Microbes play a critical role in regulating the size, composition, and turnover of dissolved organic matter (DOM), which is one of the largest pools of carbon in aquatic ecosystems. Global change may alter DOM-microbe associations with implications for biogeochemical cycles, although disentangling these complex interactions remains a major challenge. Here we develop a framework called Energy-Diversity-Trait integrative Analysis (EDTiA) to examine the associations between DOM and bacteria along temperature and nutrient gradients in a manipulative field experiment on mountainsides in contrasting subarctic and subtropical climates. In both study regions, the chemical composition of DOM correlated with bacterial communities, and was primarily controlled by nutrients and to a lesser degree by temperature. At a molecular-level, DOM-bacteria associations depended strongly on the molecular traits of DOM, with negative associations indicative of decomposition as molecules are more biolabile. Using bipartite networks, we further demonstrated that negative associations were more specialized than positive associations indicative of DOM production. Nutrient enrichment promoted specialization of positive associations, but decreased specialization of negative associations particularly at warmer temperatures in subtropical climate. These global change drivers influenced specialization of negative associations most strongly via molecular traits, while both molecular traits and bacterial diversity similarly affected positive associations. Together, our framework provides a quantitative approach to understand DOM-microbe associations and wider carbon cycling across scales under global change.
The world map of anthropogenic atmospheric nitrogen deposition and its effects on natural ecosystems is not described with equal precision everywhere. In this paper, we report atmospheric nutrient, sulphate and spheroidal carbonaceous particles (SCPs) deposition rates, based on snowpack analyses, of a formerly unexplored Siberian mountain region. Then, we discuss their potential effects on lake phytoplankton biomass limitation. We estimate that the nutrient depositions observed in the late season snowpack (40±16 mg NO-N×m and 0.58±0.13 mg TP-P·m) would correspond to yearly depositions lower than 119±71 mg NO-N·m·y and higher than 1.71±0.91 mg TP-P·m·y. These yearly deposition estimates would approximately fit the predictions of global deposition models and correspond to the very low nutrient deposition range although they are still higher than world background values. In spite of the fact that such low atmospheric nitrogen deposition rate would be enough to induce nitrogen limitation in unproductive mountain lakes, the extremely low phosphorus deposition would have made the bioavailable N:P deposition ratio to be frankly high. In the end, lake phytoplankton appeared to be hanging on the fence between phosphorus and nitrogen limitation, with a trend towards nitrogen limitation. We conclude that slight imbalances in the nutrient deposition might have important effects on the ecology of these lakes under the expected scenario of climate warming, increased winter precipitation, enhanced forest fires and shifts in anthropogenic nitrogen emissions.
The year 2020 marks the 10th anniversary of the Deepwater Horizon (DWH) disaster. From April through July 2010, an estimated total of 4.9 million barrels of oil and 250,000 metric tonnes of natural gas were discharged into the Gulf of Mexico. Not only were eleven lives lost, but the tragedy also left a lasting impact on the Gulf’s marine and coastal ecosystems and on the residents who depend on these habitats for their livelihood. After the oil spill, the Gulf of Mexico’s microbial communities played a critical role in the cleanup, contributing core hydrocarbon bioremediation services. Despite its importance, marine hydrocarbon microbiology is a young field. Prior to the spill relatively little was known about marine hydrocarbon degraders. Beginning in 2010, the development and application of genomics and bioinformatics tools enabled researchers – for the first time - to identify and examine individual microorganisms within their complex communities in unprecedented detail. Today, technical advances and new discoveries reveal a natural capacity of microbes in the Gulf of Mexico to catalyze bioremediation of petroleum hydrocarbons. This knowledge is critical to guide mitigation and restoration strategies that build on microbes’ natural bioremediation capabilities without further disturbing sensitive ecosystems. This report is based on the deliberations of experts who participated in the joint colloquium of the American Academy of Microbiology, ASM’s honorific leadership group, the American Geophysical Union (AGU), and Gulf of Mexico Research Initiative (GoMRI) in April 2019. The report highlights new research tools, methodology, data resources, collaborations, and models that will advance basic and applied research to provide data-driven solutions to environmental challenges. The report is available at www.ASM. org/microbe_oceansystem.
Known as black bread mold, R. stolonifer is a fungus commonly found in contaminated food products such as meat, preserved, and/or baked goods. Potassium sorbate is a common food preservative used to prevent fungi, mold, and mycotoxin growth by damaging the cell membrane or altering proteins in the cell. Based on background research on potassium sorbate growth prevention, it was hypothesized that a 25% concentration of potassium sorbate will most efficiently prevent R. stolonifer growth compared to lower concentrations. R. stolonifer was grown on potato dextrose agar with eight levels of potassium sorbate concentrations. During a two week period, fungal growth was observed, photographed, and the height and width of each sample were recorded. At the end of two weeks, the fungi were stained using lactophenol cotton blue dye and observed under a microscope. Qualitative observation at the cellular level showed healthy R. stolonifer solely in the control group (see Figure 1). When comparing the fungi samples across the 5% and 30% concentration groups, large areas of dead mass dominated their cellular makeup. At the end of two weeks, the 1% concentration sample group had an observed increase of 1.383 cm2 in total area, a significant decrease compared to the control group. Between the 5% and 30% concentration sample groups, there were minor changes in total area with no change exceeding 0.125 cm2. Between the 1% and 5% experimental groups, there was a significant decrease in fungal area growth, and a similarly large decrease between the 10% and 15% concentration fungi samples. Thus, it can be concluded that it is unnecessary to exceed a 1% concentration of potassium sorbate to prevent fungal growth.
Marine oxygen deficient zones (ODZs) are dynamic areas of microbial nitrogen cycling. Nitrification, the microbial oxidation of ammonia to nitrate, plays multiple roles in the biogeochemistry of these regions, including production of the greenhouse gas nitrous oxide (N2O). We present here the results of two oceanographic cruises investigating nitrification, nitrifying microorganisms, and N2O production and distribution from the offshore waters of the Eastern Tropical South Pacific (ETSP). On each cruise, high-resolution measurements of ammonium ([NH4+]), nitrite ([NO2-]), and N2O were combined with 15N tracer-based determination of ammonia oxidation, nitrite oxidation, nitrate reduction and N2O production rates. Depth-integrated inventories of NH4+ and NO2- were positively correlated with one another, and with depth-integrated primary production. Depth-integrated ammonia oxidation rates were correlated with sinking particulate organic nitrogen flux but not with primary production; ammonia oxidation rates were undetectable in trap-collected sinking particulate material. Nitrite oxidation rates exceeded ammonia oxidation rates at most mesopelagic depths. We found positive correlations between archaeal genes and ammonia oxidation rates and between -like 16S rRNA genes and nitrite oxidation rates. N2O concentrations in the upper oxycline reached values of greater than 140 nM, even at the western extent of the cruise track, supporting air-sea fluxes of up to 1.71 umol m-2 d-1. Our results suggest that a source of N2O other than ammonia oxidation may fuel high rates of nitrite oxidation in the offshore ETSP and that air-sea fluxes of N2O from this region may be higher than previously estimated.
The Amazon River discharges more than 200,000 m3 s-1 into the Western Tropical Atlantic Ocean from May to June. The low salinity surface plume extends more than 1800 km from the mouth and covers an area greater than 1 million square kilometers. We hypothesize that the plume exhibits distinct microbial community assemblages driven by plume age, nutrient supply, and light availability. We collected samples for nutrients and flow-cytometry measurements to investigate the spatial variability of the cyanobacteria Prochlorococcus spp. and Synechococcus spp., picoeukaryotes, and heterotrophic bacteria. Overall the surface salinity of the water we sampled ranged from 15.5 ppt at the southernmost station to 36.3 ppt in the open ocean station. The surface nitrate and soluble reactive phosphorus concentrations ranged from below detection limit to 3.3 µM and 2 µM, respectively. Generally, in the freshest surface plume waters (15-28 ppt) we found the highest abundances of Synechococcus spp., picoeukaryotes, and hetrotrophic bacteria with little or no Prochlorococcus spp. In the transition of surface salinities from 28 ppt to 32 ppt, a population of Prochlorococcus spp. began to form below the surface plume while Synechococcus spp. abundances at the surface remained unchanged and picoeukaryotes, and heterotrophic bacteria abundances decreased. As the surface salinity climbed over 32 ppt, the Prochlorococcus spp. abundance was uniformly high throughout the euphotic zone. On the other hand, as surface salinities increased over 32 ppt Synechococcus spp. abundances at the surface gradually decreased, while picoeukaryote and hetrotrophic bacterial abundances remained constant. We will discuss changes in the microbial community composition as a function of nutrient and light availability, as well as plume age in the Amazon Plume-Ocean continuum in both surface and deep chlorophyll maximum assemblages.
Over the past three years Stone Aerospace has developed a novel ice penetrating technology known as a Direct Laser Penetration (DLP). DLP uses laser light carried by an optical fiber to a vertically descending ice penetrator and emitted from the nose to melt the ice in front of it at extremely high power levels and melt rates. A penetrator can be made with an onboard fiber spool connected to a surface-based laser, allowing the hole to re-freeze behind, drastically increasing efficiency and providing isolation from the surface. A parallel spool can pay out a communications fiber to carry information from imagers, fiber-based sensors (e.g. temperature, pressure, seismic), and other optical sensors (e.g. fluorescence or Raman). Laser power levels of up to 100 kW (continuous) at 1070 nm wavelength are now available and can be coupled to these probes. Successful laboratory test results at Antarctic ice temperatures show that this approach could lead to the fastest ice penetration rate available to terrestrial targets, with access to any Antarctic sub-glacial lake in under 16 hours. In this way, DLP offers an alternative to traditional, logistically intense ice drilling: a small footprint system that is fast and can deploy sensor strings through the deepest ice in a short period of time. DLP also shows promise in addressing the ‘starting problem’ for extraterrestrial targets such as Europa or Mars where low pressures prevent the formation of water at the surface and thus heat transfer for traditional melt probe architectures. In order to test the effectiveness of this concept, a Europa environment ‘cryovac’ test facility has been built at Stone Aerospace in Austin, Texas. We will discuss quantitative results from initial lab and chamber tests of the DLP concept, including in an ice column at 100 K temperature subjected to vacuum.
Priming leads to the significant changes in the decomposition rate of organic matter (OM) in natural ecosystems induced by minimal treatments. A fundamental understanding of priming effects is critical to accurately predict biogeochemical dynamics and carbon/nitrogen OM cycles in natural ecosystems. However, we poorly understand how the priming effect is mechanistically induced and what factors govern the process among microbial activities and environmental constraints. Here, we propose a generalizable theory to collectively explain diverse patterns of priming effects via the cybernetic approach that accounts for regulation as key features of microbial growth. The cybernetic model treats microorganisms as dynamic systems that optimally regulate metabolic functions with respect to environmental conditions to safeguard their survival. Motivated by priming phenomenon observed in the hyporheic corridor of a riverine ecosystem, we formulated our model to investigate how the addition of exogenous labile OM primes the microbial respiration of polymeric OM. Our model accounts for interspecies interactions between various assortments of microbial groups with distinct metabolic traits to enable prediction of both increase (positive priming) and decrease (negative priming) of OM turnover using the same model structure. Our modeling framework reveals that: (1) the priming effects are manifestations of microbial regulatory response to diverse environmental conditions, and (2) priming magnitude and direction are highly dependent on the polymeric OM richness and the extent of treatment with labile OM. Beyond elucidating qualitative understanding of the phenomenon, our model also suggests that interspecies interactions between microbial groups with distinct metabolic traits (i.e., population turnover, sensitivity to labile OM, and efficiency in degrading polymeric OM) potentially drive the priming effects. By integrating contextual knowledge and a generalizable theory, our holistic modeling framework is effective for investigation and prediction of biogeochemical dynamics of natural ecosystems across diverse biological and environmental settings.
Anaerobic microbial activity in the ocean causes losses of bioavailable nitrogen and emission of nitrous oxide to the atmosphere, but its predictability at global scales remains limited. Resource ratio theory suggests that anaerobic activity becomes sustainable when the ratio of oxygen to organic matter supply is below the ratio required by aerobic metabolisms. Here, we demonstrate the relevance of this framework at the global scale using three-dimensional ocean datasets, providing a new interpretation of existing observations. Evaluations of the location and extent of anoxic zones and a diagnostic rate of pelagic nitrogen loss are consistent with previous estimates. However, we demonstrate that the flux-based threshold is qualitatively different from a threshold based solely on the ambient oxygen concentration. Since the framework is feasible for application in global biogeochemical models, it represents a way forward for more dynamic, mechanistic predictions of anaerobic activity and nitrogen loss.
The microorganisms that evolved during the Archean era had extraordinary impacts on this planet. If not for them, Earth would not have developed the oxygen-rich atmosphere needed to support the evolution of multicellular organisms. However, our direct observations of life from that time come from only fifteen known fossiliferous Archean rock formations, and the exploration of these formations is not complete. As a result, study of these formations can yield new insights into the communities of microfossils that lived in the Archean era and previously unobserved microfossil morphologies. Here we present spheroid microfossils, as well as unusually large microfossils with clublike morphologies not previously observed in Archean microorganisms. These microfossils were three-dimensionally preserved in black chert from the Gamohaan Formation, Griqualand West Basin, Kaapvaal Craton, South Africa. These microfossils were discovered in a small, domal stromatolite that formed in a shallow marine setting on a carbonate shelf system at 2.52 billion years ago (Sumner and Bowring, 1996), just one to two hundred million years before the Great Oxidation Event.
Basaltic lava caves are important Earth analogs in our search for life on Mars and other planets. Terrestrial lava caves exhibit morphologically diverse secondary mineral deposits (speleothems) often associated with liquid water. The detailed geochemical characterization of cave water and speleothems can provide valuable insights on potential biotic or abiotic mechanisms that lead to formation of these features. Our results showed that the cave water chemistry is consistent with basaltic host rock chemical composition. The water contained high levels of dissolved organic carbon and nitrogen, which could support microbial growth. The dissolved organic matter showed macromolecular structure and appears to be plant-derived, highly humified and microbially processed. Elevated nitrate in cave water may be due to agriculturally influenced regional surface water source or in situ oxidation of ammonia or organic N. Speleothems contained 29-79 wt% of crystalline, cryptocrystalline, or amorphous SiO2, and secondary minerals containing biosignature elements (Ca, Mg, Fe, Mn, S and V). This work complements the ongoing NASA BRAILLE (Biologic and Resource Analog Investigations in Low Light Environments) project to study basaltic lava tube caves as Earth analogs and ultimately provide insights for planning future missions to search for biosignature on Mars and other planetary bodies.
An emerging solution in mine waste remediation is the use of biological processes, such as microbial sulfate reduction (MSR), to immobilize metals, reducing their bioavailability and buffering the pH of acid mine drainage. Apart from laboratory tests and local observations of natural MSR in e.g. single wetlands, little is known about spatio-temporal characteristics of freshwater MSR from multiple locations within entire hydrological catchments. We here applied an isotopic fractionation (δ34S-values in SO42-) and Monte-Carlo based mixing analysis scheme to detect MSR and its variation across two major mining regions (Imetjoki, Sweden and Khibiny, Russia) in the Arctic part of Europe under different seasonal conditions. Results indicate a range of catchment-scale MSR-values in the Arctic of ~ 5-20% where the low end of the range was associated with the non-vegetated, mountainous terrain of the Khibiny catchment, having low levels of dissolved organic carbon (DOC). The high-end of the range was related to vegetated conditions provided by the Imetjoki catchment that also contains wetlands, lakes and local aquifers. These prolong hydrological residence times and support MSR hot-spots reaching values of ~40%. Present results additionally show evidence of MSR-persistence over different seasons, indicating large potential, even under relatively cold conditions, of using MSR as part of nature-based solutions to mitigate adverse impacts of (acid) mine drainage. The results call for more detailed investigations regarding potential field-scale correlations between MSR and individual landscape and hydro-climatic characteristics, which e.g. can be supported by the here utilized isotopic fractionation and mixing scheme.
Deinococcus radiodurans has been reported to show remarkable resistance to ionizing radiation, desiccation, oxidizing compounds, UV radiation and mutagens. Since the 1960s, several exposure tests on diverse bacteria in space have been conducted to study the possibility of interplanetary life transfer and this bacterium pertains to a distinct gram-negative eubacterial lineage that is considered to be most closely related to the genus Thermus. The chemical reaction of D. radiodurans after exposure to space-related radiation and vacuum was studied in the concerned research that extends the application of the Tanpopo mission conducted by Japan. Certain tests like Scanning electron microscopy demonstrated that irradiated cell shape and cellular integrity were unaffected, whereas combined proteome and metabolomic research revealed significant molecular modifications in metabolic and stress response pathways. Taking this into account reinforced with simulation studies, we propose fabrication of a wearable radiation-shielding bio-spacesuit to protect the astronauts and prevent the onset of acute radiation damage. The main focus of this study is on the idea of incorporating the organism's composition mechanisms either into the five layers of mylar or aerogel of spacesuit in order to prevent damaging radiation in space.
The Oman Drilling Project established an “Active Alteration” multi-borehole observatory in dunite and harzburgite undergoing low-temperature serpentinization in the Samail ophiolite. The highly serpentinized rocks are in contact with strongly reducing fluids. Distinct hydrological regimes, governed by differences in rock porosity and fracture density, give rise to steep redox (Eh +200 to -750 mV) and pH (pH range 8.5 to 11.2) gradients within the 300 to 400 meter deep boreholes. The serpentinites and fluids host an active subsurface ecosystem. Microbial cell abundances vary at least 6 orders of magnitude, from ≤3.5*101 cells/g to 2.9*107 cells/gram. Low levels of biological sulfate reduction (2-1000 fmol/cm3/day) can be detected in rock cores, particularly in rocks in contact with reduced groundwaters with pH <10.5. Thermodesulfovibrio is the predominant sulfate reducer identified via metagenomic sequencing of adjacent groundwater communities. We infer that transport and reaction of microbially generated sulfide with the serpentine and brucite assemblages gives rise to optical darkening and sulfide overprinting, including the formation of tochilinite-vallerite group minerals, potentially serving as an indicator that this system is inhabited by microbial life. Olivine mesh-cores replaced with ferroan brucite and minor awaruite, abundant veins containing hydroandradite garnet and polyhedral serpentine, and late-stage carbonate veins are suggested as targets for future spatially-resolved life-detection investigations. The high-quality whole-round core samples that have been preserved can be further probed to define how life distributes itself and functions within a system where chemical disequilibria are sustained by low-temperature water/rock interaction, and how biosignatures of in-situ microbial activity are generated.
The potential for molecular hydrogen (H-OH- groundwaters bearing up to 4.05 μmol⋅L-1 H2 , 3.81 μmol⋅L-1 methane (CH4) and 946 μmol⋅L-1 sulfate (SO42-) revealed an ecosystem dominated by Bacteria affiliated with the class Thermodesulfovibrionia, a group of chemolithoheterotrophs supported by H2 oxidation coupled to SO42- reduction. In shallower, oxidized Mg2+-HCO3- groundwaters, aerobic and denitrifying heterotrophs were relatively more abundant. High δ13C and δD of CH4 (up to 23.9 ‰ VPDB and 45 ‰ VSMOW , respectively), indicated microbial CH4 oxidation, particularly in Ca2+-OH- waters with evidence of mixing with Mg2+-HCO3- waters. This study demonstrates the power of spatially resolving groundwaters to probe their distinct geochemical conditions and chemosynthetic communities. Such information will help improve predictions of where microbial activity in fractured rock ecosystems might occur, including beyond Earth.
The growth of biofilms changes the hydrodynamics of porous media, which will influence the transport of bacteria and contaminants in natural and engineered systems. Traditionally, biofilms have been modeled as an impermeable domain in porous media, such that no water can enter biofilms and contaminants can only enter biofilms via molecular diffusion. Such a modeling approach is based on the assumption that the permeability of biofilms is the same as that of Extracellular Polymeric Substances (EPS), which are considered to have very low permeability. In this study, we investigate the impacts of biofilm properties on water flow using microfluidic device experiments and pore-scale modeling. E. coli biofilm was established inside a microfluidic channel packed with unisized glass beads in a single layer. A 5*5 mm2 area was live-stained and imaged via confocal microscopy at three different growth stages to represent three biofilm levels in the system. After image analysis using FIJI and AutoCAD software, the flow in the bio-clogged porous media was simulated using COMSOL Multiphysics. In these simulations, biofilm was modeled as a separate permeable domain in porous media instead of an impermeable domain. A Forchheimer-corrected version of the Brinkman equations was applied to simulate the flow in the porous biofilm regions. Two properties of biofilms, namely biofilm porosity (BPO) and biofilm permeability (BPE), were altered to examine their effects on the permeability of the system. It was found that different values of BPO and BPE clearly affect the flow paths, velocity patterns, and permeability of the system. Considering biofilms as impermeable results in significant underestimations of the flow properties. In addition, two simplified modeling scenarios, namely uniform coating and symmetric contact filling, were investigated for a possible abridging in the arduous modeling procedure of the real biofilm geometry.
We examined the biogeochemical impact of pairs of mesoscale cyclones and anticyclones in spatial proximity (<200 km apart) in the North Pacific Subtropical Gyre. While previous studies have demonstrated that upwelling associated with the intensification of cyclonic eddies supplies nutrients to the euphotic zone, we find that cyclonic eddies in their mature stage sustain plankton growth by increasing the diapycnal flux of nutrients to the lower portion of the euphotic zone. This increased supply results from enhanced vertical gradients in inorganic nutrients due to erosion of the nutricline that accompanied plankton growth during eddy intensification. From a biological standpoint, increased nutrient flux was linked with expansion of eukaryotic phytoplankton biomass and intensification of the deep chlorophyll maximum layer. This perturbation in the plankton community was associated with increased fluxes of biominerals (opal and calcium carbonate) and isotopically enriched nitrogen in particles exported in the cyclone. The time-integrated effects of thermocline uplifts and depressions were predictable deficits and surpluses of inorganic nutrients and dissolved oxygen in the lower euphotic zone. However, the stoichiometry of changes in oxygen and inorganic nutrients differed from that predicted for production and consumption of phytoplankton biomass, consistent with additional biological processes that decouple changes in oxygen and nutrient concentrations. The dynamics revealed by this study may be a common feature of oligotrophic ecosystems, where mesoscale biogeochemical perturbations are buffered by the deep chlorophyll maximum layer, which limits the ecological impact of eddies in the well-lit, near-surface ocean.
Microbial oxygenic photosynthesis in thermal habitats is thought to be performed by Bacteria in circumneutral to alkaline systems (pH > 6) and by Eukarya in acidic systems (pH < 3), yet the predominant oxygenic phototrophs in thermal environments with pH values intermediate to these extremes have received little attention. Sequencing of 16S and 18S rRNA genes was performed on samples from twelve hot springs in Yellowstone National Park (Wyoming, USA) with pH values from 3.0 to 5.5, revealing that Cyanobacteria of the genus Chlorogloeopsis and algae of the genus Cyanidioschyzon (phylum Rhodophyta) coexisted in ten of these springs. Cyanobacteria were detected at pH values as low as 3.0, challenging the paradigm of Cyanobacteria being excluded below pH values of 4.0. Cyanobacterial 16S rRNA genes were more abundant than rhodophyte 18S rRNA genes by up to 7 orders of magnitude, with rhodophyte template abundance approaching that of Cyanobacteria only at the most acidic sites. Light-driven carbon fixation was observed at two sites where chlorophyll a was detected but not at two other sites where chlorophyll a was not detected. Collectively, these observations suggest that many of the rhodophyte 18S rRNA gene sequences were from inactive cells. Fluctuations in the supply of meteoric water likely contributes to physicochemical variability in these springs, leading to transitions in photosynthetic community composition. Spatial, but perhaps not temporal, overlap in the habitat ranges of bacterial and eukaryal oxygenic phototrophs indicates that the notion of a sharp transition between these lineages with respect to pH is unwarranted.