Abstract. The aim of this work was to investigate the effect of an experimental fire used for grassland management on soil organic carbon (SOC) stocks. The study was carried out on Hyparrhenia hirta (L.) Stapf (Hh) grassland and Ampelodesmos mauritanicus (Desf.) T. Durand & Schinz (Am) grasslands located in the north of Sicily. Soil samples were collected at 0-5 cm before and after the experimental fire, and SOC was measured. During the grassland fire, soil surface temperature was monitored. Biomass of both grasses was analysed in order to determine dry weight and its chemical composition. The results showed that SOC varied significantly with vegetation type, while it is not affected in the short term by grassland fire. Am grassland stored more SOC compared with Hh grassland thanks to lower content in the biomass of the labile carbon pool. No significant difference was observed in SOC before and after fire, which could be caused by several factors: first, in both grassland types the measured soil temperature during fire was low due to thin litter layers; second, in a semiarid environment, a higher mineralization rate results in a lower soil carbon labile pool; and third, the SOC stored in the finest soil fractions, physically protected, is not affected by fire.

Seagrasses are among the most efficient sinks of carbon dioxide on Earth. While carbon sequestration in terrestrial plants is linked to the microorganisms living in their soils, the interactions of seagrasses with their rhizospheres are poorly understood. Here, we show that the seagrass, Posidonia oceanica excretes sugars, mainly sucrose, into its rhizosphere. These sugars accumulate to µM concentrations—nearly 80 times higher than previously observed in marine environments. This finding is unexpected as sugars are readily consumed by microorganisms. Our experiments indicated that under low oxygen conditions, phenolic compounds from P. oceanica inhibited microbial consumption of sucrose. Analyses of the rhizosphere community revealed that many microbes had the genes for degrading sucrose but these were only expressed by a few taxa that also expressed genes for degrading phenolics. Given that we observed high sucrose concentrations underneath three other species of marine plants, we predict that the presence of plant-produced phenolics under low oxygen conditions allows the accumulation of labile molecules across aquatic rhizospheres.

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

Abstract. The aim of this work was to investigate the effect of a experimental fire, used for grassland management, on soil organic carbon (SOC) reservoirs. The study was carried out on Hyparrhenia hirta (L.) Stapf (Hh) grassland and Ampelodesmos mauritanicus (Desf.) T. Durand and Schinz (Am) grasslands, located in the north of Sicily. Soil samples were collected at 0–5 cm before and after experimental fire and SOC was measured. During grassland fire soil surface temperature was monitored. Biomass of both grasses was analyzed in order to determine dry weight and its chemical composition. The results showed that SOC varied significantly with vegetation cover, while it is not affected in the short period by grassland fire. Am grassland stored more SOC compared with Hh grassland thanks to lower content in biomass of labile carbon pool. No significant difference was observed in SOC before and after fire which could be caused by several factors: first, in both grassland types the measured soil temperature during fire was low due to thin litter layers; second, in semiarid environment higher mineralization rate results in lower soil carbon labile pool; and third, the C stored in the finest soil fractions, physical protected, is not affected by fire.

Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software (https://sourceforge.net/projects/calis-p/). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.