N cycling and microbial dynamics in pasture soils

Pasture soils are a significant source of the greenhouse gas, nitrous oxide (N2O) and as such they contribute to global warming. It has been reported that N2O is approx. 300 times more potent than carbon dioxide (CO2) as a greenhouse gas. Thus, understanding the mechanisms for controlling N2O emissions from soil is key to developing new soil management strategies to counter or prevent climate change throughout the world. Despite this, very little is known about the key regulators of production and consumption of N2O in pasture soils, especially under urine patch conditions. To address this, we used pasture soils representing both Northern (Ireland) and Southern (New Zealand) Hemispheres in experiments designed to understand both phenotypic and genotypic characteristics associated with N2O emissions. We used a combination of gas kinetics, soil physicochemical characterization, metagenomics, 16S amplicon sequencing and quantitative PCR (of denitrifier: nirS, nirK, nosZI and nosZII; and nitrifier: bacterial and archaeal amoA genes) to link physical, chemical and biological parameters associated with emissions. This thesis work was able to show how in nitrate-amended pasture soils the rate of carbon mineralization under oxic and anoxic conditions is positively linked to the rate of denitrification. In addition, the emission ratio of N2O is negatively linked to pH. Both pH and N2O emission ratio were significantly associated with 16S microbial community composition as well as microbial richness. This result confirms that pH imposes a general selective pressure on the entire community and that this is associated with changes in emission potentials. This supports the general ecological hypothesis that with increased microbial diversity, efficiency of N2 production increases (i.e. more efficient conversation of N2O to N2). Worked performed in a simulated urine patch (oxic conditions) suggested other pathway (e.g., nitrifier-denitrification) as a source of N2O emissions. No clear trend was observed between emission ratio of N2O under urine patch condition and emission ratio under true denitrification conditions (i.e. under anoxic environment). The urine patch accelerated the rate of C mineralization about 10 times, concurrent with a decrease in prokaryotic richness and a shift in community composition. Community response identified two major groups of responders: negatively affected prokaryotes we hypothesized utilized energy from N-linked redox reaction for maintenance and positively responding populations that use this energy for growth. Overall, this study provides new insights into the N2O emissions and microbial dynamics for reduction of N2O in pasture soils

N cycling and microbial dynamics in pasture soils

Pasture soils are a significant source of the greenhouse gas, nitrous oxide (N2O) and as such they contribute to global warming. It has been reported that N2O is approx. 300 times more potent than carbon dioxide (CO2) as a greenhouse gas. Thus, understanding the mechanisms for controlling N2O emissions from soil is key to developing new soil management strategies to counter or prevent climate change throughout the world. Despite this, very little is known about the key regulators of production and consumption of N2O in pasture soils, especially under urine patch conditions. To address this, we used pasture soils representing both Northern (Ireland) and Southern (New Zealand) Hemispheres in experiments designed to understand both phenotypic and genotypic characteristics associated with N2O emissions. We used a combination of gas kinetics, soil physicochemical characterization, metagenomics, 16S amplicon sequencing and quantitative PCR (of denitrifier: nirS, nirK, nosZI and nosZII; and nitrifier: bacterial and archaeal amoA genes) to link physical, chemical and biological parameters associated with emissions. This thesis work was able to show how in nitrate-amended pasture soils the rate of carbon mineralization under oxic and anoxic conditions is positively linked to the rate of denitrification. In addition, the emission ratio of N2O is negatively linked to pH. Both pH and N2O emission ratio were significantly associated with 16S microbial community composition as well as microbial richness. This result confirms that pH imposes a general selective pressure on the entire community and that this is associated with changes in emission potentials. This supports the general ecological hypothesis that with increased microbial diversity, efficiency of N2 production increases (i.e. more efficient conversation of N2O to N2). Worked performed in a simulated urine patch (oxic conditions) suggested other pathway (e.g., nitrifier-denitrification) as a source of N2O emissions. No clear trend was observed between emission ratio of N2O under urine patch condition and emission ratio under true denitrification conditions (i.e. under anoxic environment). The urine patch accelerated the rate of C mineralization about 10 times, concurrent with a decrease in prokaryotic richness and a shift in community composition. Community response identified two major groups of responders: negatively affected prokaryotes we hypothesized utilized energy from N-linked redox reaction for maintenance and positively responding populations that use this energy for growth. Overall, this study provides new insights into the N2O emissions and microbial dynamics for reduction of N2O in pasture soils

Niche Differentiation of Host-associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their “host”. However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and phytoplankton-&-particle-associated (PPA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PPA and zooplankton associated microbes; and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PPA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analysed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PPA. Indicator species analysis showed that 9 %, 8 % 12 % and 21% unique OTUs were significantly associated with copepods, cladocerans, bacterioplankton, and PPA, respectively. Surprisingly, genera of methane oxidizing bacteria (MOB), methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PPA. Our study clearly demonstrates niche differentiation of pelagic microbes which is affected by warming with possible impact on biogeochemical cycling in freshwater systems

Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk

Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.</p

Geographical location of soil samples.

<p>Map showing origin of soil samples used in the study (a) world map, (b) Ireland [Moorepark (MP), Johnstown (JT), Solohead (SH)] and (c) New Zealand [Warepa (WP), Otokia (OT), Wingatui (WT), Tokomairiro (TM), Mayfield (MF), Lismore (LM), Templeton (TP), Manawatu (MM), Horotiu (HR), Te Kowhai (TK)]. The map was generated using open source “R-programme (packages ‘maps’ and ‘mapdata’)”.</p

Gas kinetics profile of IR and NZ soils under oxic and anoxic conditions.

<p>O₂, CO₂, NO, N₂O and N₂ emission kinetics during incubation of 13 different temperate soils (3 Ireland (a,b,c) and 10 New Zealand (d to m)) amended with 2 mM nitrate (flooding and draining immediately before incubation). Soil samples (20 g dry weight) were incubated under oxic (first 40 hours) and subsequently anoxic conditions. Dots represent three replicate vials and smooth line is the fitted line for all data.</p

Demonstration of calculation of <i>I</i>N₂O and N₂O/(N₂O+N₂).

<p>Representative curves for a) cumulative N accumulation, b) measured N, and c) N₂O production index (<i>I</i>N₂O) and N₂O/(N₂O+N₂) product ratio over time for one soil (Moorepark). N₂O production indices were calculated as . Curves represent a single flask result. Each flask contained 20 g (dry weight) soil incubated in a 120 ml serum vial under anoxic conditions. Results for all other soils can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151713#pone.0151713.s001" target="_blank">S1 Fig</a>.</p

Relationship between pH and N₂O emissions.

<p>Effect of method (extractant type) for determining soil pH on association with (a) N₂O production index (<i>I</i>N₂O) and (b) N₂O/(N₂O+N₂) ratio. Calculation of both index and ratio was based on N₂O emission within the curve (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151713#pone.0151713.s001" target="_blank">S1 Fig</a> for each sample) at 50 h under anoxic incubation. Soil pH was measured using three different extractants: i) DI water, ii) 0.01 M CaCl₂, and iii) 2M KCl. Dotted lines represent regression lines. Points represent the mean triplicate flask results.</p