In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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10 Global Biogeography of Microbial Nitrogen-Cycling Traits in Soil - Michaeline B. Nelson, Adam C. Martiny, and Jennifer B. H. Martiny
10 Global Biogeography of Microbial Nitrogen-Cycling Traits in Soil - Michaeline B. Nelson, Adam C. Martiny, and Jennifer B. H. Martiny
Pages 195-214
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From page 195... ...
The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively cor related across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample.
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. Thus, a consideration of microbial traits should improve efforts to connect biogeographic patterns and ecosystem processes (Green JL et al., 2008)
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-- would also influence compositional variation within microorganisms encoding N-cycling traits. RESULTS Metagenomic data from surface soil samples were retrieved from the metagenomics analysis server (MG-RAST)
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Habitat Agriculture Cold Desert Desert Grassland Lawn Pasture Temperate Forest Tropical Forest Tundra Wetland FIGURE 10.1 The locations (n = 118) sampled to create the soil metagenomic libraries (n = 365)
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From page 199... ...
. Bacteria and Archaea displayed similar trends in their relative frequency of N pathways except for the absence of the dissimilatory nitrite reduction to ammonium pathway in Archaea.
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From page 200... ...
Nitrate Reduction NO3 B Bacteria 10-3 10-5 10-7 10-9 Archaea 10-3 Frequency 10-5 10-7 10-9 Fungi 10-3 10-5 10-7 10-9 Assimilation Nitrite to Ammonium Nitrate to Nitrite Nitrite to Ammonium Nitrate to Nitrite Nitrogen Fixation Nitrification Denitrification Ammonia Dissimilatory Assimilatory Dissimilatory Assimilatory Pathway FIGURE 10.2 N pathways and their frequencies.
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From page 201... ...
Drivers of N Pathway Frequencies The frequency of all N-cycling traits (summing across all pathways) varied greatly among soil samples, and initial analyses revealed broad biogeographic patterns.
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For instance, denitrification frequency increased with temperature in deserts but decreased with temperature in tropical forests. Similarly, ammonia assimilation frequency increased with soil N in temperate forests but decreased with soil N in tropical forests.
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From page 203... ...
Genera carrying the pathway to complete the second half of denitrification also generally carried the first half of the pathway, dissimilatory nitrate to nitrite reduction. The same genera carryng i these denitrification pathways sometimes, but not always, carried the dissimilatory nitrite reduction to ammonium pathway, or the second part of the complete DNRA process (Fig.
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From page 204... ...
0.12 Total N 0.05 H×P <0.01 0.07 H×T 0.09 0.23 H × pH <0.01 0.09 H×C 0.1 H×N 0.17 0.49 0.06 P×T 0.02 C×N Adjusted R2 0.58 0.51 0.5 0.36 Archaea Habitat 0.08 Precipitation Temperature pH Organic Carbon Total N 0.05 H×P 0.21 H×T 0.09 0.18 H × pH H×C H×N P×T C×N 0.34 Adjusted R2 0.43 NS 0.52 NS NOTES: The models for the individual pathways are based on the residual frequencies of the pathway after correcting for the Total N pathway frequency (see text)
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Global Biogeography of Microbial Nitrogen-Cycling Traits in Soil / 205 Dissimilatory Dissimilatory Nitrite to Nitrate to N Fixation Nitrification Nitrite Denitrification Ammonia 0.29 0.11 0.06 0.09 0.02 0.02 <0.01 0.13 0.08 0.32 0.31 0.21 0.03 0.31 0.05 0.05 <0.01 <0.01 0.8 0.45 0.41 0.41 NS 0.09 0.03 0.12 <0.01 0.02 0.03 <0.01 0.04 0.09 0.33 0.13 0.12 0.06 0.63 0.22 NS 0.21 NA
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From page 206... ...
. Verrucomicrobia are known to be abundant in soils, but their ecological role remains unclear (Bergmann et al., 2011; Fierer et al., Nitrogen Cycle Pathways Dissimilatory Nitrate to Nitrite Denitrification Dissimilatory Nitrite to Ammonium Nitrification Chloro Assimilatory Nitrate to Nitrite Aqu Firm Assimilatory Nitrite to Ammonium icut es ot a Nitrogen Fixation ae rch rya Eu h arc ren Cy an Ch o Actino bacteria arc bacteria ha ea oteobacteria ma-Pr Gam Ep silo n ia er ct Ba ba ct eo er ot iod Pr ete ta- s Be De lta Pro teo Alpha-Proteobacteria FIGURE 10.4 Phylogenetic distribution of N pathways in the soil metagenomes.
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. The relative abundances of genera encoding the other six N pathways in the soil samples are reported in Fig.
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. The most abundant genera encoding the dissimilatory nitrite reduction to ammonium pathway displayed greater variability among habitats (confirming the model results in Table S1)
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From page 209... ...
We also found a high frequency of Bacteria encoding the dissimilatory nitrite reduction to ammonium pathway, which leads to recycling of N in soils. The balance between DNRA and denitrification, which leads to the loss of N to the atmosphere, is thought to be key to soil N budgets.
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From page 210... ...
in the MG-RAST database (Meyer et al., 2008) were classified into one of 10 habitat types (desert, cold desert, grassland, temperate forest, tropical forest, tundra, wetland, agriculture, pasture, and lawn)
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, dissimilatory nitrate to nitrite reduction (n = 9) , dissimilatory nitrite to ammonia reduction (n = 4)
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, we also included the following interaction terms: habitat by temperature, habitat by precipitation, habitat by soil pH, habitat by organic carbon, habitat by total N, precipitation by temperature, and organic carbon by total N To determine the relative importance of the various significant environmental factors from our model in contributing to variation in the frequency of N pathways across samples, we used a backward selection procedure (Mac Nally, 2002; Ramette, 2007)
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From page 213... ...
of the predictor variables for each pathway's composition, using a forward selection procedure. Phylogenetic Visualization We constructed a phylogenetic tree including a representative species from all genera encoding N sequences using 16S rRNA amplicon data (chosen for their sequence quality and length of ~1,400 bp)
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