Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility.

Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake.

Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows.

Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of in the Mediterranean Sea.

Niche partitioning by photosynthetic plankton as a driver of CO-fixation across the oligotrophic South Pacific Subtropical Ocean.

Oligotrophic ocean gyre ecosystems may be expanding due to rising global temperatures [1-5]. Models predicting carbon flow through these changing ecosystems require accurate descriptions of phytoplankton communities and their metabolic activities [6]. We therefore measured distributions and activities of cyanobacteria and small photosynthetic eukaryotes throughout the euphotic zone on a zonal transect through the South Pacific Ocean, focusing on the ultraoligotrophic waters of the South Pacific Gyre (SPG).

Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification.

Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB).

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone.

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April-June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128-512 µm), even though anammox bacteria were not directly associated with particles.

Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat.

Diatoms are among the few eukaryotes known to store nitrate (NO ) and to use it as an electron acceptor for respiration in the absence of light and O . Using microscopy and N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day.

Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat.

Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with sulfur reducing bacteria (SRB).

Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration.

The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years.

Author Correction: Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments.

The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation, but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor.

Anaerobic ammonium oxidation is a major N-sink in aquifer systems around the world.

Global-scale N-oxide contamination of groundwater within aquifers occurs due to the widespread use of N-bearing fertilizers and chemicals, threatening both human and environmental health. However, the conversion of these pollutants in active nitrogen (N) cycling processes in the subsurface biosphere still remains unclear. This study investigates the global occurrence of anaerobic ammonium oxidation (anammox) in aquifers, where anammox was found to be turned on and off between saturated and unsaturated soil horizons, and contributed 36.

HS events in the Peruvian oxygen minimum zone facilitate enhanced dissolved Fe concentrations.

Dissolved iron (DFe) concentrations in oxygen minimum zones (OMZs) of Eastern Boundary Upwelling Systems are enhanced as a result of high supply rates from anoxic sediments. However, pronounced variations in DFe concentrations in anoxic coastal waters of the Peruvian OMZ indicate that there are factors in addition to dissolved oxygen concentrations (O) that control Fe cycling. Our study demonstrates that sediment-derived reduced Fe (Fe(II)) forms the main DFe fraction in the anoxic/euxinic water column off Peru, which is responsible for DFe accumulations of up to 200 nmol L.

Turbulence simultaneously stimulates small- and large-scale CO sequestration by chain-forming diatoms in the sea.

Chain-forming diatoms are key CO-fixing organisms in the ocean. Under turbulent conditions they form fast-sinking aggregates that are exported from the upper sunlit ocean to the ocean interior. A decade-old paradigm states that primary production in chain-forming diatoms is stimulated by turbulence.

Filamentous Giant Beggiatoaceae from the Guaymas Basin Are Capable of both Denitrification and Dissimilatory Nitrate Reduction to Ammonium.

Filamentous large sulfur-oxidizing bacteria (FLSB) of the family are globally distributed aquatic bacteria that can control geochemical fluxes from the sediment to the water column through their metabolic activity. FLSB mats from hydrothermal sediments of Guaymas Basin, Mexico, typically have a "fried-egg" appearance, with orange filaments dominating near the center and wider white filaments at the periphery, likely reflecting areas of higher and lower sulfide fluxes, respectively. These FLSB store large quantities of intracellular nitrate that they use to oxidize sulfide.

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

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". We examined the distribution and metabolic capacity of SUP05 in Peru Upwelling waters, using a combination of oceanographic, molecular, biogeochemical and single-cell techniques.

Methane stimulates massive nitrogen loss from freshwater reservoirs in India.

The fate of the enormous amount of reactive nitrogen released to the environment by human activities in India is unknown. Here we show occurrence of seasonal stratification and generally low concentrations of dissolved inorganic combined nitrogen, and high molecular nitrogen (N) to argon ratio, thus suggesting seasonal loss to N in anoxic hypolimnia of several dam-reservoirs. However, N-experiments yielded low rates of denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium-except in the presence of methane (CH) that caused ~12-fold increase in denitrification.

Metabolic versatility of a novel N -fixing Alphaproteobacterium isolated from a marine oxygen minimum zone.

The N -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru.

Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously.

Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales.

Enhanced Nitrogen Loss by Eddy-Induced Vertical Transport in the Offshore Peruvian Oxygen Minimum Zone.

The eastern tropical South Pacific (ETSP) upwelling region is one of the ocean's largest sinks of fixed nitrogen, which is lost as N2 via the anaerobic processes of anammox and denitrification. One-third of nitrogen loss occurs in productive shelf waters stimulated by organic matter export as a result of eastern boundary upwelling. Offshore, nitrogen loss rates are lower, but due to its sheer size this area accounts for ~70% of ETSP nitrogen loss.

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle.

Microbial dinitrogen (N) fixation, the nitrogenase enzyme-catalysed reduction of N gas into biologically available ammonia, is the main source of new nitrogen (N) in the ocean. For more than 50 years, oceanic N fixation has mainly been attributed to the activity of the colonial cyanobacterium Trichodesmium. Other smaller N-fixing microorganisms (diazotrophs)-in particular the unicellular cyanobacteria group A (UCYN-A)-are, however, abundant enough to potentially contribute significantly to N fixation in the surface waters of the oceans.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs).

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments.

Most microorganisms live in environments where nutrients are limited and fluctuate over time. Cells respond to nutrient fluctuations by sensing and adapting their physiological state. Recent studies suggest phenotypic heterogeneity(1) in isogenic populations as an alternative strategy in fluctuating environments, where a subpopulation of cells express a function that allows growth under conditions that might arise in the future(2-9).