Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils

In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using 15N-labeled substrates revealed that anammox processes contributed about <2% to total N2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs

Correction : Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering

The following information is missing from the Funding section: grant number LD13046 from the Ministry of Education, Youth and Sports of the Czech Republic and the acknowledgment of funding from the EU COST action ES1103. The complete, correct Funding statement is: This project was funded by a grant from the German Academic Exchange Service (DAAD, www.daad.de) providing travel grants for VR and MS, from the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, No. LC06066, and LD13046, www.msmt.cz), from the Grant Agency of the Czech Republic (GACR, No. 526/09/1570, www.gacr.cz), and from the EU COST action ES1103, which provided funding for the author (AC) to attend a workshop

Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning

Changes in the structure of N-fixing communities from <i>nif</i>H-gene pyrosequencing across different soils and sampling times.

<p>Changes in the structure of <i>nif</i>H-gene communities and the influence of environmental parameters as revealed by RDA, considering (a) the most abundant and (b) rare sequences. The number in each axis shows the percentage of total variation explained. The length of the corresponding arrows indicated the relative importance of the geochemical factor in explaining the variation in microbial profiles. Soil samples were analyzed in four replicates at each sampling time. B, Buinen; D, Droevendaal; K, Kollumerwaard and G, Grebbedijk; Ap, April; Ju, June; Oc, October.</p

Double dendrogram and heatmap, based on the Ward minimum variance clustering method for abundant genera investigated using <i>nif</i>H gene pyrosequencing.

<p>The heatmap indicates the relative abundance of the (a) most abundant and (b) most rare genera within each sample. B, Buinen; D, Droevendaal; K, Kollumerwaard and G, Grebbedijk; Ap, April; Ju, June; Oc, October.</p

Rarefaction analysis of the diversities of <i>nif</i>H gene.

<p>Analyses of four soils across three sampling times after resampling of the sequences to the same depth (1921 sequences). The OTUs were classified at 90% similarity cutoff based on amino acid sequences. B, Buinen; D, Droevendaal; K, Kollumerwaard and G, Grebbedijk; Ap, April; Ju, June; Oc, October.</p

Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine

<div><p>Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as <i>Devosia</i>, <i>Shinella</i>, <i>Stenotrophomonas</i>, <i>Clostridium</i>, <i>Peptostreptococcus</i>, <i>Leifsonia</i>, <i>Gemmatimonas</i>, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera <i>Pseudomonas</i> and <i>Lysobacter</i>, <i>Hydrogenophaga</i>, and <i>Adhaeribacter</i> decreased in response to the repeated application of manure and SDZ.</p></div

Changes in the structure of total bacterial and N-fixing communities from DGGE fingerprints across different soils and sampling times.

<p>Changes in the structure of bacterial (a) and N-fixing (b) communities and the influence of environmental parameters, as revealed by CCA. Only statistically significant environmental variables are shown. The number in each axis shows the percentage of total variation explained. The length of the corresponding arrows indicated the relative importance of the geochemical factor in explaining the variation in microbial profiles. Soil samples were analyzed in four replicates at each sampling time. B, Buinen; D, Droevendaal; K, Kollumerwaard and G, Grebbedijk; Ap, April; Ju, June; Oc, October.</p

Composition of archaeal and bacterial communities described as relative OTU abundance of particular bacterial and archaeal taxa (phyla and classes) in different sample types.

<p>Mean relative abundances (expressed as percentages) for each taxonomical group (<i>n = 5</i>) in given sample are listed. Taxonomic units with abundance higher than 0.05% at least in one sample are shown. Significant differences (results of Tukey′s HSD test) are indicated by different letters in rows (<i>P</i> < 0.05).</p><p>Composition of archaeal and bacterial communities described as relative OTU abundance of particular bacterial and archaeal taxa (phyla and classes) in different sample types.</p

Taxa with significantly different relative abundance between manured soils with or without SDZ treatments shortly after manure addition as revealed by barcoded pyrosequencing using the reverse primer (Bonferroni adjusted p value<0.05).

<p>Bold numbers indicate taxa with significantly higher relative abundance in SDZ treated or non treated soils. Soils were collected three days after each treatment.</p