News

Editorial: Recent developments in oxygen minimum zones biogeochemistry

Abstract.

"Marine Oxygen Minimum Zones (OMZs) modulate biogeochemical cycles, and directly impact climate dynamics by influencing air-sea fluxes of the potent greenhouse gases methane and nitrous oxide (Levin, 2018). OMZs are formed in regions of weak oxygen (O2) supply from physical ventilation and high integrated microbial O2 demand fueled by downward organic flux from overlying surface waters. The ocean’s major OMZs are found in the Eastern Tropical South and North Pacific Ocean and the Arabian Sea and Bay of Bengal in the Indian Ocean (Karstensen et al., 2008; Stramma et al., 2008). [...]".

 

Source: Frontiers in Marine Science
Authors: Annie Bourbonnais et al.
DOI: https://doi.org/10.3389/fmars.2023.1333731

Read the full article here.


Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Abstract.

"Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3– to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within [...]".

 

Source: Nature
Authors: Irene H. Zhang et al.
DOI: https://doi.org/10.1038/s43705-023-00284-y

Read the full article here.


A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Abstract. 

"Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonasfrom the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0−4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. [...]".

 

Source: Nature
Authors: Massimiliano Molari et al.
DOI: https://doi.org/10.1038/s41564-023-01342-w

Read the full article here.


Insights into prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal, a pronounced Oxygen Minimum Zone

Abstract. 

"Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (≤1 μM O2) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 μM O2). [...]". 

 

Source: Microbiology Spectrum
Authors: Bowei Gu et al. 
DOI: https://doi.org/10.1128/spectrum.00892-21

Read the full article here.


Biotic induction and microbial ecological dynamics of Oceanic Anoxic Event 2

Abstract. 

"Understanding the causal mechanisms of past marine deoxygenation is critical to predicting the long-term Earth systems response to climate change. However, the processes and events preceding widespread carbon burial coincident with oceanic anoxic events remain poorly constrained. Here, we report a comprehensive biomarker inventory enveloping Oceanic Anoxic Event 2 that captures microbial communities spanning epipelagic to benthic environments in the southern proto-North Atlantic Ocean. We identify an abrupt, sustained increase in primary productivity that predates Oceanic Anoxic Event 2 by ∼220 ± 4 thousand years, well before other geochemical proxies register biogeochemical perturbations. [...]". 

 

Source: Communications Earth & Environment 
Authors: Gregory T. Connock et al. 
DOI: https://doi.org/10.1038/s43247-022-00466-x 

Read the full article here.


Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean

Abstract.

"Phytoplankton is composed of a broad-sized spectrum of phylogenetically diverse microorganisms. Assessing CO2-fixation intra- and inter-group variability is crucial in understanding how the carbon pump functions, as each group of phytoplankton may be characterized by diverse efficiencies in carbon fixation and export to the deep ocean. We measured the CO2-fixation of different groups of phytoplankton at the single-cell level around the naturally iron-fertilized Kerguelen plateau (Southern Ocean)[...]"

 

Source: The ISME Journal 
Authors: Solène Irion et al
DOI: https://doi.org/10.1038/s41396-021-00915-z

Read the full article here.


Fishing trawlers could harm water quality by disrupting seafloor microbes

"Fishing boats that drag nets along the sea floor to catch seafood can indiscriminately harm marine life and destroy habitat. Now, a new study suggests “bottom trawling” can also disrupt the ability of microbes in sediment to remove excess nutrients in coastal waters, potentially increasing that pollution. “This is one of the first papers to look at actual biogeochemical effects of bottom trawling,” says Sebastiaan van de Velde, a marine biogeochemist at the University of California, Riverside, who was not involved. “The whole angle is very novel.” [...]"

Source: Science

Read the full article here.


Discovery and Mapping of the Triton Seep Site, Redondo Knoll: Fluid Flow and Microbial Colonization Within an Oxygen Minimum Zone

Abstract.

"This paper examines a deep-water (∼900 m) cold-seep discovered in a low oxygen environment ∼30 km off the California coast in 2015 during an E/V Nautilus telepresence-enabled cruise. This Triton site was initially detected from bubble flares identified via shipboard multibeam sonar and was then confirmed visually using the remotely operated vehicle (ROV) Hercules. High resolution mapping (to 1 cm resolution) and co-registered imaging has provided us with a comprehensive site overview – both of the geologic setting and the extent of the associated microbial colonization. [...]"

Source: Frontiers in Marine Science
Authors: Jamie K. S. Wagner et al.
DOI: 10.3389/fmars.2020.00108

Read the full article here.


Interactions of anaerobic ammonium oxidizers and sulfide-oxidizing bacteria in a substrate-limited model system mimicking the marine environment

Abstract. 

"In nature anaerobic ammonium oxidation (anammox) and denitrification processes convert fixed nitrogen to gaseous nitrogen compounds, which are then released to the atmosphere. While anammox bacteria produce N2 from ammonium and nitrite, in the denitrification process nitrate and nitrite are converted to N2 and the greenhouse gas nitrous oxide (N2O). [...]"

Source: FEMS Microbiology Ecology
Authors: Lina Russ et al. 
DOI: 10.1093/femsec/fiz137

Read the full article here.


Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone

Abstract.

"Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2) and NO2 to nitrate (NO3), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). [...]"

Source: PLoS ONE
Authors: Evan Lau et al.
DOI: 10.1371/journal.pone.0217136

Read the full article here.


As oceans warm, microbes could pump more CO2 back into air, study warns

"The world's oceans soak up about a quarter of the carbon dioxide that humans pump into the air each year -- a powerful brake on the greenhouse effect. In addition to purely physical and chemical processes, a large part of this is taken up by photosynthetic plankton as they incorporate carbon into their bodies. When plankton die, they sink, taking the carbon with them. Some part of this organic rain will end up locked into the deep ocean, insulated from the atmosphere for centuries or more. [...]"

Source: EurekAlert!

Read the full article here.


Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones

Abstract.

"Marine oxygen-deficient zones (ODZs) are naturally occurring midlayer oxygen-poor regions of the ocean, sandwiched between oxygenated surface and deep layers. In the absence of oxygen, microorganisms in ODZs use other compounds, such as oxidized forms of nitrogen and sulfur, as terminal electron acceptors. [...]"

Source: PNAS
Authors: Jaclyn K. Saunders et al.
DOI: 10.1073/pnas.1818349116

Read the full article here.


Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

Abstract.

"Rich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditions. [...]"

Source: PLoS ONE
Authors: Lauren Gillies Campbell et al.
DOI: 10.1371/journal.pone.0209055

Read the full article here.

 


Microbial ecosystem dynamics drive fluctuating nitrogen loss in marine anoxic zones

Abstract.

"The dynamics of nitrogen (N) loss in the ocean’s oxygen-deficient zones (ODZs) are thought to be driven by climate impacts on ocean circulation and biological productivity. Here we analyze a data-constrained model of the microbial ecosystem in an ODZ and find that species interactions drive fluctuations in local- and regional-scale rates of N loss, even in the absence of climate variability. [...]"

Source: PNAS
Authors: Justin L. Penn et al.
DOI: 10.1073/pnas.1818014116

Read the full article here.


The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally

Abstract.

"The discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents in 1977 changed our view of biology. Chemosynthetic bacteria and archaea form the foundation of vent ecosystems by exploiting the chemical disequilibrium between reducing hydrothermal fluids and oxidizing seawater, harnessing this energy to fix inorganic carbon into biomass. [...]"

Source: Nature Reviews Microbiology
Author: Gregory J. Dick
DOI: 10.1038/s41579-019-0160-2

Read the full article here.


Unexpectedly high diversity of anammox bacteria detected in deep-sea surface sediments of the South China Sea

Abstract.

"Ca. Scalindua is an exclusive genus of anammox bacteria known to exhibit low diversity found in deep-sea ecosystems. In this study, the community composition of anammox bacteria in surface sediments of the South China Sea (SCS) was analyzed using high-throughput sequencing techniques. Results indicated that the dominant OTUs were related to three different genera of anammox bacteria, identified as Ca. Scalindua (87.29%), Ca. Brocadia (10.27%) and Ca. Kuenenia (2.44%), in order of decreasing abundance. [...]"

Source: FEMS Microbiology Ecology
Authors: Jiapeng Wu et al.
DOI: 10.1093/femsec/fiz013

Read the full article here.


Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments

Abstract.

"Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm−3 d−1) and the high sulfide treatment was not significantly different than the oxic treatment.  [...]"

Source: FEMS Microbiology Letters
Authors: Jane M. Caffrey, Stefano Bonaglia, Daniel J. Conley
DOI: 10.1093/femsle/fny288

Read the full article here.


The emergence of a globally productive biosphere

Abstract.

"A productive biosphere and oxygenated atmosphere are defining features of Earth and are fundamentally linked. Here I argue that cellular metabolism imposes central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. [...]"

Source: PeerJ Preprints
Author: Rogier Braakman
DOI: 10.7287/peerj.preprints.27269v1

Read the full article here.


Microbial niches in marine oxygen minimum zones

Abstract.

"In the ocean’s major oxygen minimum zones (OMZs), oxygen is effectively absent from sea water and life is dominated by microorganisms that use chemicals other than oxygen for respiration. Recent studies that combine advanced genomic and chemical detection methods are delineating the different metabolic niches that microorganisms can occupy in OMZs. Understanding these niches, the microorganisms that inhabit them, and their influence on marine biogeochemical cycles is crucial as OMZs expand with increasing seawater temperatures."

Source: Nature Reviews Microbiology
Authors: Anthony D. Bertagnolli & Frank J. Stewart
DOI: 10.1038/s41579-018-0087-z

Read the full article here.


Increased biofilm formation due to high-temperature adaptation in marine Roseobacter

Abstract.

"Ocean temperatures will increase significantly over the next 100 years due to global climate change. As temperatures increase beyond current ranges, it is unclear how adaptation will impact the distribution and ecological role of marine microorganisms. To address this major unknown, we imposed a stressful high-temperature regime for 500 generations on a strain from the abundant marine Roseobacter clade. High-temperature-adapted isolates significantly improved their fitness but also increased biofilm formation at the air–liquid interface.  [...]"

Source: Nature Microbiology
Authors: Alyssa G. Kent et al.
DOI: 10.1038/s41564-018-0213-8

Read the fulll article here.


Ecology and evolution of seafloor and subseafloor microbial communities

Abstract.

"Vast regions of the dark ocean have ultra-slow rates of organic matter sedimentation, and their sediments are oxygenated to great depths yet have low levels of organic matter and cells. Primary production in the oxic seabed is supported by ammonia-oxidizing archaea, whereas in anoxic sediments, novel, uncultivated groups have the potential to produce H2 and CH4, which fuel anaerobic carbon fixation. [...]"

Source: Nature Reviews Microbiology
Authors: William D. Orsi
DOI: 10.1038/s41579-018-0046-8

Read the full article here.


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

Abstract.

"Members of the gammaproteobacterial clade SUP05 couple water column sulfide oxidation to nitrate reduction in sulfidic oxygen minimum zones (OMZs). Their abundance in offshore OMZ waters devoid of detectable sulfide has led to the suggestion that local sulfate reduction fuels SUP05-mediated sulfide oxidation in a so-called “cryptic sulfur cycle”. [...]"

Source: Nature Communications
Authors: Cameron M. Callbeck et al.
DOI: 10.1038/s41467-018-04041-x

Read the full article here.


Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity

Abstract.

"The Kryos Basin is a deep-sea hypersaline anoxic basin (DHAB) located in the Eastern Mediterranean Sea (34.98°N 22.04°E). It is filled with brine of re-dissolved Messinian evaporites and is nearly saturated with MgCl2-equivalents, which makes this habitat extremely challenging for life. The strong density difference between the anoxic brine and the overlying oxic Mediterranean seawater impedes mixing, giving rise to a narrow chemocline. [...]"

Source: The ISME Journal
Authors: Lea Steinle et al.
DOI: 10.1038/s41396-018-0107-z

Read the full article here.


The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Abstract.

"Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic ‘Candidatus Methanothrix paradoxum’, which is active in oxic soils. [...]"

Source: FEMS Microbiology Ecology
Authors: Michiel H in ‘t Zandt et al.
DOI: 10.1093/femsec/fiy064


Coccolithovirus facilitation of carbon export in the North Atlantic

Abstract.

"Marine phytoplankton account for approximately half of global primary productivity, making their fate an important driver of the marine carbon cycle. Viruses are thought to recycle more than one-quarter of oceanic photosynthetically fixed organic carbon, which can stimulate nutrient regeneration, primary production and upper ocean respiration2 via lytic infection and the ‘virus shunt’. [...]"

Source: Nature Microbiology
Authors: Christien P. Laber
DOI: 10.1038/s41564-018-0128-4

Read the full article here.


A missing link in the estuarine nitrogen cycle?: Coupled nitrification-denitrification mediated by suspended particulate matter

Abstract.

"In estuarine and coastal ecosystems, the majority of previous studies have considered coupled nitrification-denitrification (CND) processes to be exclusively sediment based, with little focus on suspended particulate matter (SPM) in the water column. Here, we present evidence of CND processes in the water column of Hangzhou Bay, one of the largest macrotidal embayments in the world. [...]"

Source: Scientific Reports
Authors: Weijing Zhu et al.
DOI: 10.1038/s41598-018-20688-4

Read the full article here.


The microbial nitrogen-cycling network

Abstract.

"Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth. [...]"

Source: Nature Reviews Microbiology
Authors: Marcel M. M. Kuypers, Hannah K. Marchant & Boran Kartal
DOI: 10.1038/nrmicro.2018.9

Read the full article here.


Insights into the metabolic functioning of a multipartner ciliate symbiosis from oxygen-depleted sediments

Abstract.

"Symbioses between anaerobic or microaerophilic protists and prokaryotes are common in anoxic and oxygen-depleted habitats ranging from marine sediments to gastrointestinal tracts. Nevertheless, little is known about the mechanisms of metabolic interaction between partners. In these putatively syntrophic associations, consumption of fermentative end products (e.g., hydrogen) by the prokaryotic symbionts is thought to facilitate protistan anaerobic metabolism.  [...]"

Source: Molecular Ecology
Authors: R. A. Beinart et al.
DOI: 10.1111/mec.14465

Read the full article here.


Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients

Abstract.

"Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant “microbial dark matter” phylum Marinimicrobia along defined energy gradients. [...]"

Source: Nature Communications
Authors: Alyse K. Hawley et al.
DOI: 10.1038/s41467-017-01376-9

Read the full article here.


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