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Current mass balances of C, N, and P were estimated using a model (Fluxin = Fluxout + ΔFlux) from Gamak Bay, Korea, in August 2017, where eutrophication and reducing conditions are prevalent. To examine the current fluxes of particulate organic carbon (POC), nitrogen (PON), and phosphorus (POP), sinking and re-floating sediment traps were deployed, a sediment oxygen demand (SOD) chamber experiment and ex-situ nutrient incubation experiment were conducted, and Fick’s first law of diffusion was applied. The principal component analysis and cluster analysis were performed to identify the three groups of water masses based on the characteristics of the bay, including the effects of the reducing environment due to the anoxic water mass using 14 bottom water quality parameters. In the reducing environment (sampling point GA4), the SOD20 flux was 3047.2 mg O2/m2/d. Additionally, the net sinking POC flux was 861.0 mg C/m2/d, while 131.8% of the net sinking POC flux (1134.5 mg C/m2/d) was removed toward the overlying water. This indicates that the organic matter that had been deposited was decomposed as a flux of 273.6 mg C/m2/d. The net sinking PON flux was 187.9 mg N/m2/d, whereas 15.8% of the net sinking PON flux was eluted, and 84.2% remained in the surface sediments. The dissolved inorganic nitrogen (DIN) elution flux from the surface sediments consisted of NH4+ elution (33.7 mg N/m2/d) and NOx− elution (−4.1 mg N/m2/d) fluxes. Despite the net sinking POP flux being 26.0 mg P/m2/d, the 47.7 mg P/m2/d of DIP elution flux (179.5% of the net sinking POP flux) was eluted to the overlying water. Similar to C mass balance, the additional elution flux occurred. Therefore, severe eutrophication (16.5 of the Okaichi eutrophication index) with the lowest N:P ratio (2.6) in GA4 was noted. This indicates that not only the freshly exported organic matter to the surface sediments but also the biochemical processes under anoxic conditions played an essential role as a remarkable nutrient source–particularly P–for eutrophication in Gamak Bay, Korea.

In ocean waters, anaerobic microbial respiration should be confined to the anoxic waters found in coastal regions and tropical oxygen minimum zones, where it is energetically favourable. However, recent molecular and geochemical evidence has pointed to a much broader distribution of denitrifying and sulfate-reducing microbes. Anaerobic metabolisms are thought to thrive in microenvironments that develop inside sinking organic aggregates, but the global distribution and geochemical significance of these microenvironments is poorly understood. Here, we develop a new size-resolved particle model to predict anaerobic respiration from aggregate properties and seawater chemistry. Constrained by observations of the size spectrum of sinking particles, the model predicts that denitrification and sulfate reduction can be sustained throughout vast, hypoxic expanses of the ocean, and could explain the trace metal enrichment observed in particles due to sulfide precipitation. Globally, the expansion of the anaerobic niche due to particle microenvironments doubles the rate of water column denitrification compared with estimates based on anoxic zones alone, and changes the sensitivity of the marine nitrogen cycle to deoxygenation in a warming climate.

Oxygen deprivation and hydrogen sulfide toxicity are considered potent kill mechanisms during the mass extinction just before the Permian–Triassic boundary (~251.9 million years ago). However, the mechanism that drove vast stretches of the ocean to an anoxic state is unclear. Here, we present palaeoredox and phosphorus speciation data for a marine bathymetric transect from Svalbard. This shows that, before the extinction, enhanced weathering driven by Siberian Traps volcanism increased the influx of phosphorus, thus enhancing marine primary productivity and oxygen depletion in proximal shelf settings. However, this non-sulfidic state efficiently sequestered phosphorus in the sediment in association with iron minerals, thus restricting the intensity and spatial extent of oxygen-depleted waters. The collapse of vegetation on land immediately before the marine extinction changed the relative weathering influx of iron and sulfate. The resulting transition to euxinic (sulfidic) conditions led to enhanced remobilization of bioavailable phosphorus, initiating a feedback that caused the spread of anoxic waters across large portions of the shelf. This reconciles a lag of >0.3 million years between the onset of enhanced weathering and the development of widespread, but geographically variable, ocean anoxia, with major implications for extinction selectivity.Phosphorus remobilized from seafloor sediments due to a reduced influx of iron-oxide from land led to widespread anoxia during the end-Permian mass extinction, according to palaeoredox and phosphorus speciation proxy records from Svalbard.

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and δ13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere.

The aquatic networks that connect soils with oceans receive each year 5.1 Pg of terrestrial carbon to transport, bury and process. Stagnant sections of aquatic networks often become anoxic. Mineral surfaces attract specific components of organic carbon, which are released under anoxic conditions to the pool of dissolved organic matter (DOM). The impact of the anoxic release on DOM molecular composition and reactivity in inland waters is unknown. Here, we report concurrent release of iron and DOM in anoxic bottom waters of northern lakes, removing DOM from the protection of iron oxides and remobilizing previously buried carbon to the water column. The deprotected DOM appears to be highly reactive, terrestrially derived and molecularly distinct, generating an ambient DOM pool that relieves energetic constraints that are often assumed to limit carbon turnover in anoxic waters. The Fe-to-C stoichiometry during anoxic mobilization differs from that after oxic precipitation, suggesting that up to 21% of buried OM escapes a lake-internal release-precipitation cycle, and can instead be exported downstream. Although anoxic habitats are transient and comprise relatively small volumes of water on the landscape scale, our results show that they may play a major role in structuring the reactivity and molecular composition of DOM transiting through aquatic networks and reaching the oceans.

The ocean is a net source of N 2 O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N 2 O via microbial N 2 O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand N 2 O consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic seawater for the first time. We find that the substrate affinity, O 2 tolerance, and community composition of N 2 O-consuming microbes in oxic waters differ from those in the underlying anoxic layers. Kinetic parameters determined here are used to model in situ N 2 O production and consumption rates. Estimated in situ rates differ from measured rates, confirming the necessity to consider kinetics when predicting N 2 O cycling. Microbes from the oxic layer consume N 2 O under anoxic conditions at a much faster rate than microbes from anoxic zones. These experimental results are in keeping with model results which indicate that N 2 O consumption likely takes place above the oxygen deficient zone (ODZ). Thus, the dynamic layer with steep O 2 and N 2 O gradients right above the ODZ is a previously ignored potential gatekeeper of N 2 O and should be accounted for in the marine N 2 O budget.

Methane (CH4) emissions from reservoirs are responsible for most of the atmospheric climatic forcing of these aquatic ecosystems, comparable to emissions from paddies or biomass burning. Primarily, CH4 is produced during the anaerobic mineralization of organic carbon in anoxic sediments by methanogenic archaea. However, the origin of the recurrent and ubiquitous CH4 supersaturation in oxic waters (i.e., the methane paradox) is still controversial. Here, we determined the dissolved CH4 concentration in the water column of 12 reservoirs during summer stratification and winter mixing to explore CH4 sources in oxic waters. Reservoir sizes ranged from 1.18 to 26.13 km(2). We found that dissolved CH4 in the water column varied by up to 4 orders of magnitude (0.02-213.64 mu mol L-1), and all oxic depths were consistently supersaturated in both periods. Phytoplanktonic sources appear to determine the concentration of CH4 in these reservoirs primarily. In anoxic waters, the depth-cumulative chlorophyll a concentration, a proxy for the phytoplanktonic biomass exported to sediments, was correlated to CH4 concentration. In oxic waters, the photosynthetic picoeukaryotes' abundance was significantly correlated to the dissolved CH4 concentration during both the stratification and the mixing. The mean depth of the reservoirs, as a surrogate of the vertical CH4 transport from sediment to the oxic waters, also contributed notably to the CH4 concentration in oxic waters. Our findings suggest that photosynthetic picoeukaryotes can play a significant role in determining CH4 concentration in oxic waters, although their role as CH4 sources to explain the methane paradox has been poorly explored.

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria , or in unclassified archaeal viruses predicted to infect Thaumarchaeota . Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.