Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0–5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals–organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change.

It has proven difficult, when focused only on biological determinants, to explain why some plant species become naturalized in or invade new locations, whereas others fail. We analyzed the invasion of Trifolium (true clover) species into New Zealand, assessing a range of human, biogeographic, and biological influences at three key invasion stages: introduction, naturalization, and spread. We used sparse principal component analysis (SPCA) to define suites of related attributes and aggregated boosted trees to model relationships with invasion outcomes. Human and biogeographic attributes were strongly associated with success at all stages. Whereas biogeographic attributes, notably large native range, were consistently associated with success, different human factors appeared to favor success at different stages, such as presence in early trade/immigration hotspots (introduction), intentional largescale planting (naturalization), and frequent presence as a seed contaminant (relative spread rate). Biological traits were less strongly associated with success for introduction and spread and little if at all for naturalization; we found that tall perennials with long flowering periods were more frequently selected for introduction, whereas species with extended flowering in New Zealand spread more rapidly. In addition to causal relationships, the importance of human factors may reflect indirect associations, including ecological traits associated with both human use and invasion. Nevertheless, our results highlight key roles that humans can play in facilitating plant invasion via two pathways: (i) commercial introduction leading to widespread planting and concomitant naturalization and spread and (ii) unintentional introduction and spread of species associated with human activities, such as seed contaminants.alien ͉ naturalization ͉ spread ͉ transition ͉ stage

The retroviral integrase protein catalyzes the insertion of linear viral DNA ends into the host cell DNA. Although integration in vivo is not site-specific, the detection of local and regional preferences within cellular DNA suggests that the integration reaction can be influenced by specific features of host DNA or chromatin. Here we describe highly preferred in vitro integration sites for avian sarcoma virus and human immunodeficiency virus-1 integrases within the stems of plasmid DNA cruciform structures. The preferred sites are adjacent to the loops in the cruciform and are strand-specific. We suggest that the observed preference is due to the end-like character of the stem loop structure that allows DNA unpairing. From these results we propose that such unpairing may enhance both the processing and the joining steps in the integration reaction, and perhaps other cellular recombination reactions as well.The integration of retroviral DNA into the host cell chromosome is an obligatory step in the retroviral replication cycle and is catalyzed by a virus-encoded protein, integrase (IN) 1 (1-3). With respect to viral DNA, integration is site-specific and occurs at the ends of the linear DNA. In contrast, many sites in host DNA can be targets for integration. IN is sufficient to perform the integration reaction in vitro, and two well defined steps have been described. In the first step, the "processing" reaction, linear viral DNA is nicked 3Ј of a conserved dinucleotide (5Ј-CA-3Ј) that is usually located two nucleotides from the 3Ј-ends of the viral DNA strands (4, 5). In the second step, "joining" (5, 6), the same active site (7, 8) is used to catalyze a coupled cleavage-ligation reaction via the direct attack on host DNA phosphates by the newly formed CA 3Ј-OH groups at the viral DNA ends (9). The two target DNA phosphates selected for joining are staggered by 4 -6 base pairs on the two DNA strands. IN functions as a multimer that may facilitate the positioning of the two viral DNA ends at the integration site. Subsequent repair and sealing of the 5Ј-ends of the viral DNA strands gives rise to the characteristic 4 -6-base pair duplication of host sequences flanking the integration site. This joining of 5Ј-ends of the viral strands is thought to be carried out by host mechanisms. In vitro, IN can utilize synthetic duplex viral DNA substrates whose sequence corresponds to a single viral DNA terminus, as well as longer substrates that contain two viral-like DNA ends. To study the latter concerted reaction, we have also constructed substrates comprised of two viral DNA ends held together by a single-stranded DNA tether (10).Although purified IN can join 3Ј-ends of viral DNA strands to naked target DNA in vitro, the in vivo reaction is likely influenced by components of host chromatin or DNA structure. In a recent study (11), it was found that many regions of avian host DNA are accessible for ASLV integration in vivo. Within these regions, preferred integration sites were observed, and it was suggested that such pr...

Propagule dispersal biology is a crucial avenue of research for rare plant species, especially those adapted to disturbance, such as northern blazing star (Liatris scariosa var. novae-angliae), a rare, early-successional New England grassland perennial. We examined the dispersal ability of northern blazing star propagules collected from 14 populations covering the entire latitudinal range of the taxon. Multiple regression demonstrated that dispersal ability, as measured by drop time in still air and flight distance in a low-speed wind tunnel, decreased significantly with propagule size and achene length, and increased with achene width and (for flight distance) pappus length. We used this multiple regression model to test for differences in predicted dispersal capability among maternal families, populations, and inland, coastal, and island habitats. Dispersal capability differed significantly among families and populations but not regions, and allometric relationships between morphological measurements were consistent across populations. Overall, dispersal capability was negatively correlated with germination success in a common greenhouse environment. However, germination success for a given dispersal ability, as well as achene shape, differed among populations. These results suggest specific populations to be targeted for management efforts promoting dispersal and establishment.