Publications

We estimated organic carbon (OC) burial over the past century in 40 impoundments in one of the most intensively agricultural regions of the world. The volume of sediment deposited per unit time varied as a function of lake and watershed size, but smaller impoundments had greater deposition and accumulation rates per unit area. Annual water storage losses varied from 0.1–20% and were negatively correlated with impoundment size. Estimated sediment OC content was greatest in lakes with low ratios of watershed to impoundment area. Sediment OC burial rates were higher than those assumed for fertile impoundments by previous studies and were much higher than those measured in natural lakes. OC burial ranged from a high of 17,000 g C m −2 a −1 to a low of 148 g C m −2 a −1 and was significantly greater in small impoundments than large ones. The OC buried in these lakes originates in both autochthonous and allochthonous production. These analyses suggest that OC sequestration in moderate to large impoundments may be double the rate assumed in previous analyses. Extrapolation suggests that they may bury 4 times as much carbon (C) as the world's oceans. The world's farm ponds alone may bury more OC than the oceans and 33% as much as the world's rivers deliver to the sea.

Seagrass meadows are natural carbon sinks, and their conservation and restoration play a crucial role in climate change mitigation and adaptation. However, blue carbon projects are hindered, in most nations, by major gaps in understanding the distribution and extent of seagrasses. Here, we show how satellite tracking of green turtles ( Chelonia mydas ) provided a major advance in identifying novel seagrass blue carbon resources in the Red Sea. By tracking 53 nesting green turtles, we identified 38 distinctive foraging sites. All ground-truthed foraging sites (100%) identified a seagrass meadow, surpassing the 40% ( n = 30) accuracy of satellite imagery-based inferences. Sampling from these turtle-derived locations represents a greater range of depths than previously sampled in the Red Sea providing a carbon stock estimate of 4.89 ± 0.83 kg C org (organic carbon) m −2 . By improving estimates of seagrass extent and associated blue carbon, our approach can support the conservation of blue carbon resources in data-deficient regions worldwide.

The content of volatile and semivolatile organic compounds (VOC and SOC), measured as exchangeable dissolved organic carbon (EDOC), was quantified in 9 phytoplanktonic species that spanned 4 orders of magnitude in cell volume, by disrupting the cells and quantifying the gaseous organic carbon released. EDOC content varied 4 orders of magnitude, from 0.0015 to 14.12 pg C cell-1 in the species studied and increased linearly with increasing phytoplankton cell volume following the equation EDOC (pg C cell-1) = -2.35 x cellular volume (CV, µm3 cell-1) 0.90 (± 0.3), with a slope (0.90) not different from 1 indicating a constant increase in volatile carbon as the cell size of phytoplankton increased. The percentage of EDOC relative to total cellular carbon was small but varied 20 fold from 0.28 % to 5.17 %, and no obvious taxonomic pattern in the content of EDOC was appreciable for the species tested. The cell release rate of EDOC is small compared to the amount of carbon in the cell and difficult to capture. Nonetheless, the results point to a potential flux of volatile and semivolatile phytoplankton-derived organic carbon to the atmosphere that has been largely underestimated and deserves further attention in the future.

Abstract Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require access to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data. We illustrate the capacities KMAP provides through the re-assembly of ~ 27,000 public metagenomic samples captured in ~ 450 studies sampled across ~ 77 diverse habitats. A small subset of these metagenomic assemblies is used in this pilot study grouped into 36 new habitat-specific gene catalogs, all based on full-length (complete) genes. Extensive taxonomic and gene annotations are stored in Gene Information Tables (GITs), a simple tractable data integration format useful for analysis through command line or for database management. KMAP pilot study provides the exploration and comparison of microbial GITs across different habitats with over 275 million genes. KMAP access to data and analyses is available at https://www.cbrc.kaust.edu.sa/aamg/kmap.start .

Abstract Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal‐like”‐ abundant and ubiquitous; “logistic”‐ globally rare, present in few sites; and “bimodal”‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal‐like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal‐like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.

Abstract The study of a Posidonia australis sediment archive has provided a record of ecosystem dynamics and processes over the last 600 years in Oyster Harbour ( SW Australia). Ecosystem shifts are a widespread phenomenon in coastal areas, and this study identifies baseline conditions and the time‐course of ecological change (cycles, trends, resilience and thresholds of ecosystem change) under environmental stress in seagrass‐dominated ecosystem. The shifts in the concentrations of chemical elements, carbonates, sediments <0.125 mm and stable carbon isotope signatures ( δ 13 C) of the organic matter were detected between 1850s and 1920s, whereas the shift detected in P concentration occurred several decades later (1960s). The first degradation phase (1850s–1950s) follows the onset of European settlement in Australia and was characterized by a strong increase in sediment accumulation rates and fine‐grained particles, driven primarily by enhanced run‐off due to land clearance and agriculture in the catchment. About 80% of total seagrass area at Oyster Harbour was lost during the second phase of environmental degradation (1960s until present). The sharp increase in P concentration and the increasing contribution of algae and terrestrial inputs into the sedimentary organic matter pool around 1960s provides compelling evidence of the documented eutrophication of the estuary and the subsequent loss of seagrass meadows. The results presented demonstrate the power of seagrass sedimentary archives to reconstruct the trajectories of anthropogenic pressures on estuarine ecosystem and the associated regime shifts, which can be used to improve the capacity of scientists and environmental managers to understand, predict and better manage ecological change in these ecosystems.

The characterization, control, and reporting of environmental conditions in mammalian cell cultures is fundamental to ensure physiological relevance and reproducibility in basic and preclinical biomedical research. The potential issue of environment instability in routine cell cultures in affecting biomedical experiments was identified many decades ago. Despite existing evidence showing variable environmental conditions can affect a suite of cellular responses and key experimental readouts, the underreporting of critical parameters affecting cell culture environments in published experiments remains a serious problem. Here, we outline the main sources of potential problems, improved guidelines for reporting, and deliver recommendations to facilitate improved culture-system based research. Addressing the lack of attention paid to culture environments is critical to improve the reproducibility and translation of preclinical research, but constitutes only an initial step towards enhancing the relevance of in vitro cell cultures towards in vivo physiology.

Corrigendum: Metagenomic probing toward an atlas of the taxonomic and metabolic foundations of the global ocean genome