Association of earthworm-denitrifier interactions with increased emission of nitrous oxide from soil mesocosms amended with crop residue.

Earthworm activity is known to increase emissions of nitrous oxide (N(2)O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N(2)O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N(2)O emissions from the soil. We set up a 90-day mesocosm experiment in which (15)N-labeled maize (Zea mays L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm Lumbricus rubellus and/or the endogeic earthworm Aporrectodea caliginosa. We measured N(2)O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes nirS and nosZ through real-time quantitative PCR. Compared to the control, L. rubellus increased denitrification enzyme activity and N(2)O emissions on days 21 and 90 (day 21, P = 0.034 and P = 0.002, respectively; day 90, P = 0.001 and P = 0.007, respectively), as well as cumulative N(2)O emissions (76%; P = 0.014). A. caliginosa activity led to a transient increase of N(2)O emissions on days 8 to 18 of the experiment. Abundance of nosZ was significantly increased (100%) on day 90 in the treatment mixture containing L. rubellus alone. We conclude that L. rubellus increased cumulative N(2)O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.

Backbone amide dynamics studies of Apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the (15)N NMR relaxation profiles of wild-type and A77V mutant Apo-TrpR repressors.

Backbone amide dynamics studies were conducted on a temperature-sensitive mutant (L75F-TrpR) of the tryptophan repressor protein (TrpR) of Escherichia coli in its apo (i.e., no l-tryptophan corepressor-bound) form. The (15)N NMR relaxation profiles of apo-L75F-TrpR were analyzed and compared to those of wild-type (WT) and super-repressor mutant (A77V) TrpR proteins, also in their apo forms. The (15)N NMR relaxation data ((15)N-T(1), (15)N-T(2), and heteronuclear (15)N-{(1)H}-nOe) recorded on all three aporepressors at a magnetic field strength of 600 MHz ((1)H Larmor frequency) were analyzed to extract dynamics parameters, including diffusion tensor ratios (D(∥)/D(⊥)), correlation times (τ(m)) for overall reorientations of the proteins in solution, reduced spectral density terms [J(eff)(0), J(0.87ω(H)), J(ω(N))], and generalized order parameters (S(2)), which report on protein internal motions on the picosecond to nanosecond and slower microsecond to millisecond chemical exchange time scales. Our results indicate that all three aporepressors exhibit comparable D(∥)/D(⊥) ratios and characteristic time constants, τ(m), for overall global reorientation, indicating that in solution, all three apoproteins display very similar overall shape, structure, and rotational diffusion properties. Comparison of (15)N NMR relaxation data, reduced spectral density profiles, and generalized S(2) order parameters indicated that these parameters are quite uniform for backbone amides positioned within the four (A-C and F) core α-helices of all three aporepressors. In contrast, small but noticeable differences in internal dynamics were observed for backbone amides located within the helix D-turn-helix E DNA-binding domain of the apo-TrpR proteins. The significance of these dynamics differences in terms of the biophysical characteristics and ligand binding properties of the three apo-TrpR proteins is discussed.