PH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical–chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and “spillover effects” of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.

It has been shown that cover crops can enhance soil nitrous oxide (N(2)O) emissions, but the magnitude of increase depends on the quantity and quality of the crop residues. Therefore, this study aimed to evaluate the effect of long-term (19 and 21 years) no-till maize crop rotations including grass [black oat (Avena strigosa Schreb)] and legume cover crops [vetch (Vigna sativa L), cowpea (Vigna unguiculata L. Walp), pigeon pea (Cajanus cajan L. Millsp.) and lablab (Dolichos lablab)] on annual soil N(2)O emissions in a subtropical Acrisol in Southern Brazil. Greater soil N(2)O emissions were observed in the first 45 days after the cover crop residue management in all crop rotations, varying from -20.2 +/- 1.9 to 163.9 +/- 24.3 mu g N m(-2) h(-1). Legume-based crop rotations had the largest cumulative emissions in this period, which were directly related to the quantity of N (r(2) = 0.60, p = 0.13)and inversely related to the lignin:N ratio(r(2) = 0.89,p = 0.01) of the cover crop residues. After this period, the mean fluxes were smaller and were closely related to the total soil N stocks (r(2) = 0.96, p = 0.002). The annual soil N(2)O emission represented 0.39-0.75% of the total N added by the legume cover crops. Management-control led soil variables such as mineral N (NO(3)(-) and NH(4)(+)) and dissolved organic C influenced more the N(2)O fluxes than environmental-related variables as water-filled pore space and air and soil temperature. Consequently, the synchronization between N mineralization and N uptake by plants seems to be the main challenge to reduce N(2)O emissions while maintaining the environmental and agronomic services provided by legume cover crops in agricultural systems. (C) 2009 Elsevier B.V. All rights reserved