The evolution of Earth’s biogeochemical nitrogen cycle

Financial support during the compilation of this manuscript was provided by the NASA postdoctoral program (EES), the NSF Graduate Research Fellowship Program (MAK), the Agouron Institute (MCK, RB) and the NSF FESD program (grant number 1338810, subcontract to RB).Nitrogen is an essential nutrient for all life on Earth and it acts as a major control on biological productivity in the modern ocean. Accurate reconstructions of the evolution of life over the course of the last four billion years therefore demand a better understanding of nitrogen bioavailability and speciation through time. The biogeochemical nitrogen cycle has evidently been closely tied to the redox state of the ocean and atmosphere. Multiple lines of evidence indicate that the Earth’s surface has passed in a non-linear fashion from an anoxic state in the Hadean to an oxic state in the later Phanerozoic. It is therefore likely that the nitrogen cycle has changed markedly over time, with potentially severe implications for the productivity and evolution of the biosphere. Here we compile nitrogen isotope data from the literature and review our current understanding of the evolution of the nitrogen cycle, with particular emphasis on the Precambrian. Combined with recent work on redox conditions, trace metal availability, sulfur and iron cycling on the early Earth, we then use the nitrogen isotope record as a platform to test existing and new hypotheses about biogeochemical pathways that may have controlled nitrogen availability through time. Among other things, we conclude that (a) abiotic nitrogen sources were likely insufficient to sustain a large biosphere, thus favoring an early origin of biological N2 fixation, (b) evidence of nitrate in the Neoarchean and Paleoproterozoic confirm current views of increasing surface oxygen levels at those times, (c) abundant ferrous iron and sulfide in the mid-Precambrian ocean may have affected the speciation and size of the fixed nitrogen reservoir, and (d) nitrate availability alone was not a major driver of eukaryotic evolution.PostprintPeer reviewe

Spatial and temporal trends in Precambrian nitrogen cycling: a Mesoproterozoic offshore nitrate minimum

We thank NSF EAR FESD grant #1338810 (RB), NASA grant NNX16AI37G (RB), the Agouron Institute (RB), the NASA Astrobiology Institute’s Virtual Planetary Laboratory (RB), the NSF Graduate Research Fellowship Program (MAK), and the Department of Earth and Space Sciences, University of Washington Goodspeed Geology Fellowship (MCK), Misch Fellowship (MCK), and the Kenneth C. Robbins Field Study Fellowship (2014, MCK) for funding.Fixed nitrogen is an essential nutrient for eukaryotes. As N2 fixation and assimilation of nitrate are catalyzed by metalloenzymes, it has been hypothesized that in Mesoproterozoic oceans nitrate was limited in offshore environments by low trace metal concentrations and high rates of denitrification in anoxic and episodically euxinic deep water masses, restricting eukaryotes to near-shore environments and limiting their evolutionary innovation. To date this hypothesis has only been tested in the Belt Supergroup (∼1.4 Ga), with results that support an onshore-offshore nitrate gradient as a potential control on eukaryote ecology. Here we present bulk nitrogen and organic carbon isotopic data from non-isochronous cross-basinal facies across the Bangemall (∼1.5 Ga) and the Roper (∼1.4-1.5 Ga) basins to better understand the extent and variability of onshore-offshore nitrogen isotope gradients in the Mesoproterozoic. Both basins show an average ∼1-2‰ enrichment in δ15Nbulk from deep to shallow facies, with a maximum range from -1‰ offshore to +7.5‰ onshore. Unlike the Belt basin, the Bangemall and Roper basins show some offshore δ15Nbulk values that are enriched beyond the isotopic range induced by biological N2 fixation alone. This suggests a mixture of aerobic and anaerobic metabolisms offshore. In shallow waters, where δ15Nbulk enrichment peaks, an aerobic nitrogen cycle was evidently operating vigorously. Even though isotopic signatures of aerobic nitrogen cycling are seen in all parts of the Bangemall and Roper basins, our data are consistent with a lateral gradient in nitrate availability within the photic zone, with higher concentrations in near-shore environments than offshore. The variability in δ15Nbulk values in each depositional environment and the consistently low δ15N values from Mesoproterozoic units compared to the Paleoproterozoic and Neoproterozoic suggest that nitrate concentrations in the global ocean were likely low. This trend is now seen in all three Mesoproterozoic basins so far examined, and contrasts with the Paleoproterozoic and Neoproterozoic where nearly all δ15Nbulk data plot above the N2 fixation window. Thus, we propose that the Mesoproterozoic ocean was characterized by a nitrate minimum between the Paleo- and Neoproterozoic, with the lowest concentrations in offshore environments. This inference is consistent with a Mesoproterozoic O2 decline following a temporary Paleoproterozoic O2 peak, and it further supports the idea that nitrate limitation offshore may have contributed to the restriction of photosynthetic eukaryotes to near-shore environments, delaying their rise to ecological dominance until the Neoproterozoic Era.PostprintPeer reviewe

Cover crop planting practices determine their performance in the U.S. Corn Belt

Cover crop growing periods in the western U.S. Corn Belt could be extended by planting earlier. We evaluated both pre-harvest broadcast interseeding and post-harvest drilling of the following cover crops: (a) cereal rye (Secale cereale L.) [RYE]; (b) a mix of rye + legumes + brassicas [MIX1], (c) a mix of rye + oat [Avena sativa L.] + legumes + brassicas (MIX2), (d) legumes [LEGU]) and (e) a no cover crop control. These were tested in continuous corn (Zea mays L.) [corn–corn] and soybean [Glycine max (L.) Merr.]–corn systems [soybean–corn] at three sites in Nebraska for their effect on cover crop productivity, soil nutrients, and subsequent corn performance. At the sites with wet fall weather, pre-harvest broadcasting increased cover crop biomass by 90%, to 1.29 Mg ha−1 for RYE and 0.87 Mg ha−1 for MIX1 in soybean–corn, and to 0.56 Mg ha−1 and 0.39 Mg ha−1 in corn–corn, respectively. At the drier site, post-harvest drilling increased biomass of RYE and MIX1 by 95% to 0.80 Mg ha−1 in soybean–corn. Biomass N uptake was highest in pre-harvest RYE and MIX1 at two sites in soybean–corn (35 kg ha−1). RYE and sometimes mixes reduced soil N, but effects on P, K, and soil organic C were inconsistent. In soybean–corn, corn yields decreased by 4% after RYE, and in corn–corn, by 4% after pre-harvest cover crops. Site-specific selection of cover crops and planting practices can increase their performance while minimizing impacts on corn

Friedrich Heinrich Jacobi: O Spinozinu nauku u pismima Mosesu Mendelssohnu / Spisi o sporu o božanskim stvarima i njihovoj objavi

Understanding how and when Earth's surface became oxygenated is essential for understanding its biogeochemical evolution. Incipient oxygenation of Earth's surface environments before the Great Oxidation Event (GOE; 2.4 Ga) has been well-documented, but the nature of these redox changes, whether protracted or transient, is poorly understood. We present nitrogen isotope ratios, selenium abundances, and selenium isotope ratios from the Jeerinah Formation (2.66 Ga; Fortescue Group, Western Australia) that represent (i) high-resolution evidence of transient surface ocean oxygenation 260 My before the GOE, (ii) a possible muted pulse of oxidative continental weathering, and (iii) the oldest firm evidence for nitrification and denitrification metabolisms. These results, in concert with previous studies, highlight the variability in mechanisms and magnitudes of Neoarchean oxygen fluctuations.Many paleoredox proxies indicate low-level and dynamic incipient oxygenation of Earth's surface environments during the Neoarchean (2.8textendash2.5 Ga) before the Great Oxidation Event (GOE) at 2.4 Ga. The mode, tempo, and scale of these redox changes are poorly understood, because data from various locations and ages suggest both protracted and transient oxygenation. Here, we present bulk rock and kerogen-bound nitrogen isotope ratios as well as bulk rock selenium abundances and isotope ratios from drill cores sampled at high stratigraphic resolution through the Jeerinah Formation (2.66 Ga; Fortescue Group, Western Australia) to test for changes in the redox state of the surface environment. We find that both shallow and deep depositional facies in the Jeerinah Formation display episodes of positive primary δ15N values ranging from +4 to +6textperthousand, recording aerobic nitrogen cycling that requires free O2 in the upper water column. Moderate selenium enrichments up to 5.4 ppm in the near-shore core may indicate coincident oxidative weathering of sulfide minerals on land, although not to the extent seen in the younger Mt. McRae Shale that records a well-documented textquotedblleftwhifftextquotedblright of atmospheric oxygen at 2.5 Ga. Unlike the Mt. McRae Shale, Jeerinah selenium isotopes do not show a significant excursion concurrent with the positive δ15N values. Our data are thus most parsimoniously interpreted as evidence for transient surface ocean oxygenation lasting less than 50 My, extending over hundreds of kilometers, and occurring well before the GOE. The nitrogen isotope data clearly record nitrification and denitrification, providing the oldest firm evidence for these microbial metabolisms.PostprintPeer reviewe

Cover crop productivity and subsequent soybean yield in the western Corn Belt

Cover crops (CC) in corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotations may prevent N loss and provide other ecosystem services but CC productivity in the western Corn Belt is limited by the short growing season. Our objective was to assess CC treatment and planting practice effects on CC biomass, spring soil nitrate concentrations, and soybean yield at two rainfed sites in eastern and one irrigated site in south-central Nebraska over 4 yr. Cover crop treatments (cereal rye [Secale cereale L.] [RYE] and a mix of rye, legume, and brassica species [MIX]) were planted by broadcast interseeding into corn stands in September (pre-harvest broadcast) or drilling after corn harvest (post-harvest drilled) and terminated 2 wk before planting soybean. Cover crop biomass and N uptake varied between years, but generally at the eastern sites, pre-harvest broadcasting produced more biomass than post-harvest drilling (1.64 and 0.79 Mg ha−1, respectively) and had greater N uptake (37 and 24 kg ha−1, respectively). At the south-central site, post-harvest drilling produced more than pre-harvest broadcasting (1.44 and 1.20 Mg ha−1, respectively). RYE had more biomass than MIX (1.41 and 1.09 Mg ha−1, respectively), but the same N uptake. Soil nitrate reductions after CC were small. In 3 of 12 site-years, soybean yielded less after pre-harvest CC. Yield reductions were not correlated to CC biomass, but were likely due to greater weed pressure. High CC productivity is necessary for high N uptake, and requires site-specific selection of planting practice and CC treatments

Cover Crops have Negligible Impact on Soil Water in Nebraska Maize–Soybean Rotation

One perceived cost of integrating winter cover cropping in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotation systems is the potential negative impact on soil water storage available for primary crop production. The objective of this 3-yr study was to evaluate the effects of winter cover crops on soil water storage and cover crop biomass production following no-till maize and soybean rotations. Locations were near Brule (west-central), Clay Center (south-central), Concord (northeast), and Mead (east-central), NE. Treatments included crop residue only (no cover crop) and a multi-species cover crop mix, both broadcast-seeded before primary crop harvest and drilled following harvest. Pre-harvest broadcast-seeded cereal rye (Secale cereale L.) was also included in the last year of the study because rye was observed to be the dominant component of the mix in spring biomass samples. Soil water content was monitored using neutron probe or gravimetric techniques. Mean aboveground cover crop biomass ranged from practically 0 to ~3,200 kg ha–1 across locations and cover crop treatments. Differences in the change in soil water storage between autumn and spring among treatments occurred in 4 of 20 location–rotation phase–years for the top 0.3 m of soil and 3 of 20 location–rotation phase–years for the 1.2-m soil profile. However, these differences were small (profile). In conclusion, winter cover crops did not have an effect on soil water content that would impact maize and soybean crop production

Inflammasome-Mediated IL-1β Production in Humans with Cystic Fibrosis

Inflammation and infection are major determinants of disease severity and consequently, the quality of life and outcome for patients with cystic fibrosis (CF). Interleukin-1 beta (IL-1β) is a key inflammatory mediator. Secretion of biologically active IL-1β involves inflammasome-mediated processing. Little is known about the contribution of IL-1β and the inflammasomes in CF inflammatory disease. This study examines inflammasome-mediated IL-1β production in CF bronchial epithelial cell lines and human patients with CF.Bronchial epithelial cell lines were found to produce negligible amounts of basal or stimulated IL-1β compared to hematopoeitic cells and they did not significantly upregulate caspase-1 activity upon inflammasome stimulation. In contrast, peripheral blood mononuclear cells (PBMCs) from both CF and healthy control subjects produced large amounts of IL-1β and strongly upregulated caspase-1 activity upon inflammasome stimulation. PBMCs from CF patients and controls displayed similar levels of caspase-1 activation and IL-1β production when stimulated with inflammasome activators. This IL-1β production was dependent on NF-κB activity and could be enhanced by priming with LPS. Finally, chemical inhibition of CFTR activity in control PBMCs and THP-1 cells did not significantly alter IL-1β or IL-8 production in response to P. aeruginosa.Hematopoeitic cells appear to be the predominant source of inflammasome-induced pro-inflammatory IL-1β in CF. PBMCs derived from CF subjects display preserved inflammasome activation and IL-1β secretion in response to the major CF pathogen Pseudomonas aeruginosa. However, our data do not support the hypothesis that increased IL-1β production in CF subjects is due to an intrinsic increase in NF-κB activity through loss of CFTR function

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity