Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

UNLABELLED: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. AVAILABILITY AND IMPLEMENTATION: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. CONTACT: shallam@mail.ubc.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fossil steroids record the appearance of Demospongiae during the Cryogenian period.

The Neoproterozoic era (1,000-542 Myr ago) was an era of climatic extremes and biological evolutionary developments culminating in the emergence of animals (Metazoa) and new ecosystems. Here we show that abundant sedimentary 24-isopropylcholestanes, the hydrocarbon remains of C(30) sterols produced by marine demosponges, record the presence of Metazoa in the geological record before the end of the Marinoan glaciation ( approximately 635 Myr ago). These sterane biomarkers are abundant in all formations of the Huqf Supergroup, South Oman Salt Basin, and, based on a new high-precision geochronology, constitute a continuous 100-Myr-long chemical fossil record of demosponges through the terminal Neoproterozoic and into the Early Cambrian epoch. The demosponge steranes occur in strata that underlie the Marinoan cap carbonate (>635 Myr ago). They currently represent the oldest evidence for animals in the fossil record, and are evidence for animals pre-dating the termination of the Marinoan glaciation. This suggests that shallow shelf waters in some late Cryogenian ocean basins (>635 Myr ago) contained dissolved oxygen in concentrations sufficient to support basal metazoan life at least 100 Myr before the rapid diversification of bilaterians during the Cambrian explosion. Biomarker analysis has yet to reveal any convincing evidence for ancient sponges pre-dating the first globally extensive Neoproterozoic glacial episode (the Sturtian, approximately 713 Myr ago in Oman).

Continuous summer export of nitrogen-rich organic matter from the Greenland Ice Sheet inferred by ultrahigh resolution mass spectrometry.

Runoff from glaciers and ice sheets has been acknowledged as a potential source of bioavailable dissolved organic matter (DOM) to downstream ecosystems. This source may become increasingly significant as glacial melt rates increase in response to future climate change. Recent work has identified significant concentrations of bioavailable carbon and iron in Greenland Ice Sheet (GrIS) runoff. The flux characteristics and export of N-rich DOM are poorly understood. Here, we employed electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to determine the elemental compositions of DOM molecules in supraglacial water and subglacial runoff from a large GrIS outlet glacier. We provide the first detailed temporal analysis of the molecular composition of DOM exported over a full melt season. We find that DOM pools in supraglacial and subglacial runoff are compositionally diverse and that N-rich material is continuously exported throughout the melt season, as the snowline retreats further inland. Identification of protein-like compounds and a high proportion of N-rich DOM, accounting for 27-41% of the DOM molecules identified by ESI FT-ICR MS, may suggest a microbial provenance and high bioavailability of glacially exported DOM to downstream microbial communities.

A Leak in the Academic Pipeline: Identity and Health Among Postdoctoral Women.

Several challenges (e.g., sexism, parental leave, the glass ceiling, etc.) disproportionately affect women in academia (and beyond), and thus perpetuate the leaky pipeline metaphor for women who opt-out of an academic career. Although this pattern can be seen at all levels of the academic hierarchy, a critical time for women facing such challenges is during the postdoctoral stage, when personal life transitions and professional ambitions collide. Using a social identity approach, we explore factors affecting the mental health of postdoctoral women, including identity development (e.g., as a mother, a scientist) and lack of control (uncertainty about one's future personal and professional prospects), which likely contribute to the leak from academia. In this mixed-method research, Study 1 comprised interviews with postdoctoral women in North America (n = 13) and Europe (n = 8) across a range disciplines (e.g., psychology, physics, political science). Common themes included the negative impact of career uncertainty, gender-based challenges (especially sexism and maternity leave), and work-life balance on mental and physical health. However, interviewees also described attempts to overcome gender inequality and institutional barriers by drawing on support networks. Study 2 comprised an online survey of postdoctoral women (N = 146) from a range of countries and academic disciplines to assess the relationships between social identification (e.g., disciplinary, gender, social group), perceived control (i.e., over work and life), and mental health (i.e., depression, anxiety, stress, and life satisfaction). Postdoctoral women showed mild levels of stress and depression, and were only slightly satisfied with life. They also showed only moderate levels of perceived control over one's life and work. However, hierarchical regression analyses revealed that strongly identifying with one's discipline was most consistently positively associated with both perceived control and mental health. Collectively, these findings implicate the postdoctoral stage as being stressful and tenuous for women regardless of academic background or nationality. They also highlight the importance of disciplinary identity as a potentially protective factor for mental health that, in turn, may diminish the rate at which postdoctoral women leak from the academic pipeline.

Author Correction: A compendium of geochemical information from the Saanich Inlet water column.

In Table 3 of this Data Descriptor the units of Mean_N2O and Mean_CH4 are incorrectly stated as "Nanomolar (µM)". This should instead read "Nanomolar (nM)".

A compendium of geochemical information from the Saanich Inlet water column.

Extensive and expanding oxygen minimum zones (OMZs) exist at variable depths in coastal and open ocean waters. As oxygen levels decline, nutrients and energy are increasingly diverted away from higher trophic levels into microbial community metabolism, resulting in fixed nitrogen loss and production of climate active trace gases including nitrous oxide and methane. While ocean deoxygenation has been reported on a global scale, our understanding of OMZ biology and geochemistry is limited by a lack of time-resolved data sets. Here, we present a historical dataset of oxygen concentrations spanning fifty years and nine years of monthly geochemical time series observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique geochemical framework for evaluating long-term trends in biogeochemical cycling in OMZ waters.

A compendium of multi-omic sequence information from the Saanich Inlet water column.

Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.

Effect of carbon addition and predation on acetate-assimilating bacterial cells in groundwater.

Groundwater microbial community dynamics are poorly understood due to the challenges associated with accessing subsurface environments. In particular, microbial interactions and their impact on the subsurface carbon cycle remain unclear. In the present project, stable isotope probing with uniformly labeled [(13)C]-acetate was used to identify metabolically active and inactive bacterial populations based on their ability to assimilate acetate and/or its metabolites. Furthermore, we assessed whether substrate availability (bottom-up control) or grazing mortality (top-down control) played a greater role in shaping bacterial community composition by separately manipulating the organic carbon supply and the protozoan grazer population. A community fingerprinting technique, terminal restriction fragment length polymorphism, revealed that the bacterial community was not affected by changes in acetate availability but was significantly altered by the removal of protozoan grazers. In silico identification of terminal restriction fragments and 16S rRNA gene sequences from clone libraries revealed a bacterial community dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Elucidation of the factors that structure the bacterial community will improve our understanding of the bacterial role in the carbon cycle of this important subterranean environment.

Fracture propagation to the base of the Greenland Ice Sheet during supraglacial lake drainage.

Surface meltwater that reaches the base of an ice sheet creates a mechanism for the rapid response of ice flow to climate change. The process whereby such a pathway is created through thick, cold ice has not, however, been previously observed. We describe the rapid (<2 hours) drainage of a large supraglacial lake down 980 meters through to the bed of the Greenland Ice Sheet initiated by water-driven fracture propagation evolving into moulin flow. Drainage coincided with increased seismicity, transient acceleration, ice-sheet uplift, and horizontal displacement. Subsidence and deceleration occurred over the subsequent 24 hours. The short-lived dynamic response suggests that an efficient drainage system dispersed the meltwater subglacially. The integrated effect of multiple lake drainages could explain the observed net regional summer ice speedup.

Distinct bacterial communities exist beneath a high Arctic polythermal glacier.

Bacterial communities reside in basal ice, sediment, and meltwater in the supra-, sub-, and proglacial environments of John Evans Glacier, Nunavut, Canada. We examined whether the subglacial bacterial community shares common members with the pro- and supraglacial communities, and by inference, whether it could be derived from communities in either of these environments (e.g., by ice overriding proglacial sediments or by in-wash of surface meltwaters). Terminal restriction fragment length polymorphism analysis of bacterial 16S rRNA genes amplified from these environments revealed that the subglacial water, basal ice, and sediment communities were distinct from those detected in supraglacial meltwater and proglacial sediments, with 60 of 142 unique terminal restriction fragments (T-RFs) detected exclusively in subglacial samples and only 8 T-RFs detected in all three environments. Supraglacial waters shared some T-RFs with subglacial water and ice, likely reflecting the seasonal flow of surface meltwater into the subglacial drainage system, whereas supraglacial and proglacial communities shared the fewest T-RFs. Thus, the subglacial community at John Evans Glacier appears to be predominantly autochthonous rather than allochthonous, and it may be adapted to subglacial conditions. Chemical analysis of water and melted ice also revealed differences between the supraglacial and proglacial environments, particularly regarding electrical conductivity and nitrate, sulfate, and dissolved organic carbon concentrations. Whereas the potential exists for common bacterial types to be broadly distributed throughout the glacial system, we have observed distinct bacterial communities in physically and chemically different glacial environments.