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1. Microbial mechanisms and ecosystem flux estimation for aerobic NO _y emissions from deciduous forest soils

   https://doi.org/10.1073/pnas.1814632116  

   Mushinski, Ryan M. ; Phillips, Richard P. ; Payne, Zachary C. ; Abney, Rebecca B. ; Jo, Insu ; Fei, Songlin ; Pusede, Sally E. ; White, Jeffrey R. ; Rusch, Douglas B. ; Raff, Jonathan D. ( February 2019 , Proceedings of the National Academy of Sciences)

   Reactive nitrogen oxides (NO_y; NO_y= NO + NO₂+ HONO) decrease air quality and impact radiative forcing, yet the factors responsible for their emission from nonpoint sources (i.e., soils) remain poorly understood. We investigated the factors that control the production of aerobic NO_yin forest soils using molecular techniques, process-based assays, and inhibitor experiments. We subsequently used these data to identify hotspots for gas emissions across forests of the eastern United States. Here, we show that nitrogen oxide soil emissions are mediated by microbial community structure (e.g., ammonium oxidizer abundances), soil chemical characteristics (pH and C:N), and nitrogen (N) transformation rates (netmore »nitrification). We find that, while nitrification rates are controlled primarily by chemoautotrophic ammonia-oxidizing archaea (AOA), the production of NO_yis mediated in large part by chemoautotrophic ammonia-oxidizing bacteria (AOB). Variation in nitrification rates and nitrogen oxide emissions tracked variation in forest communities, as stands dominated by arbuscular mycorrhizal (AM) trees had greater N transformation rates and NO_yfluxes than stands dominated by ectomycorrhizal (ECM) trees. Given mapped distributions of AM and ECM trees from 78,000 forest inventory plots, we estimate that broadleaf forests of the Midwest and the eastern United States as well as the Mississippi River corridor may be considered hotspots of biogenic NO_yemissions. Together, our results greatly improve our understanding of NO_yfluxes from forests, which should lead to improved predictions about the atmospheric consequences of tree species shifts owing to land management and climate change.

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2. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

   https://doi.org/10.1038/s41598-019-53679-0  

   Orellana, Luis H. ; Hatt, Janet K. ; Iyer, Ramsunder ; Chourey, Karuna ; Hettich, Robert L. ; Spain, Jim C. ; Yang, Wendy H. ; Chee-Sanford, Joanne C. ; Sanford, Robert A. ; Löffler, Frank E. ; et al ( November 2019 , Scientific Reports)

   To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO₃⁻g⁻¹dry soil d⁻¹) and accumulation of N₂O after 192 hours of incubation. Nitrification activity (NH₄⁺ → NH₂OH → NO → NO₂^- → NO₃⁻) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable genemore »expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

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3. Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers

   https://doi.org/10.1128/mbio.02379-21  

   Podowski, Justin C. ; Paver, Sara F. ; Newton, Ryan J. ; Coleman, Maureen L. ( June 2022 , mBio)

   Giovannoni, Stephen J. (Ed.)

   ABSTRACT Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, whichmore »could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “ Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change. IMPORTANCE Microorganisms play critical roles in Earth’s nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth’s largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low-nutrient waters and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy by using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals the unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.« less
4. Imprint of trace dissolved oxygen on prokaryoplankton community structure in an oxygen minimum zone

   https://doi.org/doi:10.3389/fmars.2020.00360  

   Medina Faull, L. ; Mara, Paraskevi ; Taylor, G.T. ; Edgcomb, V.P. ( January 2020 , Frontiers in marine science)

   The Eastern Tropical North Pacific (ETNP) is a large, persistent, and intensifying oxygen minimum zone (OMZ) that accounts for almost half of the total area of global OMZs. Within the OMZ core (350–700 m depth), dissolved oxygen is typically near or below the analytical detection limit of modern sensors (10 nM). Steep oxygen gradients above and below the OMZ core lead to vertical structuring of microbial communities that also vary between particle-associated (PA) and free-living (FL) size fractions. Here, we use 16S amplicon sequencing (iTags) to analyze the diversity and distribution of prokaryotic populations between FL and PA size fractionsmore »and among the range of ambient redox conditions. The hydrographic conditions at our study area were distinct from those previously reported in the ETNP and other OMZs, such as the ETSP. Trace oxygen concentrations (0.35 mM) were present throughout the OMZ core at our sampling location. Consequently, nitrite accumulations typically reported for OMZ cores were absent as were sequences for anammox bacteria (Brocadiales genus Candidatus Scalindua), which are commonly found across oxic-anoxic boundaries in other systems. However, ammonia-oxidizing bacteria (AOB) and archaea (AOA) distributions and maximal autotrophic carbon assimilation rates (1.4 mM C d􀀀1) coincided with a pronounced ammonium concentration maximum near the top of the OMZ core. In addition, members of the genus Nitrospina, a dominant nitrite-oxidizing bacterial (NOB) clade were present suggesting that both ammonia and nitrite oxidation occur at trace oxygen concentrations. Analysis of similarity test (ANOSIM) and Non-metric Dimensional Scaling (nMDS) revealed that bacterial and archaeal phylogenetic representations were significantly different between size fractions. Based on ANOSIM and iTag profiles, composition of PA assemblages was less influenced by the prevailing depth-dependent biogeochemical regime than the FL fraction. Based on the presence of AOA, NOB and trace oxygen in the OMZ core we suggest that nitrification is an active process in the nitrogen cycle of this region of the ETNP OMZ.« less
5. Isotopic signals in an agricultural watershed suggest denitrification is locally intensive in riparian areas but extensive in upland soils

   https://doi.org/10.1007/s10533-022-00898-9  

   Sigler, W. A. ; Ewing, S. A. ; Wankel, S. D. ; Jones, C. A. ; Leuthold, S. ; Brookshire, E. N. ; Payn, R. A. ( March 2022 , Biogeochemistry)

   Abstract Nitrogen loss from cultivated soils threatens the economic and environmental sustainability of agriculture. Nitrate (NO 3 − ) derived from nitrification of nitrogen fertilizer and ammonified soil organic nitrogen may be lost from soils via denitrification, producing dinitrogen gas (N 2 ) or the greenhouse gas nitrous oxide (N 2 O). Nitrate that accumulates in soils is also subject to leaching loss, which can degrade water quality and make NO 3 − available for downstream denitrification. Here we use patterns in the isotopic composition of NO 3 − observed from 2012 to 2017 to characterize N loss to denitrificationmore »within soils, groundwater, and stream riparian corridors of a non-irrigated agroecosystem in the northern Great Plains (Judith River Watershed, Montana, USA). We find evidence for denitrification across these domains, expressed as a positive linear relationship between δ 15 N and δ 18 O values of NO 3 − , as well as increasing δ 15 N values with decreasing NO 3 − concentration. In soils, isotopic evidence of denitrification was present during fallow periods (no crop growing), despite net accumulation of NO 3 − from the nitrification of ammonified soil organic nitrogen. We combine previous results for soil NO 3 − mass balance with δ 15 N mass balance to estimate denitrification rates in soil relative to groundwater and streams. Substantial denitrification from soils during fallow periods may be masked by nitrification of ammonified soil organic nitrogen, representing a hidden loss of soil organic nitrogen and an under-quantified flux of N to the atmosphere. Globally, cultivated land spends ca. 50% of time in a fallow condition; denitrification in fallow soils may be an overlooked but globally significant source of agricultural N 2 O emissions, which must be reduced along-side other emissions to meet Paris Agreement goals for slowing global temperature increase.« less