A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features

Standard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a next-generation sequencing library. The ladder can be spiked into a DNA sample, and act as an internal scale that measures quantitative genetics features. Unlike previous spike-ins, the ladder is encoded within a single molecule, and can be equivalently and independently synthesized by different laboratories. We show how the ladder can measure diverse quantitative features, including human genetic variation and microbial abundance, and also estimate uncertainty due to technical variation and improve normalization between libraries. This ladder provides an independent quantitative unit that can be used with any organism, application or technology, thereby providing a common metric by which genomes can be measured

Natural and regenerated saltmarshes exhibit similar soil and belowground organic carbon stocks, root production and soil respiration

Saltmarshes provide many valuable ecosystem services including storage of a large amount of ‘blue carbon’ within their soils. To date, up to 50% of the world’s saltmarshes have been lost or severely degraded primarily due to a variety of anthropogenic pressures. Previous efforts have aimed to restore saltmarshes and their ecosystem functions, but the success of these efforts is rarely evaluated. To fill this gap, we used a range of metrics, including organic carbon stocks, root production, soil respiration and microbial communities to compare natural and a 20-year restoration effort in saltmarsh habitats within the Sydney Olympic Park in New South Wales, Australia. We addressed four main questions: (1) Have above- and belowground plant biomass recovered to natural levels? (2) Have organic carbon stocks of soils recovered? (3) Are microbial communities similar between natural and regenerated saltmarshes? and (4) Are microbial communities at both habitats associated to ecosystem characteristics? For both soil organic carbon stocks and belowground biomass, we found no significant differences between natural and regenerated habitats (F = 0.47, p = 0.5; F = 0.08, p = 0.76). Aboveground biomass was higher in the natural habitat compared to the regenerated habitat (F = 27.3, p < 0.0001), which may result from a site-specific effect: protection from erosion offered by a fringing mangrove forest in the natural habitat but not the regenerated habitat. Our microbial community assessment indicated that restored and natural saltmarsh habitats were similar at a phylum level, with the exception of a higher proportion of Proteobacteria in the rhizosphere of saltmarshes from the regenerated habitat (p < 0.01). Abundance of both Desulfuromonas and Geobacter was associated with high carbon and nitrogen densities in soils indicating that these genera may be key for the recovery of ecosystem characteristics in saltmarshes. Our restored and natural saltmarsh soils store at 30\ua0cm depth similar levels of organic carbon: 47.9\ua0Mg OC ha to 64.6\ua0Mg OC ha. Conservation of urban saltmarshes could be important for ‘blue carbon’ programmes aimed at mitigating atmospheric carbon dioxide