Appendix A. Additional materials and methods, including a diagram showing the chambers used in the methane flux measurements, photographs of the waterfowl exclosures, and a table showing potential methane oxidation and production, soil moisture content, soil organic matter content, soil density per month in the exclosed and control plots, and the results of a repeated-measures ANOVA for these soil characteristics.

Additional materials and methods, including a diagram showing the chambers used in the methane flux measurements, photographs of the waterfowl exclosures, and a table showing potential methane oxidation and production, soil moisture content, soil organic matter content, soil density per month in the exclosed and control plots, and the results of a repeated-measures ANOVA for these soil characteristics

Correlation between total CH₄ flux, soil properties and rice yield.

<p>*<i>p<0.05, **p<0.01</i> and <i>***p<0.001</i>.</p><p>Correlation between total CH₄ flux, soil properties and rice yield.</p

Phylogenetic_signal_blomberg_JEB

This file includes the results of each individual Blomberg's K signal calculation used to create figure 1 and table S1. In addition test statistic values are given as well

Cattle Manure Enhances Methanogens Diversity and Methane Emissions Compared to Swine Manure under Rice Paddy

<div><p>Livestock manures are broadly used in agriculture to improve soil quality. However, manure application can increase the availability of organic carbon, thereby facilitating methane (CH₄) production. Cattle and swine manures are expected to have different CH₄ emission characteristics in rice paddy soil due to the inherent differences in composition as a result of contrasting diets and digestive physiology between the two livestock types. To compare the effect of ruminant and non-ruminant animal manure applications on CH₄ emissions and methanogenic archaeal diversity during rice cultivation (June to September, 2009), fresh cattle and swine manures were applied into experimental pots at 0, 20 and 40 Mg fresh weight (FW) ha⁻¹ in a greenhouse. Applications of manures significantly enhanced total CH₄ emissions as compared to chemical fertilization, with cattle manure leading to higher emissions than swine manure. Total organic C contents in cattle (466 g kg⁻¹) and swine (460 g kg⁻¹) manures were of comparable results. Soil organic C (SOC) contents were also similar between the two manure treatments, but dissolved organic C (DOC) was significantly higher in cattle than swine manure. The <i>mcr</i>A gene copy numbers were significantly higher in cattle than swine manure. Diverse groups of methanogens which belong to <i>Methanomicrobiaceae</i> were detected only in cattle-manured but not in swine-manured soil. Methanogens were transferred from cattle manure to rice paddy soils through fresh excrement. In conclusion, cattle manure application can significantly increase CH₄ emissions in rice paddy soil during cultivation, and its pretreatment to suppress methanogenic activity without decreasing rice productivity should be considered.</p></div

Read.me

This file includes a description of sequences which have been used

Analysis of methanogen community composition by <i>mcr</i>A based T-RFLP under different manure application during rice cultivation.

<p>The number indicated Shannon diversity index (<i>H</i>).</p

Changes in DOC concentration with time (A) and numbers of total <i>mcr</i>A gene copies (B) in soils incorporated with different manures.

<p>Bars represent standard errors (n = 3). Different letters at the same stage indicate significant difference (One-way ANOVA, <i>p<0.05</i>).</p

Relationships between CH₄ emission rate, DOC concentration (A) and <i>mcr</i>A gene copy number (B), and Shannon diversity index (C) in soils during rice cultivation.

<p>Relationships between CH₄ emission rate, DOC concentration (A) and <i>mcr</i>A gene copy number (B), and Shannon diversity index (C) in soils during rice cultivation.</p

Visual representation of the DGGE fingerprints.

<p>Each vertical line of pixels represents the DGGE lane of a single sample. Lower bin numbers correspond to the top of the DGGE gel. Higher relative intensities of DGGE bins are represented with darker pixels. The clustering dendrogram shows the relation between samples. The sample fraction, sampling station, amendment and redox condition of each sample is color- coded between the dendrogram and the fingerprints (fraction: bulk DNA = white, whole-cell DNA = blue, RNA = black; station: LF1 = white, LF1.5 = yellow, LF3 = blue, LF5 = black; amendment: control = white, CNP = black, in situ = yellow; redox: oxic = white, anoxic = black, in situ = yellow).</p

Effect of Redox Conditions on Bacterial Community Structure in Baltic Sea Sediments with Contrasting Phosphorus Fluxes

<div><p>Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.</p></div