Functional and genetic diversities of soil and plant associated microbial communities across variable spatial scales in semiarid ecological regions

Functional and genetic diversities studies of soil and plant associated microbial communities across variable spatial scales are of a great interest especially for the reclamation efforts of degraded and landscapes. These studies are significant in understanding the mechanisms of soil/plant/microbial relationships and in identification of possible management options relevant to plant fitness. Arid and semiarid ecological regions pose specific challenges but at the same time offer unique opportunities such as high stress conditions, immediate response, and biotic and abiotic gradients. It is hypothesized that endophytes are distributed across the soil-plant continuum, suggesting either or both plant recruitment of environmental microorganisms and soil inoculation with plant endophytes. Leaf and seeds of Atriplex spp. in addition to rhizosphere and bulk soils were sampled at three arid locations, one in New Mexico, USA (Jornada LTER) and two in the Al-Badia region of Jordan (JUST and Al-Khanasri). Tag-encoded FLX amplicon pyrosequencing and sequence alignment were used to determine diversity and distribution of bacterial and fungal populations across the soil to plant continuum. Of the total bacterial OTUs 0.17% at Al-Khanasri, 0.16% at JUST, and 0.42% at Jornada LTER were common across all plant and soil compartments. For fungal OTUs the same was true for 1.56% at JUST and 0.86% at Jornada. For Al-Khanasri 12.08% were found in at least one soil and one plant compartment. Arthrobacter, Sporosarcina , and Cladosporium were distributed across the soil-plant continuum at all three sites. Proteobacteria and Actinobacteria members were recovered along all soil and plant compartments. Ascomycota amplicons, mainly Didymellaceae, Pleosporaceae and Davidiellaceae, were identified across all compartments at all sites. Continuum communities for the Al-Badia locations were similar to each other and both quite distinct from the Jornada LTER location. This confirms the ubiquity of certain bacteria and fungi across soil and plant compartments, while also suggesting either plant species and/or geographic specificity. The second study evaluated the potential of the catabolic profiling MicroRespTM method to estimate divergence in microbial activities of old and more recently surface coalmine remediated areas in direct comparison with a non-disturbed reference site of tablelands in the Arizona/New Mexico Plateau. Results revealed that standard fertility parameters were lower in the remediated soils versus the undisturbed reference site with a noticeable gradient with the older remediated site more similar to the undisturbed site. The organic matter content was larger in all soil layers of the undisturbed site. While the same was true for the active microbial biomass (MB) the differences were less drastic suggesting a faster recovery of microbial activity potential than what can be inferred from the simple soil organic matter content values. The more recently remediated site had consistently larger metabolic quotient (qCO2) values suggesting less efficient carbon utilization. This also explains the slow recovery of the total organic matter. Total soil physiological activity profiles were consistent across sites in the crust samples except for cellulose degradation potential which was distinctly different from the catabolic potentials for all other substrates. This suggests relatively uniform degradation rates across substrate types indicating a wide range of potential enzymatic activity in the soil crust. For subsoil samples, the CLPP profiles induced a somewhat distinct clustering of the undisturbed soil samples, from the sample sets collected from the two remediated sites. The undisturbed site samples were associated with an increase in catabolic potential for most substrates but were less distinct across remediation age. Most catabolic potential indicators for the deep subsurface soil except for cellulose and L-histidine, were distinct between the undisturbed and remediated sites and were larger for the undisturbed soil. The non-rhizosphere soils at the two remediated sites had rather similar CLPP profiles despite the significant difference in their remediation age and distance from the central plant as well. The rhizosphere catabolic potentials of undisturbed soils were larger across the tested substrates. The unclear separation of the some tested soils based on their remediation status and age may be due to the quick recovery of the disturbed sites bringing them to equivalent to the control site.