Actinobacterial Nitrate Reducers and Proteobacterial Denitrifiers Are Abundant in N2O-Metabolizing Palsa Peat

Palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N2O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland. In situ N2O fluxes were spatially variable, ranging from 0.01 to -0.02 μmol of N2O m-2 h-1. Fertilization with nitrate stimulated in situ N2O emissions and N2O production in anoxic microcosms without apparent delay. N2O was subsequently consumed in microcosms. Maximal reaction velocities (vmax) of nitrate-dependent denitrification approx-imated 3 and 1 nmol of N2O per h per gram (dry weight [gDW]) in soil from 0 to 20 cm and below 20 cm of depth, respectively. vmax values of nitrite-dependent denitrification were 2- to 5-fold higher than the vmax nitrate-dependent denitrification, and vmax of N2O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N2O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) of narG, nirK and nirS, and nosZ were retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected spe- cies, as well as Actino-, Alpha-, and Betaproteobacteria. Copy numbers of nirS always outnumbered those of nirK by 2 orders of magnitude. Copy numbers of nirS tended to be higher, while copy numbers of narG and nosZ tended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N2O are associated with denitrification, (ii) actinobacterial nitrate reducers and nirS-type and nosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent reservoirs of diverse acid-tolerant denitrifiers associated with N2O fluxes. Copyright 2012, American Society for Microbiology

Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers

Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of ≥97% had a narG or nosZ similarity of ≥67% or ≥80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent. Copyright © 2009, American Society for Microbiology. All Rights Reserved

Association of Novel and Highly Diverse Acid-Tolerant Denitrifiers with N2O Fluxes of an Acidic Fen

Wetlands are sources of denitriflcation-derived nitrous oxide (N 2O). Thus, the denitrifler community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitriflers approximated 10 11 cells · gDW-1 (where DW is dry weight) and 108 cells • gDW-1, respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (vma-) values for denitriflcation in anoxic microcosms ranged from 1 to 24 and - 19 to - 105 nmol N2O h-1 • gDW-1, with maximal values occurring in the upper soil layers. Denitriflcation was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitriflcation. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomie units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifler diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifler community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifler communities capable of complete denitriflcation and consumption of atmospheric N2O at in situ pH. Copyright © 2010, American Society for Microbiology. All Rights Reserved

Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen

Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen

Denitrification activity of a remarkably diverse fen denitrifier community in Finnish Lapland is N-Oxide limited

Peatlands cover more than 30% of the Finnish land area and impact N2O fluxes. Denitrifiers release N2O as an intermediate or end product. In situ N2O emissions of a near pH neutral pristine fen soil in Finnish Lapland were marginal during gas chamber measurements. However, nitrate and ammonium fertilization significantly stimulated in situ N2O emissions. Stimulation with nitrate was stronger than with ammonium. N2O was produced and subsequently consumed in gas chambers. In unsupplemented anoxic microcosms, fen soil produced N2O only when acetylene was added to block nitrous oxide reductase, suggesting complete denitrification. Nitrate and nitrite stimulated denitrification in fen soil, and maximal reaction velocities (vmax) of nitrate or nitrite dependent denitrification where 18 and 52 nmol N2O h-1 gDW-1, respectively. N2O was below 30% of total produced N gases in fen soil when concentrations of nitrate and nitrite were <500 μM. vmax for N2O consumption was up to 36 nmol N2O h-1 gDW-1. Denitrifier diversity was assessed by analyses of narG, nirK/nirS, and nosZ (encoding nitrate-, nitrite-, and nitrous oxide reductases, respectively) by barcoded amplicon pyrosequencing. Analyses of ~14,000 quality filtered sequences indicated up to 25 species-level operational taxonomic units (OTUs), and up to 359 OTUs at 97% sequence similarity, suggesting diverse denitrifiers. Phylogenetic analyses revealed clusters distantly related to publicly available sequences, suggesting hitherto unknown denitrifiers. Representatives of species-level OTUs were affiliated with sequences of unknown soil bacteria and Actinobacterial, Alpha-, Beta-, Gamma-, and Delta-Proteobacterial sequences. Comparison of the 4 gene markers at 97% similarity indicated a higher diversity of narG than for the other gene markers based on Shannon indices and observed number of OTUs. The collective data indicate (i) a high denitrification and N2O consumption potential, and (ii) a highly diverse, nitrate limited denitrifier community associated with potential N2O fluxes in a pH-neutral fen soil

Einfluss einer platzierten N-Düngung und eines Nitrifikationshemmstoffs auf die N2O-Freisetzung im Gemüsebau

Es wurden ganzjährige Untersuchungen zum Einfluss eines Nitrifikationshemm-stoffs (NI, DMPP) bzw. einer N-Depot-düngung auf die N2O-Freisetzung aus einer gemüsebaulich genutzten Parabraun¬erde nahe Hohenheim durchgeführt. Als Kontrolle diente eine breitwürfige N-Düngung gleicher Düngerhöhe. In beiden Versuchsjahren konnte die annuelle N2O-Emission gegenüber der Kontrollvariante mittels NI um 40% reduziert werden. Dabei zeigte sich auch ein emissionsmindernder Effekt im Winterhalbjahr. Der Grund dafür ist bisher unklar. Im Gegensatz zum NI-Einsatz konnte die annuelle Emission mit platzierter N-Düngung nicht vermindert werden, obwohl eine Hemmung der Nitrifikation im Düngerdepot aufgrund der hohen NH4+-Konzentration nachgewiesen wurde

Persistent Pesticides in Human Breast Milk and Cryptorchidism

INTRODUCTION: Prenatal exposure to some pesticides can adversely affect male reproductive health in animals. We investigated a possible human association between maternal exposure to 27 organochlorine compounds used as pesticides and cryptorchidism among male children. DESIGN: Within a prospective birth cohort, we performed a case–control study; 62 milk samples from mothers of cryptorchid boys and 68 from mothers of healthy boys were selected. Milk was collected as individual pools between 1 and 3 months postpartum and analyzed for 27 organochlorine pesticides. RESULTS: Eight organochlorine pesticides were measurable in all samples (medians; nanograms per gram lipid) for cases/controls: 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (p,p′-DDE): 97.3/83.8; β-hexachlorocyclohexane (β-HCH): 13.6/12.3; hexachlorobenzene (HCB): 10.6/8.8; α -endosulfan: 7.0/6.7; oxychlordane: 4.5/4.1; 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (p,p′-DDT): 4.6/4.0; dieldrin: 4.1/3.1; cis-heptachloroepoxide (cis-HE): 2.5/2.2. Five compounds [octachlorostyrene (OCS); pentachlorobenzene, 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane (p,p′-DDD); o,p′-DDT; mirex] were measurable in most samples (detection rates 90.8–99.2%) but in lower concentrations. For methoxychlor, cis-chlordane, pentachloroanisole (PCA), γ -HCH, 1,1-dichloro-2-(2-chlorophenyl)-2,2(4-chlorophenyl)ethane, trans-chlordane, α -HCH, and o,p′-DDE, both concentrations and detection rates were low (26.5–71.5%). Heptachlor, HCH (δ, ɛ ), aldrin, β-endosulfan and trans-heptachloroepoxide were detected at negligible concentrations and low detection rates and were not analyzed further. Seventeen of 21 organochlorine pesticides [p,p′-DDT, p,p′-DDE, p,p′-DDD, o,p′-DDT, HCH (α , β, γ ), HCB, PCA, α -endosulfan, cis-HE, chlordane (cis-, trans-) oxychlordane, methoxychlor, OCS, and dieldrin] were measured in higher median concentrations in case milk than in control milk. Apart from trans-chlordane (p = 0.012), there were no significant differences between cryptorchid and healthy boys for individual chemicals. However, combined statistical analysis of the eight most abundant persistent pesticides showed that pesticide levels in breast milk were significantly higher in boys with cryptorchidism (p = 0.032). CONCLUSION: The association between congenital cryptorchidism and some persistent pesticides in breast milk as a proxy for maternal exposure suggests that testicular descent in the fetus may be adversely affected

AmericasNLI: Machine translation and natural language inference systems for Indigenous languages of the Americas

Little attention has been paid to the development of human language technology for truly low-resource languages—i.e., languages with limited amounts of digitally available text data, such as Indigenous languages. However, it has been shown that pretrained multilingual models are able to perform crosslingual transfer in a zero-shot setting even for low-resource languages which are unseen during pretraining. Yet, prior work evaluating performance on unseen languages has largely been limited to shallow token-level tasks. It remains unclear if zero-shot learning of deeper semantic tasks is possible for unseen languages. To explore this question, we present AmericasNLI, a natural language inference dataset covering 10 Indigenous languages of the Americas. We conduct experiments with pretrained models, exploring zero-shot learning in combination with model adaptation. Furthermore, as AmericasNLI is a multiway parallel dataset, we use it to benchmark the performance of different machine translation models for those languages. Finally, using a standard transformer model, we explore translation-based approaches for natural language inference. We find that the zero-shot performance of pretrained models without adaptation is poor for all languages in AmericasNLI, but model adaptation via continued pretraining results in improvements. All machine translation models are rather weak, but, surprisingly, translation-based approaches to natural language inference outperform all other models on that task