13 research outputs found
Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production
<div><p>The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus <em>Rubellimicrobium</em> of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable <em>vs</em>. non-sustainable agricultural practices in the Pampa region.</p> </div
Soil characteristics according to site and agricultural management at the first sampling date, in June 2009.
1<p>Mat: Mean annual temperature.</p>2<p>MAP: mean annual precipitation.</p
Venn diagram of the overlap of OTUs from the different soil management practices at four geographical locations.
<p>The numbers of overlapping tag sequences are indicated in the graph. Management practices are indicated at the bottom of each diagram: GAP: Good no-till Agricultural Practices, PAP: Poor no-till Agricultural Practices; NE: Natural Environment. Location labels are indicated with B (Bengolea), MB (Monte Buey), P (Pergamino) and V (Viale).</p
Ordination diagram from Canonical Correspondence Analysis of bacterial taxa identified as indicators using IndVal.
<p>Only OTUs identified with IndVal values higher than 0.75 were used in this analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051075#pone.0051075.s009" target="_blank">Table S6</a>). The 2-D ordination diagram CCA accounts for 66% of inertia. Samples are indicated by circles and site labels. OTUs are indicated by crosses, names are omitted. Arrows for quantitative variables show the direction of increase of each variable, and the length of the arrow indicates the degree of correlation with the ordination axes. Colors indicate soil management type: Poor no-till Agricultural Practices in red, Good no-till Agricultural Practices in blue; Natural Environment in green. Location labels are indicated with: B (Bengolea), MB (Monte Buey), P (Pergamino) and V (Viale).</p
Results of indicator species analysis.
<p>For each of the taxa, we indicate the total number of sequences corresponding to the OTU that represents the specific groups of samples (size), the Indicator Value index (IndVal), the number of samples that contain the taxon (Freq), the statistical significance of the association (p-value), the chance of reporting a false-positive result (q-value), and the lowest taxonomic rank assigned with a bootstrap confidence greater than 80%. Agricultural managements GAP and PAP are defined in the main text. Results were sorted according to Size. Only OTUs containing 20 or more sequences are shown in this table. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051075#pone.0051075.s009" target="_blank">Table S6</a> for a complete list of significant indicators with IndVal values ≥0.75.</p
Indicator values for samples of soils under different agricultural management.
<p>The geographic sites are indicated in the box. In each site bars are ordered from left to right to the successive sampling dates: June 2009, February 2010, September 2010 and February 2011. PAP, Poor no-till Agricultural Practices (red) and GAP, Good no-till Agricultural Practices (blue). Shadow areas are 95% confidence intervals of indicator of GAP (0.24, 0.71) and PAP (−1.31, −0.41). Error bars are standard error.</p
Quantitative phylogenetic group abundance of the OTUs targeted with a set of primers specific for Acidobacteria GP1A (panel A) and <i>Rubellimicrobium</i> genus (panel B).
<p>Each soil sample subjected to the indicated management in the four geographical locations was sampled at the date showed in the boxes. Bars correspond to the average qPCR data of three independent samples. Colors indicate soil management type: Poor no-till Agricultural Practices in red, Good no-till Agricultural Practices in blue, and Natural Environment in green. Error bars are standard error.</p
Description of the agricultural management and crop yield, averaged over the five years before the first sampling date, in June 2009 (2005–2009).
a<p>Number of soybean cycles to number of maize cycles over the last 5years.</p>b<p>Percentage of winters that wheat was planted as a winter crop.</p>c<p>Percentage of winters that a cover crop (<i>Vicia</i> sp., <i>Melilotus alba</i> or <i>Lolium perenne</i>) was planted. Cover crops were chemically burned before summer crops are planted.</p>d<p>Calculated as liters of low-toxicity herbicides plus liters of moderate-toxicity herbicides weighted by two. Toxicity was defined according to EPA Toxicity Categories. Unit: total liters over 5 years.</p>e<p>No maize was planted in the last 5 years.</p
Ordination diagram from the Correspondence Analysis of the relative abundances for taxa defined at 0.05 distance.
<p>The 2-D CA diagram account for 29% of inertia. Locations of soils are indicated by squares (Bengolea, B), circles (Monte Buey, MB), diamond (Pergamino, P) and triangles (Viale, V). Colors indicate soil management type: Poor no-till Agricultural Practices in red, Good no-till Agricultural Practices in blue and Natural Environment in green. Standard error ellipses show 95% confidence areas.</p
scFv C5 intrabody expression in T. <i>brucei</i>.
<p><b>A.</b> Western blot detection of C5 intrabody expression at 0, 24 and 72 hours in six different clones. C5 was detected by an anti-Myc antibody. The loading control ALD was detected by an anti-aldolase antibody. <b>B.</b> Averaged densitometry analysis of intrabody expression (***; p<0.001). <b>C.</b> Averaged growth rate curve of the six different clones induced and un-induced C5 intrabody parasites (***; p<0.001).</p