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Transfer of electronic excitation energy (sensitized fluorescence) between donor and acceptor fluorophores separately attached to dimer or tetramer proteins is used to demonstrate the exchange of subunits among the undissociated particles. In dimers subjected to a pressure that produces half-dissociation, the exchange occurs at a rate that approaches the rate of dissociation. In the tetramers of glyceraldehydephosphate dehydrogenase and lactate dehydrogenase at 0 degrees C, the times for subunit exchange are nearly 2 orders of magnitude, and at room temperature 5-10 times longer than the time required to reach the dissociation equilibrium. By application of a novel method, pressure is shown to preferentially increase the rate of dissociation in dimers and decrease the rate of association in tetramers. From these observations, we conclude that the tetramers constitute a heterogeneous population, the members of which are dissociated by pressure according to individual molecular properties that can be retained over periods of time much longer than the time for equilibration of the dissociation. The dissociation of dimers exhibits the characteristics of the classical stochastic chemical equilibria, while those of the tetramers, like the more complex protein aggregates, must already be considered similar to the deterministic mechanical equilibria of macroscopic bodies.

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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 Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non-sustainable agricultural practices in the Pampa region.

The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyse bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on β-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower β-diversity and narrower breadth compared with distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of β-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region was likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity.

Understanding the processes that generate patterns of community structure is a central focus of ecological research. With that aim, we manipulated the structure of bacterial activated sludge to test the influence of the species richness and composition of bacterial communities on the dynamics of activated sludge floc assembly in lab-scale bioreactors. Bacterial community structure was analyzed using denaturing gradient gel electrophoresis of RT-PCR amplified 16S rRNA. Fingerprinting of four parallel reactors, started with the same source communities added in different proportions, converged to patterns that were more similar than expected by chance, suggesting a deterministic selection in floc development. Evidence for neutral dynamics was suggested by the dependence of the rate of replacement of species (bacterial taxa-time relationships) on the number of available species in the source community. Further indication of stochastic dynamics was obtained by the application of the Sloan neutral model for prokaryotes. The fitting of the observed data to the model predictions revealed that the importance of the stochastic component increased with the size of the reservoir of species richness from which the community is drawn. Taken together, the results illustrate how both neutral and deterministic dynamics operate simultaneously in the assembly of the bacterial floc and show that the balance of the two depends on the richness of the source community.

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The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.