotrophic
bacteria and bacteriovorous protozoa in oceanic macroaggregates, Science,
218, 795–797, 1982.
Castelle, C., Wrighton, K., Thomas, B., Hug, L., Brown, C., Wilkins, M.,
Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C.,
Williams, K. H., and Banfield, J. F.: Genomic expansion of domain archaea
highlights roles for organisms from new phyla in anaerobic carbon cycling,
Curr. Biol., 25, 690–701, 2015.
Chen, M., Liu, H., Song, S., and Sun, J.: Size-fractionated mesozooplankton
biomass and grazing impact on phytoplankton in northern South China Sea
during four seasons, Deep-Sea Res. Pt. II., 117, 108–118, 2015.
Chen, W., Cai, P., Dai, M., and Wei, J.: 234Th ∕ 238U disequilibrium
and particulate organic carbon export in the northern South China Sea,
J. Oceanogr., 64, 417–428, 2008.
Chen, Y. L., Chen, H. Y., Karl, D. M., and Takahashi, M.: Nitrogen modulates
phytoplankton growth in spring in the South China Sea, Cont. Shelf Res., 24,
527–541, 2004.
Cram, J. A., Weber, T., Leung, S. W., McDonnell, A. M. P., Liang, J. H., and Deutsch,
C.: The role of particle size, ballast, temperature, and oxygen in the
sinking flux to the deep sea, Global Biogeochem. Cy., 32, 858–876,
2018.
Crespo, B. G., Pommier, T., Fernadez-Gomez, B., and Pedros-Alio, C.:
Taxonomic composition of the particle-attached and free-living bacterial
assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of
the 16S rRNA, Microbiology Open, 2, 541–552, 2013.
Crump, B. C., Baross, J. A., and Simenstad, C. A.: Dominance of
particle-attached bacteria in the Columbia River estuary, USA, Aquat.
Microb. Ecol., 14, 7–18, 1998.
D'Ambrosio, L., Ziervogel, K., MacGregor, B., Teske, A., and Arnosti, C.:
Composition and enzymatic function of particle-associated and free-living
bacteria: a coastal/offshore comparison, ISME J., 8, 2167–2179,
https://doi.org/10.1038/ismej.2014.67, 2014.
DeLong, E. F., Franks, D. G., and Alldredge, A. L.: Phylogenetic diversity of
aggregate-attached vs. free-living marine bacterial assemblages, Limnol.
Oceanogr., 38, 924–934, 1993.
Dilly, O., Bloem, J., Vos, A., and Munch, J. C.: Bacterial diversity in
agricultural soils during litter decomposition, Appl. Environ. Microbiol.,
70, 468–474, 2004.
Doxaran, D., Ehn, J., Bélanger, S., Matsuoka, A., Hooker, S., and Babin, M.:
Optical characterisation of suspended particles in the Mackenzie River plume
(Canadian Arctic Ocean) and implications for ocean colour remote sensing,
Biogeosciences, 9, 3213–3229, https://doi.org/10.5194/bg-9-3213-2012, 2012.
Eloe, E. A., Shulse, C. N., Fadrosh, D. W., Williamson, S. J., Allen, E. E., and
Bartlett, D. H.: Compositional differences in particle-associated and
free-living microbial assemblages from an extreme deep-ocean environment,
Env. Microbiol. Rep., 3, 449–458, 2011.
Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., and
Golding, S. D., and Tyson, G. W.: Methane metabolism in the archaeal phylum
bathyarchaeota revealed by genome-centric metagenomics, Science, 350,
434–438, 2015.
Fuchsman, C. A., Staley, J. T., Oakley, B. B., Kirkpatrick, J. B., and Murray,
J. W.: Free-living and aggregate-associated Planctomycetes in the Black Sea,
FEMS Microbiol. Ecol., 80, 402–416, 2012.
Fuhrman, J. A. and Davis, A. A.: Widespread Archaea and novel Bacteria from
the deep sea as shown by 16S rRNA gene sequences, Mar. Ecol. Prog. Ser.,
150, 275–285, 1997.
Galand, P. E., Lovejoy, C., Pouliot, J., and Vincent, W. F.: Heterogeneous
archaeal communities in the particle rich environment of an arctic shelf
ecosystem, J. Mar. Syst., 74, 774–782, 2008.
Galand, P. E., Casamayor, E. O., Kirchman, D. L., Potvin, M., and Lovejoy, C.:
Unique archaeal assemblages in the Arctic Ocean unveiled by massively
parallel tag sequencing, ISME J., 3, 860–869, 2009.
Galand, P. E., Gutiérrez-Provecho, C., Massana, R., Gasol, J. M., and
Casamayor, E. O.: Inter-annual recurrence of archaeal assemblages in the
coastal NW Mediterranean Sea (Blanes Bay microbial observatory), Limnol.
Oceanogr., 55, 2117–2125, 2010.
Garneau, M.È., Vincent, W. F., Terrado, R., and Lovejoy, C.: Importance of
particle-associated bacterial heterotrophy in a coastal Arctic ecosystem, J.
Mar. Syst., 75, 185–197, 2009.
Ganesh, S., Parris, D. J., DeLong, E. F., and Stewart, F. J.: Metagenomic analysis
of size-fractionated picoplankton in a marine oxygen minimum zone, ISME J.,
8, 187–211, https://doi.org/10.1038/ismej.2013.144, 2014.
Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A., and Rodriguez-Valera, F.:
Metagenomics uncovers a new group of low GC and ultra-small marine
Actinobacteria, Sci. Rep., 3, 2471, https://doi.org/10.1038/srep02471, 2013.
Ghiglione, J. F., Mevel, G., Pujo-Pay, M., Mousseau, L., Lebaron, P., and
Goutx, M.: Diel and seasonal variations in abundance, activity, and
community structure of particle-attached and free-living bacteria in NW
Mediterranean Sea, Microb. Ecol., 54, 217–231, 2007.
Ghiglione, J. F., Conan, P., and Pujo-Pay, M.: Diversity of total and active
free-living vs. particle-attached bacteria in the euphotic zone of the NW
Mediterranean Sea, FEMS Microbiol. Lett., 299, 9–21, 2009.
Giovannoni, S. J. and Stingl, U.: Molecular diversity and ecology of
microbial plankton, Nature, 437, 343–348, https://doi.org/10.1038/nature04158, 2005.
Giovannoni, S. J., Cameron, Thrash J., and Temperton, B.: Implications of
streamlining theory for microbial ecology, ISME J., 8, 1553–1565,
https://doi.org/10.1038/ismej.2014.60, 2014.
Gómez-Pereira, P. R., Kennaway, G., Fuchs, B. M., Tarran, G. A., and
Zubkov, M. V.: Flow cytometric identification of Mamiellales clade II in the
Southern Atlantic Ocean, FEMS Microbiol. Ecol., 83, 664–671, 2013.
Gong, G. C., Liu, K. K., Liu, C. T., Pai, and S. C.: The chemical hydrography of the
South China Sea west of Luzon and a comparison with the West Philippine Sea,
Terr. Atmos. Ocean Sci., 3, 587–602, 1992.
Gonzalez, J. M., Fernandez-Gomez, B., Fernandez-Guerra, A., Gomez-Consarnau,
L., Sanchez, O., and Coll-Llado, M.: Genome analysis of the
proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria),
P. Natl. Acad. Sci. USA, 105, 8724–8729, 2008.
Green, P. N.: Methylobacterium, in: The Prokaryotes: A Handbook on the Biology of Bacteria,
edited by: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K. H., and
Stackebrandt, E., Springer, New York, 5, 257–265, 2006.
Griffith, P., Shiah, F., Gloersen, K., Ducklow, H. W., and Fletcher, M.: Activity
and distribution of attached bacteria in Chesapeake Bay, Mar. Ecol. Prog.
Ser., 108, 1–10, 1994.
Grossart, H. P.: Ecological consequences of bacterioplankton lifestyles:
changes in concepts are needed, Env. Microbiol. Rep., 2, 706–714, 2010.
Grossart, H. P., Kiorboe, T., Tang, K., Allgaier, M., Yam, E. M., and Ploug, H.:
Interactions between marine snow and heterotrophic bacteria: aggregate
formation and microbial dynamics, Aquat. Microb. Ecol., 42, 19–26, 2006.
Grossart, H.-P., Tang, K. W., Kiørboe, T., and Ploug, H.: Comparison of
cell-specific activity between free-living and attached bacteria using
isolates and natural assemblages, FEMS Microbiol. Lett., 266, 194–200, 2007.
Grote, J., Thrash, J. C., Huggett, M. J., Landry, Z. C., Carini, P.,
Giovannoni, S. J., and Rappé, M. S.: Streamlining and core genome
conservation among highly divergent members of the SAR11 clade, mBio, 3,
e00252-12, https://doi.org/10.1128/mBio.00252-12, 2012.
Haro-Moreno, J. M., Rodriguez-Valera, F., López-García,
Purificación, Moreira, D., and Martin-Cuadrado, A. B.: New insights into
marine group III Euryarchaeota, from dark to light, ISME J., 11,
1102–1117, 2017.
He, X., Xu, D., Bai, Y., Pan, D., Chen, T. A., Chen, X., and Gong, F.:
Eddy-entrained Pearl River plume into the oligotrophic basin of the South
China Sea, Cont. Shelf Res., 124, 117–124, 2016.
Hollibaugh, J. T., Wong, P. S., and Murrell, M. C.: Similarity of
particle-associated and free-living bacterial communities in northern San
Francisco Bay, California, Aquat. Microb. Ecol., 21, 103–114, 2000.
Huang, Y. N., Chen, F. J., Zhao, H., Zeng, Z., and Chen, J. F.: Concentration
distribution and structural features of nutrients in the northwest of South
China Sea in winter 2012, J. Appl. Oceanogr., 34, 310–316,
2015.
Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L.,
and Armbrust, E. V.: Untangling genomes from metagenomes: revealing an uncultured
class of marine Euryarchaeota, Science, 335, 587–590, 2012.
Jiao, N., Luo, T., Zhang, R., Yan, W., Lin, Y., Johnson, Z. I., Tian, J., Yuan, D., Yang, Q., Zheng, Q., Sun, J., Hu, D., and Wang, P.: Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean, Biogeosciences, 11, 2391–2400, https://doi.org/10.5194/bg-11-2391-2014, 2014.
Jing, H., Zhu, W., Liu, H., Zheng, L., and Zhang, Y.: Particle-attached and free-living archaeal communities in the benthic boundary layer of the Mariana Trench, Front. Microbiol., 9, 2821, https://doi.org/10.3389/fmicb.2018.02821, 2018.
Karner, M. and Herndl, G. J.: Extracellular enzymatic activity and secondary
production in free-living and marine-snow-associated bacteria, Mar.
Biol., 113, 341–347, 1992.
Karner, M. B., DeLong, E. F., and Karl, D. M.: Archaeal dominance in the
mesopelagic zone of the Pacific Ocean, Nature, 409, 507–510, 2001.
Kiorboe, T. and Jackson, G. A.: Marine snow, organic solute plumes, and
optimal chemosensory behavior of bacteria, Limnol. Oceanogr., 46, 1309–1318,
2001.
Koblížek, M., Béjà, O., Bidigare, R. R., Christensen, S.,
Benitez-Nelson, B., Vetriani, C., Kolber, M. K., Falkowski, P. G., and Kolber,
Z. S.: Isolation and characterization of Erythrobacter sp. strains from the upper ocean,
Arch. Microbiol., 180, 327–338, https://doi.org/10.1007/s00203-003-0596-6,
2003.
Kolber, Z. S., Van Dover, C. L., Niederman, R. A., and Falkowski, P. G.: Bacterial
photosynthesis in surface waters of the open ocean, Nature, 407, 177–179,
2000.
Könneke M, Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury,
J. B., and Stahl, D. A.: Isolation of an autotrophic ammonia-oxidizing marine
archaeon, Nature, 437, 543–546, 2005.
Laufkötter, C., John, J. G., Stock, C. A., and Dunne, J. P.: Temperature
and oxygen dependence of the remineralization of organic matter, Global
Biogeochem. Cy., 31, 1038–1050, 2017.
Lauro, F. M., McDougald, D., Thomas, T., Williams, T. J., Egan, S., Rice, S., DeMaere, M. Z., Ting, L., Ertan, H., Johnson, J., Ferriera, S., Lapidus, A., Anderson, I., Kyrpides, N., Munk, A. C., Detter, C., Han, C. S., Brown, M. V., Robb, F. T., Kjelleberg, S., and Cavicchioli, R.: The genomic basis of trophic strategy in marine bacteria, P. Natl. Acad. Sci. USA, 106, 15527–15533, https://doi.org/10.1073/pnas.0903507106, 2009.
Lee, C., Wakeham, S., and Arnosti, C.: Particulate organic matter in the sea:
the composition conundrum, Ambio, 33, 566–575, 2004.
Lee, Z. M.-P., Bussema, C., and Schmidt, T. M.: rrnDB: documenting the number
of rRNA and tRNA genes in bacteria and archaea, Nucl. Acid. Res., 37,
489–493, 2009.
Li, J., Wei, B., Wang, J., Liu, Y., Dasgupta, S., and Zhang, L.: Variation in
abundance and community structure of particle-attached and free-living
bacteria in the South China Sea, Deep-Sea Res. Pt. II,
122, 64–73, https://doi.org/10.1016/j.dsr2.2015.07.006, 2015.
Liang, W., Tang, D., and Luo, X.: Phytoplankton size structure in the western
South China Sea under the influence of a “jet-eddy system”, J. Mar.
Syst., 187, 82–95, 2018.
Lipsewers, Y. A., Hopmans, E. C., Sinninghe Damsté, J. S., and Villanueva,
L.: Potential recycling of thaumarchaeotal lipids by DPANN Archaea in
seasonally hypoxic surface marine sediments, Org. Geochem., 119, 101–109, 2018.
Liu, R. L., Wang, L., Liu, Q. F., Wang, Z. X., Li, Z. Z., and Fang, J. S.:
Depth-resolved distribution of particle-attached and free-living bacterial
communities in the water column of the New Britain Trench, Front.
Microbiol., 9, 625, https://doi.org/10.3389/fmicb.2018.00625, 2018a.
Liu, S., Riesen, A., and Liu, Z.: Differentiating the role of
different-sized microorganisms in peptide decomposition during incubations
using size-fractioned coastal seawater, J. Exp. Mar.
Biol. Ecol., 472, 97–106, 2015.
Liu, X., Li, M., Castelle, C. J., Probst, A. J., Zhou, Z., and Pan, J.:
Insights into the ecology, evolution, and metabolism of the widespread
woesearchaeotal lineages, Microbiome, 6, 102, https://doi.org/10.1186/s40168-018-0488-2, 2018b.
Long, R. A. and Azam, F.: Microscale patchiness of bacterioplankton
assemblage richness in seawater, Aquat. Microb. Ecol., 26, 103–113,
https://doi.org/10.3354/ame026103, 2001.
Martin-Cuadrado, A.-B., Rodriguez-Valera, F., Moreira, D., Alba, J. C.,
Ivars-Martinez, E., and Henn, M. R.: Hindsight in the relative abundance,
metabolic potential and genome dynamics of uncultivated marine archaea from
comparative metagenomic analyses of bathypelagic plankton of different
oceanic regions, ISME J., 2, 865–886, 2008.
Martin-Cuadrado, A.-B., Garcia-Heredia, I., Moltó, A.G.,
López-Úbeda, R., Kimes, N., López-García, P., Moreira, D.,
and Rodriguez-Valera, F.: A new class of marine euryarchaeota group II from the
Mediterranean deep chlorophyll maximum, ISME J., 9, 1619–1634,
https://doi.org/10.1038/ismej.2014.249, 2015.
Massana, R., Delong, E. F., and Pedros-Alio, C.: A few cosmopolitan
phylotypes dominate planktonic archaeal assemblages in widely different
oceanic provinces, Appl. Environ. Microbiol., 66, 1777–1787,
2000.
Meng, F., Dai, M., Cao, Z., Wu, K., Zhao, X., Li, X., Chen, J., and Gan, J.:
Seasonal dynamics of dissolved organic carbon under complex circulation
schemes on a large continental shelf: the northern South China Sea, J.
Geophys. Res.-Ocean., 122, 9415–9428, 2017.
Mestre, M., Ruiz-Gonzalez, C., Logares, R., Duarte, C. M., Gasol, J. M., and
Sala, M. M.: Sinking particles promote vertical connectivity in the ocean
microbiome, P. Natl. Acad. Sci. USA, 115, 6799–6807, 2018.
Mevel, G., Vernet, M., Goutx, M., and Ghiglione, J. F.: Seasonal to hour
variation scales in abundance and production of total and particle-attached
bacteria in the open NW Mediterranean Sea (0–1000 m), Biogeosciences, 5,
1573–1586, https://doi.org/10.5194/bg-5-1573-2008, 2008.
Milici, M., Deng, Z. L., Tomasch, J., Decelle, J., Wos-Oxley, M. L., Wang H.,
Jáuregui, R., Plumeier, I., Giebel, H. A., Badewien, T. H., Wurst, M.,
Pieper, D. H., Simon, M., and Wagner-Döbler, I.: Co-occurrence analysis of
microbial taxa in the Atlantic Ocean reveals high connectivity in the
free-living bacterioplankton, Front. Microbiol., 7, 649,
https://doi.org/10.3389/fmicb.2016.00649, 2016.
Milici, M., Vital, M., Tomasch, J., Badewien, T. H., Giebel, H. A., and Plumeier,
I.: Diversity and community composition of particle-associated and
free-living bacteria in mesopelagic and bathypelagic Southern Ocean water
masses: evidence of dispersal limitation in the Bransfield Strait, Limnol.
Oceanogr., 62, 1080–1095, https://doi.org/10.1002/lno.10487, 2017.
Mincer, T. J., Church, M. J., Taylor, L. T., Preston, C., Karl, D. M., and DeLong,
E. F.: Quantitative distribution of presumptive archaeal and bacterial
nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre, Environ.
Microbiol., 9, 1162–1175, 2007.
Mizuno, C. M., Rodriguez-Valera, F., and Ghai, R.: Genomes of planktonic acidimicrobiales: widening horizons for marine actinobacteria by metagenomics, mBio, 6, e02083-14, https://doi.org/10.1128/mBio.02083-14, 2015
Moeseneder, M. M., Winter, C., and Herndl, G. J.: Horizontal and vertical
complexity of attached and free-living bacteria of the eastern Mediterranean
Sea, determined by 16S rDNA and 16S rRNA fingerprints, Limnol. Oceanagr.,
46, 95–107, 2001.
Mönnich, J., Tebben, J., Bergemann, J., Case, R., Wohlrab, S., and Harder, T.: Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible, ISME J., 14, 1614–1625, https://doi.org/10.1038/s41396-020-0631-5, 2020.
Morris, S. A., Radajewski, S., Willison, T. W., and Murrell, J. C.: Identification
of the functionally active methanotroph population in a peat soil microcosm
by stable-isotope probing, Appl. Environ. Microbiol., 68, 1446–1453, 2002.
Ohene-Adjei, S., Teather, R. M., Ivan, M., and Forster, R. J.: Postinoculation protozoan establishment and association patterns of methanogenic Archaea in the ovine rumen, Appl. Environ. Microbiol., 73, 4609–4618, 2007.
Orsi, W. D., Smith, J. M., Wilcox, H. M., Swalwell, J. E., Carini, P., and Worden,
A. Z.: Ecophysiology of uncultivated marine euryarchaea is linked to
particulate organic matter, ISME J., 9, 1747–1763, 2015.
Orsi, W. D., Smith, J. M., Liu, S., Liu, Z., Sakamoto, C. M., Wilken, S., Poirier, C., Richards, T. A., Keeling, P. J., Worden, A. Z., and Santoro, A. E.: Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean, ISME J., 10, 2158–2173, https://doi.org/10.1038/ismej.2016.20, 2016.
Ortega-Retuerta, E., Joux, F., Jeffrey, W. H., and Ghiglione, J. F.: Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic), Biogeosciences, 10, 2747–2759, https://doi.org/10.5194/bg-10-2747-2013, 2013.
Peoples, L. M., Sierra, D., Oladayo, O., Qing, X., Alex, N., and Jessica, B.:
Vertically distinct microbial communities in the Mariana and Kermadec
Trenches, PLOS ONE, 13, e0195102, https://doi.org/10.1371/journal.pone.0195102, 2018.
Poretsky, R. S., Sun, S., Mou, X., and Moran, M. A.: Transporter genes
expressed by coastal bacterioplankton in response to dissolved organic
carbon, Environ. Microbiol., 12, 616–627, 2010.
Probst, A. J., Castelle, C. J., Singh, A., Brown, C. T., Anantharaman, K.,
Sharon, I., Hug, L. A., Burstein, D., Emerson, J. B., Thomas, B. C., and Banfield,
B. F.: Genomic resolution of a cold subsurface aquifer community provides
metabolic insights for novel microbes adapted to high CO2 concentrations,
Environ. Microbiol., 19, 459–74, 2017.
Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M.,
García-Villadangos, M., Moreno-Paz, M., Blanco, Y., and Parro, V.: Viable
cyanobacteria in the deep continental subsurface, P. Natl. Acad. Sci.
USA, 115, 10702–10707, https://doi.org/10.1073/pnas.1808176115, 2018.
Qin, W., Amin, S. A., Martens-Habbena, W., Walker, C. B., Urakawa, H., and Devol,
A. H.: Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy
and wide ecotypic variation, P. Natl. Acad. Sci. USA, 111, 12504–12509,
2014.
Qin, W., Heal, K. R., Ramdasi, R., Kobelt, J. N., Martens-Habbena, W.,
Bertagnolli, A. D., Amin, S. A., Walker, C. B., Urakawa, H.,
Könneke, M., Devol, A. H., Moffett, J. W., Armbrust, E. V.,
Jensen, G. J., Ingalls, A. E., and Stahl, D. A.: Nitrosopumilus maritimus gen. nov., sp.
nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing
archaea of the phylum Thaumarchaeota, Int. J. Syst. Evol. Microbiol., 67,
5067–5079, 2017.
Rieck, A., Herlemann, D. P. R., Jürgens, K., and Grossart, H.-P.:
Particle-associated differ from free-living bacteria in surface waters of
the Baltic Sea, Front. Microbiol., 6, 1297, https://doi.org/10.3389/fmicb.2015.01297, 2015.
Rinke, C., Rubino, F., Messer, L. F., Youssef, N., Parks, D. H.,
Chuvochina, M., Brown, M., Jeffries, T., Tyson, G. W., Seymour, J. R.,
and Hugenholtz, P.: A phylogenomic and ecological analysis of the globally
abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.), ISME
J., 13, 663–675, 2019.
Rinta-Kanto, J. M., Sun, S., Sharma, S., Kiene, R. P., and Moran, M. A.:
Bacterial community transcription patterns during a marine phytoplankton
bloom, Environ. Microbiol., 14, 228–239, 2012.
Salazar, G., Cornejo-Castillo, F. M., Borrull, E., Díez-Vives, C., Lara,
E., Vaqué, D., Arrieta, J. M., Duarte, C. M., Gasol, J. M., and Acinas, S. G.:
Particle-association lifestyle is a phylogenetically conserved trait in
bathypelagic prokaryotes, Mol. Ecol., 24, 5692–5706, 2015.
Salazar, G., Cornejo-Castillo, F. M., Benítez-Barrios, V., Fraile-Nuez,
E., Álvarez-Salgado, X. A., Duarte, C. M., Gasol, J. M., and Acinas, S. G.:
Global diversity and biogeography of deep-sea pelagic prokaryotes, ISME J.,
10, 596–608, 2016.
Simon, M., Grossart, H. P., Schweitzer, B., and Ploug, H.: Microbial ecology
of organic aggregates in aquatic ecosystems, Aquat. Microb. Ecol., 28,
175–211, 2002.
Smith, D. C., Simon, M., Alldredge, A. L., and Azam, F.: Intense hydrolytic
enzyme activity on marine aggregates and implications for rapid particle
dissolution, Nature, 359, 139–142, 1992.
Smith, M. W., Allen, L. Z., Allen, A. E., Herfort, L., and Simon, H. M.:
Contrasting genomic properties of free-living and particle-attached
microbial assemblages within a coastal ecosystem, Front. Microbiol.,
4, 120, https://doi.org/10.3389/fmicb.2013.00120, 2013.
Sun, F., Wang, Y., Wu, M., Jiang, Z., Sun, C., and Cheng, H.: Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea, PLoS ONE, 9, e111892, https://doi.org/10.1371/journal.pone.0111892, 2014.
Suter, E. A., Pachiadaki, M., Taylor, G. T., Astor, Y., and Edgcomb, V. P.:
Free-living chemoautotrophic and particle-attached heterotrophic prokaryotes
dominate microbial assemblages along a pelagic redox gradient, Environ.
Microbiol., 20, 693–712, 2018.
Suzuki, S., Kaneko, R., Kodama, T., Hashihama, F., Suwa, S., Tanita, I.,
Furuya, K., and Hamasaki, K.: Comparison of community structures between
particle-associated and free-living prokaryotes in tropical and subtropical
Pacific Ocean surface waters, J. Oceanogr., 73, 383–395, 2017.
Takai, K. and Horikoshi, K.: Genetic diversity of archaea in deep-sea
hydrothermal vent environments, Genetics, 152, 1285–1297, 1999.
Tarn, J., Peoples, L. M., Hardy, K., Cameron, J., and Bartlett, D. H.:
Identification of free-living and particle-associated microbial communities
present in hadal regions of the Mariana Trench, Front. Microbiol., 7, 665,
https://doi.org/10.3389/fmicb.2016.00665, 2016.
Teeling, H., Fuchs, B. M., Becher, D., Klockow, C., Gardebrecht, A., Bennke, C. M., Kassabgy, M., Huang, S., Mann, A. J., Waldmann, J., Weber, M., Klindworth, A., Otto, A., Lange, J., Bernhardt, J., Reinsch, C., Hecker, M., Peplies, J., Bockelmann, F. D., Callies, U., Gerdts, G., Wichels, A., Wiltshire, K. H., Glöckner, F. O., Schweder, T., and Amann, R.:
Substrate-controlled succession of marine bacterioplankton populations
induced by a phytoplankton bloom, Science, 336, 608–611, 2012.
Tully, B. J.: Metabolic diversity within the globally abundant Marine Group
II Euryarchaea offers insight into ecological patterns, Nat. Commun., 10,
271, https://doi.org/10.1038/s41467-018-07840-4, 2019.
Turley, C. M. and Mackie, P. J.: Biogeochemical significance of attached and
free-living bacteria and the flux of particles in the NE Atlantic Ocean,
Mar. Ecol. Prog. Ser., 115, 191–203, https://doi.org/10.3354/meps115191, 1994.
Turley, C. M. and Stutt, E. D.: Depth-related cell-specific bacterial leucine
incorporation rates on particles and its biogeochemical significance in the
Northwest Mediterranean, Limnol. Oceanogr., 45, 419–425,
https://doi.org/10.4319/lo.2000.45.2.0419, 2000.
Varela, M. M., Vanaken, H. M., Sintes, E., and Herndl, G.: Latitudinal trends of
Crenarchaeota, and bacteria, in the meso- and bathypelagic water masses of
the eastern north Atlantic, Environ. Microbiol., 10, 110–124, 2008.
Wang, Y., Wang, B., Dann, L. M., Mitchell, J. G., Hu, X., Tang, H., Zhang,
H., and Shen, Y.: Bacterial community structure in the Bohai Strait provides
insights into organic matter niche partitioning, Cont. Shelf Res.,
169, 46–54, 2018.
Wright, T. D., Vergin, K. L., Boyd, P. W., and Giovannoni, S. J.: A novel
delta-subdivision proteobacterial lineage from the lower ocean surface
layer, Appl. Environ. Microbiol., 63, 1441–1448, 1997.
Wu, J., Chung, S. W., Wen, L. S., Liu, K. K., Chen, Y. L. L., Chen, H. Y.,
and Karl, D. M.: Dissolved inorganic phosphorus, dissolved iron, and
trichodesmium in the oligotrophic South China Sea, Global Biogeochem.
Cy., 17, 1008, https://doi.org/10.1029/2002GB001924, 2003.
Yawata, Y., Cordero, O. X., Menolascina, F., Hehemann, J.-H., Polz, M. F.,
and Stocker, R.: Competition-dispersal tradeoff ecologically differentiates
recently speciated marine bacterioplankton populations, P. Natl. Acad.
Sci. USA, 111, 5622–5627, https://doi.org/10.1073/pnas.1318943111, 2014.
Yilmaz, P., Yarza, P., Rapp, J. Z., and Glöckner, F. O.: Expanding the
world of marine bacterial and archaeal clades, Front. Microbiol., 6, 1524,
https://doi.org/10.3389/fmicb.2015.01524, 2016.
Yung, C.-M., Ward, C. S., Davis, K. M., Johnson, Z. I., and Hunt, D. E.:
Insensitivity of diverse and temporally variable particle-associated
microbial communities to bulk seawater environmental parameters, Appl.
Environ. Microbiol., 82, 3431–3437, 2016.
Zhang, R., Liu, B., Lau, S. C. K., Ki, J. S., and Qian, P.: Particle-attached
and free-living bacterial communities in a contrasting marine environment:
Victoria Harbor, Hong Kong, FEMS Microbiol. Ecol., 61, 496–508, 2007.
Zhang, Y., Xiao, W., and Jiao, N.: Linking biochemical properties of
particles to particle-attached and free-living bacterial community structure
along the particle density gradient from freshwater to open ocean, J.
Geophys. Res.-Biogeo., 121, 2261–2274, https://doi.org/10.1002/2016JG003390, 2016.
Zhang, H., Wang, K., Shen, L., Chen, H., Hou, F., Zhou, X., Zhang, D., and Zhu, X.: Microbial community dynamics and assembly follow trajectories of an early-spring diatom bloom in a semienclosed bay, Appl. Environ. Microbiol., 84, e01000-18, https://doi.org/10.1128/AEM.01000-18, 2018.
Short summary
Few studies have focused on the particle-attached (PA) and free-living (FL) microbes of the deep ocean. Here we determined PA and FL microbial communities along depth profiles of the SCS. PA and FL fractions accommodated divergent microbial compositions, and most of them are potentially generalists with PA and FL dual lifestyles. A potential vertical connectivity between surface-specific microbes and those in the deep ocean was indicated, likely through microbial attachment to sinking particles.
Few studies have focused on the particle-attached (PA) and free-living (FL) microbes of the deep...
Altmetrics
Final-revised paper
Preprint