Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities

In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes

In agriculture, adoption of reduced tillage practices is a widespread adaptation to global change. The cessation of plowing reduces erosion, slows soil organic matter oxidation, and promotes soil carbon accrual, but it can also result in the development of potential N2O spots from denitrification activity. In this study, we hypothesized that 16S rRNA-based composition of bacterial-archaeal assemblages would differ in agricultural soils subjected for forty years to a range of disturbance intensities, with annual moldboard plowing (MP) being the most intensive. No-till planting (NT) represented tillage management with the least amount of disturbance, while chisel-disking (CD), a type of conservation tillage, was intermediate. All long-term tillage plots had been planted with the same crops grown in a three-year crop rotation (corn-soybean-small grain+cover crop), and both bulk and rhizosphere soils were analyzed from the corn and soybean years. We also evaluated denitrification gene markers by quantitative PCR at multiple points (three growth stages of corn and soybean). Tillage intensity, soil compartment (bulk or rhizosphere), crop year, growth stage, and interactions all exerted effects on community diversity and composition. Compared to MP and CD, NT soils had lower abundances of denitrification genes, higher abundances of nitrate ammonification genes, and higher abundances of taxa at the family level associated with the inorganic N cycle processes of archaeal nitrification and anammox. Soybean rhizospheres exerted stronger selection on community composition and diversity relative to corn rhizospheres. Interactions between crop year, management, and soil compartment had differential impacts on N gene abundances related to denitrification and nitrate ammonification. Opportunities for managing hot spots or hot moments for N losses from agricultural soils may be discernible through improved understanding of tillage intensity effects, although weather and crop type are also important factors influencing how tillage influences microbial assemblages and N use.

Soil N2O flux and nitrification and denitrification gene responses to feed-induced differences in the composition of dairy cow faeces

Faeces from cows with different milk yield and non-lactating cows were applied to soil to investigate whether soil N2O efflux is related to feeding-induced differences in faecal microbiome and abundances of nitrification and denitrification genes. Fungal 18S-rRNA gene abundance was the highest in the faeces of the non-lactating group. The 18S-rRNA/ergosterol ratio showed a strong positive correlation with the 18S-rRNA/fungal glucosamine ratio. The milk-yield groups did not affect the gene abundances of bacterial 16S rRNA, AOB amoA, nirS and nosZ clade I, or the 16S-rRNA/muramic acid (MurN) ratio. In contrast, nirK gene abundance was generally the lowest in the high-yield group. The 16S-rRNA/MurN ratio showed a strong positive correlation with the 16S-rRNA/bacterial PLFA ratio. Cow faeces application to soil increased microbial biomass and ergosterol contents as well as the gene abundances of 18S-rRNA and nosZ clade I, compared with the non-amended control soil. Cumulative ΣCO2 efflux was roughly twice as high as the control, without differences between the faeces treatments. Cumulative ΣN2O efflux showed a 16-fold increase after applying high-yield cow faeces to soil, which was above the sevenfold increase in the non-lactating faeces treatment. The ΣN2O efflux from soil was positively related to faecal MurN and total PLFA concentration but also to soil nirK at day 14. The comparison of genome markers with cell wall (glucosamine) and cell membrane components (ergosterol) showed that the fungal cells were much larger in energy-rich faeces than in C-limited soil. A cow diet reduced in protein decreased the ΣN2O efflux from faeces amended soil.

Gross rates of soil N2O emission and uptake and denitrification gene abundance in temperate cropland agroforestry and monoculture systems

<p>Monoculture croplands are considered as major sources of the greenhouse gas, nitrous oxide (N<sub>2</sub>O). The conversion of monoculture croplands to agroforestry systems, e.g., integrating trees within croplands, is an essential climate-smart management system through extra C sequestration and can potentially mitigate N<sub>2</sub>O emissions. So far, no study has systematically compared gross rates of N<sub>2</sub>O emission and uptake between cropland agroforestry and monoculture. In this study, we used an in-situ <sup>15</sup>N<sub>2</sub>O pool dilution technique to simultaneously measure gross N<sub>2</sub>O emission and uptake over two consecutive growing seasons (2018 - 2019) at three sites in Germany: two sites were on Phaeozem and Cambisol soils with each site having a pair of cropland agroforestry and monoculture systems, and an additional site with only monoculture on an Arenosol soil prone to high nitrate leaching. Our results showed that cropland agroforestry had lower gross N<sub>2</sub>O emissions and higher gross N<sub>2</sub>O uptake than in monoculture at the site with Phaeozem soil (P ≤ 0.018 – 0.025) and did not differ in gross N<sub>2</sub>O emissions and uptake with cropland monoculture at the site with Cambisol soil (P ≥ 0.36). Gross N<sub>2</sub>O emissions were positively correlated with soil mineral N and heterotrophic respiration which, in turn, were correlated with soil temperature, and with water-filled pore space (WFPS) (r = 0.24 ‒ 0.54, P < 0.01). Gross N<sub>2</sub>O emissions were also negatively correlated with nosZ clade I gene abundance (involved in N<sub>2</sub>O-to-N<sub>2</sub> reduction, r = -0.20, P < 0.05). These findings showed that across sites and management systems changes in gross N<sub>2</sub>O emissions were driven by changes in substrate availability and aeration condition (i.e., soil mineral N, C availability, and WFPS), which also influenced denitrification gene abundance. The strong regression values between gross N<sub>2</sub>O emissions and net N<sub>2</sub>O emissions (R<sup>2 </sup>≥ 0.96, P < 0.001) indicated that gross N<sub>2</sub>O emissions largely drove net soil N<sub>2</sub>O emissions. Across sites and management systems, annual soil gross N<sub>2</sub>O emissions and uptake were controlled by clay contents which, in turn, correlated with indices of soil fertility (i.e., effective cation exchange capacity, total N, and C/N ratio) (Spearman rank’s rho = -0.76 – 0.86, P ≤ 0.05). The lower gross N<sub>2</sub>O emissions from the agroforestry tree rows at two sites indicated the potential of agroforestry in reducing soil N<sub>2</sub>O emissions, supporting the need for temperate cropland agroforestry to be considered in greenhouse gas mitigation policies.</p>

Genomic analysis of the meningococcal ST-4821 complex–Western clade, potential sexual transmission and predicted antibiotic susceptibility and vaccine coverage

Introduction The ST-4821 complex (cc4821) is a leading cause of serogroup C and serogroup B invasive meningococcal disease in China where diverse strains in two phylogenetic groups (groups 1 and 2) have acquired fluoroquinolone resistance. cc4821 was recently prevalent among carriage isolates in men who have sex with men in New York City (USA). Genome-level population studies have thus far been limited to Chinese isolates. The aim of the present study was to build upon these with an extended panel of international cc4821 isolates. Methods Genomes of isolates from Asia (1972 to 2017), Europe (2011 to 2018), North America (2007), and South America (2014) were sequenced or obtained from the PubMLST Neisseria database. Core genome comparisons were performed in PubMLST. Results Four lineages were identified. Western isolates formed a distinct, mainly serogroup B sublineage with alleles associated with fluoroquinolone susceptibility (MIC <0.03 mg/L) and reduced penicillin susceptibility (MIC 0.094 to 1 mg/L). A third of these were from anogenital sites in men who have sex with men and had unique denitrification gene alleles. Generally 4CMenB vaccine strain coverage was reliant on strain-specific NHBA peptides. Discussion The previously identified cc4821 group 2 was resolved into three separate lineages. Clustering of western isolates was surprising given the overall diversity of cc4821. Possible association of this cluster with the anogenital niche is worthy of monitoring given concerns surrounding antibiotic resistance and potential subcapsular vaccine escape.

Edaphic factors and plants influence denitrification in soils from a long-term arable experiment

Factors influencing production of greenhouse gases nitrous oxide (N2O) and nitrogen (N2) in arable soils include high nitrate, moisture and plants; we investigate how differences in the soil microbiome due to antecedent soil treatment additionally influence denitrification. Microbial communities, denitrification gene abundance and gas production in soils from tilled arable plots with contrasting fertilizer inputs (no N, mineral N, FYM) and regenerated woodland in the long-term Broadbalk field experiment were investigated. Soil was transferred to pots, kept bare or planted with wheat and after 6 weeks, transferred to sealed chambers with or without K15NO3 fertilizer for 4 days; N2O and N2 were measured daily. Concentrations of N2O were higher when fertilizer was added, lower in the presence of plants, whilst N2 increased over time and with plants. Prior soil treatment but not exposure to N-fertiliser or plants during the experiment influenced denitrification gene (nirK, nirS, nosZI, nosZII) relative abundance. Under our experimental conditions, denitrification generated mostly N2; N2O was around 2% of total gaseous N2 + N2O. Prior long-term soil management influenced the soil microbiome and abundance of denitrification genes. The production of N2O was driven by nitrate availability and N2 generation increased in the presence of plants.

Dinitrogen (N2) pulse emissions during freeze-thaw cycles from montane grassland soil

Short-lived pulses of soil nitrous oxide (N2O) emissions during freeze-thaw periods can dominate annual cumulative N2O fluxes from temperate managed and natural soils. However, the effects of freeze thaw cycles (FTCs) on dinitrogen (N2) emissions, i.e., the dominant terminal product of the denitrification process, and ratios of N2/N2O emissions have remained largely unknown because methodological difficulties were so far hampering detailed studies. Here, we quantified both N2 and N2O emissions of montane grassland soils exposed to three subsequent FTCs under two different soil moisture levels (40 and 80% WFPS) and under manure addition at 80% WFPS. In addition, we also quantified abundance and expression of functional genes involved in nitrification and denitrification to better understand microbial drivers of gaseous N losses. Our study shows that each freeze thaw cycle was associated with pulse emissions of both N2O and N2, with soil N2 emissions exceeding N2O emissions by a factor of 5–30. Increasing soil moisture from 40 to 80% WFPS and addition of cow slurry increased the cumulative FTC N2 emissions by 102% and 77%, respectively. For N2O, increasing soil moisture from 40 to 80% WFPS and addition of slurry increased the cumulative emissions by 147% and 42%, respectively. Denitrification gene cnorB and nosZ clade I transcript levels showed high explanatory power for N2O and N2 emissions, thereby reflecting both N gas flux dynamics due to FTC and effects of different water availability and fertilizer addition. In agreement with several other studies for various ecosystems, we show here for mountainous grassland soils that pulse emissions of N2O were observed during freeze-thaw. More importantly, this study shows that the freeze-thaw N2 pulse emissions strongly exceeded those of N2O in magnitude, which indicates that N2 emissions during FTCs could represent an important N loss pathway within the grassland N mass balances. However, their actual significance needs to be assessed under field conditions using intact plant-soil systems.

Patterns of Denitrification and Methanogenesis Rates from Vernal Pools in a Temperate Forest Driven by Seasonal, Microbial Functional Gene Abundances, and Soil Chemistry

Due to their relatively small sizes, temperate forest vernal pools are less studied than other wetlands, despite being potential biogeochemical hotspots in landscapes. We investigated spatial and temporal factors driving N2O and CH4 emission rates from vernal pools in a temperate forest. We determined higher N2O (3.66 ± 0.53 × 10−6, μg N2O/m2/h) and CH4 (2.10 ± 0.7 × 10−3, μg N2O/m2/h) rates in spring relative to fall (~50% and 77% lower for N2O and CH4 rates, respectively) and winter (~70% and 94% lower for N2O and CH4 rates, respectively). Soil organic matter, nitrate content and bacterial 16S rDNA, nirS, and norB gene abundances emerged as significant drivers of N2O rates, whereas, soil pH, organic matter content and mcrA abundance were significant drivers of CH4 rates. Denitrification gene abundances were negatively correlated with N2O rates, whereas mcrA abundance correlated positively with CH4 rates. Results suggest that CH4 rates may be directly coupled to methanogen abundance, whereas N2O rates may be directly impacted by a variety of abiotic variables and indirectly coupled to the abundance of potential denitrifier assemblages. Overall, additional studies examining these dynamics over extended periods are needed to provide more insights into their control.