Evidence for suboxic nitrification in recent marine sediments

The classical scheme of biogeochemical zones (BGZ) is known to be an oversimplification of the microbial processes that occur in organic-rich marine sediments. Results from a coupled deployment of pore-water gel probes in Loch Duich, Scotland, provide direct evidence for rapid recycling within the iron reduction (FeR) and sulphate reduction (SR) zones. High resolution porewater profiles obtained using diffusive equilibrium in thin films (DET) gel probes found a nitrate peak at the boundary between the FeR and SR zones. This non-steady state feature is consistent with recycling of reduced N occurring throughout the FeR zone. Both conventional pore-water iron profiles and results from diffusive gradient in thin films (DGT) probes indicate that iron is solubilised and precipitated in rapid Fe/S recycling reactions throughout the SR zone. The presence of such complex recycling reactions confirms the oversimplification of the classical BGZ scheme

High-resolution pore-water sampling with a gel sampler

Sediment pore-water profiles were sampled at high resolution (millimeter scale) with a polyacrylamide gel probe. This simple procedure involves inserting a 1-mm-thick gel held in a plastic probe into sediment. The gel reaches diffusive equilibrium in <1-2 h. For anions, the gel was sectioned, back-equilibrated into distilled-deionized water, and anions determined by high-performance liquid chromatography. Laboratory trials showed recovery of 104+/-4% Cl, 102+/-2% NO3, 101+/-1% SO4, and 102+/-2% NH4. For Fe and Mn, the gel was fixed in 0.01 M NaOH for similar to 3 h, subsectioned, extracted with 1 M HNO3, and analyzed by atomic absorption spectrometry. Field trials were undertaken in Esthwaite Water, a seasonally anoxic lake in the English Lake District. Gel probe data compared well with conventional pore-water extractions

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Citation: Serba, D. D., Uppalapati, S. R., Krom, N., Mukherjee, S., Tang, Y. H., Mysore, K. S., & Saha, M. C. (2016). Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. Bmc Genomics, 17, 14. doi:10.1186/s12864-016-3377-8Background: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1. 1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At >= 100x coverage and >= 5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions: The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion

Direct Discharges of Domestic Wastewater are a Major Source of Phosphorus and Nitrogen to the Mediterranean Sea

Direct discharges of treated and untreated wastewater are important sources of nutrients to coastal marine ecosystems and contribute to their eutrophication. Here, we estimate the spatially distributed annual inputs of phosphorus (P) and nitrogen (N) associated with direct domestic wastewater discharges from coastal cities to the Mediterranean Sea (MS). According to our best estimates, in 2003 these inputs amounted to 0.9 × 10⁹ mol P yr-1 and 15 × 10⁹ mol N yr-1, that is, values on the same order of magnitude as riverine inputs of P and N to the MS. By 2050, in the absence of any mitigation, population growth plus higher per capita protein intake and increased connectivity to the sewer system are projected to increase P inputs to the MS via direct wastewater discharges by 254, 163, and 32% for South, East, and North Mediterranean countries, respectively. Complete conversion to tertiary wastewater treatment would reduce the 2050 inputs to below their 2003 levels, but at an estimated additional cost of over €2 billion yr-1. Management of coastal eutrophication may be best achieved by targeting tertiary treatment upgrades to the most affected near-shore areas, while simultaneously implementing legislation limiting P in detergents and increasing wastewater reuse across the entire basin