BEST Variables explaining variation between soils in bacterial <i>amoA</i> MspI terminal restriction fragment profiles^a.

a<p>Variables included in correlation indicated by “X”. Abbreviations: P = Phosphorus; K = Potassium; S = Sulphur; B = Boron; Mn = Manganese; Fe = Iron, Cu = Copper; Al = Aluminium; Na, Sodium; BD, Bulk Density; OC, Organic Carbon.</p

Neighbor joining consensus tree of bacterial AmoA phylotypes.

<p>Colored branches indicate the <i>Nitrosomonas</i> cluster (green) and <i>Nitrosospira</i> cluster (blue). Boot strap values are indicated at nodes. Values in red are cluster designations following the classification of Avrahami et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089568#pone.0089568-Avrahami1" target="_blank">[48]</a> based on amino acid alignment of bacterial AmoA.</p

Principle coordinate plot of archaeal <i>amoA</i> clone libraries (Panel A) and bacterial <i>amoA</i> clone libraries (Panel B).

<p>Symbol colors correspond to soil pH: red, acidic (pH<6); green, circum-neutral (pH 6.2, 6.6), blue, alkaline (pH 7.8, 8.2), purple, multiple pH. Letters indicate soil names that are abbreviated as: A, Arena; B, Brasso; E, Ecclesville; P, Piarco; R, River Estate; S, St. Augustine; T, Talparo; W, Princes Town.</p

Non-metric multidimensional scaling plots of bacterial <i>amoA</i> terminal restriction fragment profiles generated by digestion with MspI (Panel A) or RsaI (Panel B).

<p>Symbol colors correspond to soil types, letters indicate soil names and values are the replicate number from the indicated soil. Soil name abbreviations: A, Arena; B, Brasso; E, Ecclesville; P, Piarco; R, River Estate; S, St. Augustine; T, Talparo; W, Princes Town.</p

BEST variables explaining variation between soils in archaeal <i>amoA</i> RsaI terminal restriction fragment profiles^a.

a<p>Variables included in correlation indicated by “X”. Abbreviations: P, Phosphorus; Zn, Zinc; TC, Total Carbon; TN, Total Nitrogen; TKN, Total Kjeldahl Nitrogen.</p

Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

<div><p>Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (<i>ca.</i> 10⁵ to 10⁶ copies archaeal <i>amoA</i> g⁻¹ soil), but AOB levels were low and bacterial <i>amoA</i> was infrequently detected. AOA abundance showed a significant negative correlation (<i>p</i><0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by <i>amoA</i> terminal restriction fragment (TRF) analysis, differed significantly between soils (<i>p</i><0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (<i>p</i><0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (<i>p</i><0.01). In clone libraries, phylotypes of archaeal <i>amoA</i> (predominantly <i>Nitrososphaera</i>) and bacterial <i>amoA</i> (predominanatly <i>Nitrosospira</i>) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (<i>p</i><0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.</p></div

Box and whisker plots of gene abundance determined by qPCR.

<p>Panel A, Archaeal <i>amoA</i>; Panel B, Archaeal 16S rRNA; Panel C, Bacterial 16S rRNA. Symbol colors correspond to soil types: red, sandy loam; blue, silty loam; green, clay. Soil name abbreviations are: A, Arena; B, Brasso; E, Ecclesville; P, Piarco; R, River Estate; S, St. Augustine; T, Talparo; W, Princes Town.</p

Nitrification Potential^a.

a<p>N = NO₃-N+NO₂-N, <i>p</i><0.001, LSD (5%) = 0.17, SEM = 0.06.</p

Soil Elemental Properties^a.

a<p>Abbreviations: P = Phosphorus; K = Potassium; Ca = Calcium; Mg = Magnesium; S = Sulphur; Zn = Zinc, B = Boron;</p><p>Mn = Manganese; Fe = Iron, Cu = Copper; Al = Aluminium; Na = Sodium.</p

Neighbour joining consensus tree of archaeal <i>amoA</i> phylotypes.

<p>Colored branches indicate the <i>Nitrosotalea</i> cluster (green) and <i>Nitrososphaera</i> cluster (blue). Boot strap values are indicated at nodes. Cluster designations follow the classification of Pester et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089568#pone.0089568-Pester1" target="_blank">[25]</a> based on nucleic acid alignment of archaeal <i>amoA</i>.</p