Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.

Eye Movement and Pupil Measures: A Review

Our subjective visual experiences involve complex interaction between our eyes, our brain, and the surrounding world. It gives us the sense of sight, color, stereopsis, distance, pattern recognition, motor coordination, and more. The increasing ubiquity of gaze-aware technology brings with it the ability to track gaze and pupil measures with varying degrees of fidelity. With this in mind, a review that considers the various gaze measures becomes increasingly relevant, especially considering our ability to make sense of these signals given different spatio-temporal sampling capacities. In this paper, we selectively review prior work on eye movements and pupil measures. We first describe the main oculomotor events studied in the literature, and their characteristics exploited by different measures. Next, we review various eye movement and pupil measures from prior literature. Finally, we discuss our observations based on applications of these measures, the benefits and practical challenges involving these measures, and our recommendations on future eye-tracking research directions.

The sensitivity of pCO₂ reconstructions in the Southern Ocean to sampling scales: a semi-idealized model sampling and reconstruction approach

The Southern Ocean is a complex system yet is sparsely sampled in both space and time. These factors raise questions about the confidence in present sampling strategies and associated machine learning (ML) reconstructions. Previous studies have not yielded a clear understanding of the origin of uncertainties and biases for the reconstructions of the partial pressure of carbon dioxide (pCO2) at the surface ocean (pCO2ocean). Here, we examine these questions by investigating the sensitivity of pCO2ocean reconstruction uncertainties and biases to a series of semi-idealized observing system simulation experiments (OSSEs) that simulate spatio-temporal sampling scales of surface ocean pCO2 in ways that are comparable to ocean CO2 observing platforms (Ship, Waveglider, Carbon-float, Saildrone). These experiments sampled a high spatial resolution (±10 km) coupled physical and biogeochemical model (NEMO-PISCES) within a sub-domain representative of the Sub-Antarctic and Polar Frontal Zones in the Southern Ocean. The reconstructions were done using a two-member ensemble approach that consisted of two machine learning (ML) methods, (1) the feed-forward neural network and (2) the gradient boosting machines. With the baseline observations being from the simulated ships mimicking observations from the Surface Ocean CO2 Atlas (SOCAT), we applied to each of the scale-sampling simulation scenarios the two-member ensemble method ML2, to reconstruct the full sub-domain pCO2ocean and assess the reconstruction skill through a statistical comparison of reconstructed pCO2ocean and model domain mean. The analysis shows that uncertainties and biases for pCO2ocean reconstructions are very sensitive to both the spatial and temporal scales of pCO2 sampling in the model domain. The four key findings from our investigation are the following: (1) improving ML-based pCO2 reconstructions in the Southern Ocean requires simultaneous high resolution observations of the meridional and the seasonal cycle (< 3 days) of pCO2ocean; (2) Saildrones stand out as the optimal platforms to simultaneously address these requirements; (3) Wavegliders with hourly/daily resolution in pseudo-mooring mode improve on Carbon-floats (10-day period), which suggests that sampling aliases from the low temporal frequency have a greater negative impact on their uncertainties, biases and reconstruction means; and (4) the present summer seasonal sampling biases in SOCAT data in the Southern Ocean may be behind a significant winter bias in the reconstructed seasonal cycle of pCO2ocean.

From 1/4° to 1/8°: Influence of Spatial Resolution on Eddy Detection Using Altimeter Data

A substantial portion of ocean eddies, especially small ones, may be missed due to insufficient spatial or temporal sampling by satellite altimetry. In order to illustrate the influence of spatial resolution on eddy detection, this study provides a comparison of eddy identification, tracking, and analysis between two sets of merged altimeter data with spatial resolutions of 1/4° and 1/8°. One main study area (the Mediterranean Sea), and three confirmatory areas (the South-China Sea, the North-West Pacific, and the South-East Pacific) are chosen. The results show that the number and density of eddies captured by the 1/8° data are about twice as much as those captured by the 1/4° data, while the ratios of corresponding eddy parameters, i.e., radius, amplitude, (eddy kinetic energy (EKE)) are about 0.6–0.8 (1.3) for the two datasets (1/8° ÷ 1/4°). Long-term eddy tracking (1993–2018) is conducted in the Mediterranean Sea, indicating that the improvement in spatial resolution will increase the observed values of both the lifetime and the propagation distance of robust eddies. The number of eddies identified using the 1/4° data only accounts for ~30% to 60% of those identified using the 1/8° data. However, for eddies that can be detected using the two datasets, ~5% to 10% present errors (i.e., confusion). In comparison between the four regions, we find that for the enclosed seas with complex conditions, the increase in spatial resolution may lead to more significant improvements in the efficiency and accuracy of eddy detection.

Quantitative Precipitation Estimation over Antarctica Using Different Ze-SR Relationships Based on Snowfall Classification Combining Ground Observations

Snow plays a crucial role in the hydrological cycle and energy budget of the Earth, and remote sensing instruments with the necessary spatial coverage, resolution, and temporal sampling are essential for snowfall monitoring. Among such instruments, ground-radars have scanning capability and a resolution that make it possible to obtain a 3D structure of precipitating systems or vertical profiles when used in profiling mode. Radars from space have a lower spatial resolution, but they provide a global view. However, radar-based quantitative estimates of solid precipitation are still a challenge due to the variability of the microphysical, geometrical, and electrical features of snow particles. Estimations of snowfall rate are usually accomplished using empirical, long-term relationships between the equivalent radar reflectivity factor (Ze) and the liquid-equivalent snowfall rate (SR). Nevertheless, very few relationships take advantage of the direct estimation of the microphysical characteristics of snowflakes. In this work, we used a K-band vertically pointing radar collocated with a laser disdrometer to develop Ze-SR relationships as a function of snow classification. The two instruments were located at the Italian Antarctic Station Mario Zucchelli. The K-band radar probes the low-level atmospheric layers, recording power spectra at 32 vertical range gates. It was set at a high vertical resolution (35 m), with the first trusted range gate at a height of only 100 m. The disdrometer was able to provide information on the particle size distribution just below the trusted radar gate. Snow particles were classified into six categories (aggregate, dendrite aggregate, plate aggregate, pristine, dendrite pristine, plate pristine). The method was applied to the snowfall events of the Antarctic summer seasons of 2018–2019 and 2019–2020, with a total of 23,566 min of precipitation, 15.3% of which was recognized as showing aggregate features, 33.3% dendrite aggregate, 7.3% plates aggregate, 12.5% pristine, 24% dendrite pristine, and 7.6% plate pristine. Applying the appropriate Ze-SR relationship in each snow category, we calculated a total of 87 mm water equivalent, differing from the total found by applying a unique Ze-SR. Our estimates were also benchmarked against a colocated Alter-shielded weighing gauge, resulting in a difference of 3% in the analyzed periods.

Estimating the movements of terrestrial animal populations using broad-scale occurrence data

As human and automated sensor networks collect increasingly massive volumes of animal observations, new opportunities have arisen to use these data to infer or track species movements. Sources of broad scale occurrence datasets include crowdsourced databases, such as eBird and iNaturalist, weather surveillance radars, and passive automated sensors including acoustic monitoring units and camera trap networks. Such data resources represent static observations, typically at the species level, at a given location. Nonetheless, by combining multiple observations across many locations and times it is possible to infer spatially continuous population-level movements. Population-level movement characterizes the aggregated movement of individuals comprising a population, such as range contractions, expansions, climate tracking, or migration, that can result from physical, behavioral, or demographic processes. A desire to model population movements from such forms of occurrence data has led to an evolving field that has created new analytical and statistical approaches that can account for spatial and temporal sampling bias in the observations. The insights generated from the growth of population-level movement research can complement the insights from focal tracking studies, and elucidate mechanisms driving changes in population distributions at potentially larger spatial and temporal scales. This review will summarize current broad-scale occurrence datasets, discuss the latest approaches for utilizing them in population-level movement analyses, and highlight studies where such analyses have provided ecological insights. We outline the conceptual approaches and common methodological steps to infer movements from spatially distributed occurrence data that currently exist for terrestrial animals, though similar approaches may be applicable to plants, freshwater, or marine organisms.

Reconstructing the diet, trophic level and migration pattern of mysticete whales based on baleen isotopic composition

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of δ 13 C and δ 15 N values from bulk baleen have been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations between regions as it is difficult to determine variations in isotopic shifts without temporal sampling of prey items. Here, we apply analysis of δ 15 N values of amino acids to five baleen plates belonging to three species, revealing novel insights on trophic position, metabolic state and migration between regions. Humpback and minke whales had higher reconstructed trophic levels than fin whales (3.7–3.8 versus 3–3.2, respectively) as expected due to different feeding specialization. Isotopic niche areas between baleen minima and maxima were well separated, indicating regional resource use for individuals during migration that aligned with isotopic gradients in Atlantic Ocean particulate organic matter. Phenylanine δ 15 N values confirmed regional separation between the niche areas for two fin whales as migrations occurred and elevated glycine and threonine δ 15 N values suggested physiological changes due to fasting. Simultaneous resolution of trophic level and physiological changes allow for identification of regional migrations in mysticetes.

Probing the association between resting state brain network dynamics and psychological resilience

This study aimed at replicating a previously reported negative correlation between node flexibility and psychological resilience, i.e., the ability to retain mental health in the face of stress and adversity. To this end, we used multiband resting-state BOLD fMRI (TR = .675 sec) from 52 participants who had filled out three psychological questionnaires assessing resilience. Time-resolved functional connectivity was calculated by performing a sliding window approach on averaged time series parcellated according to different established atlases. Multilayer modularity detection was performed to track network reconfigurations over time and node flexibility was calculated as the number of times a node changes community assignment. In addition, node promiscuity (the fraction of communities a node participates in) and node degree (as proxy for time-varying connectivity) were calculated to extend previous work. We found no substantial correlations between resilience and node flexibility. We observed a small number of correlations between the two other brain measures and resilience scores, that were however very inconsistently distributed across brain measures, differences in temporal sampling, and parcellation schemes. This heterogeneity calls into question the existence of previously postulated associations between resilience and brain network flexibility and highlights how results may be influenced by specific analysis choices.

The TROPOSIF global sun-induced fluorescence dataset from the Sentinel-5P TROPOMI mission

The first satellite-based global retrievals of terrestrial sun-induced chlorophyll fluorescence (SIF) were achieved in 2011. Since then, a number of global SIF datasets with different spectral, spatial, and temporal sampling characteristics have become available to the scientific community. These datasets have been useful to monitor the dynamics and productivity of a range of vegetated areas worldwide, but the coarse spatiotemporal sampling and low signal-to-noise ratio of the data hamper their application over small or fragmented ecosystems. The recent advent of the Copernicus Sentinel-5P TROPOMI mission and the high quality of its data products promise to alleviate this situation, as TROPOMI provides daily global measurements at a much denser spatial and temporal sampling than earlier satellite instruments. In this work, we present a global SIF dataset produced from TROPOMI measurements within the TROPOSIF project funded by the European Space Agency. The current version of the TROPOSIF dataset covers the time period between May 2018 and April 2021. Baseline SIF retrievals are derived from the 743–758 nm window. A secondary SIF dataset derived from an extended fitting window (735–758 nm window) is included. This provides an enhanced signal-to-noise ratio at the expense of a higher sensitivity to atmospheric effects. Spectral reflectance spectra at seven 3 nm windows devoid of atmospheric absorption within the 665–785 nm range are also included in the TROPOSIF dataset as an important ancillary variable to be used in combination with SIF. The methodology to derive SIF and ancillary data as well as results from an initial data quality assessment are presented in this work. The TROPOSIF dataset is available through the following digital object identifier (DOI): https://doi.org/10.5270/esa-s5p_innovation-sif-20180501_20210320-v2.1-202104 (Guanter et al., 2021).

The Effect of Spatial Resolution and Temporal Sampling Schemes on the Measurement Error for a Moon-Based Earth Radiation Observatory

The Moon-based Earth radiation observatory (MERO) is a new platform, which is expected to advance current Earth radiation budget (ERB) research with better observations. For the instrument design of a MERO system, ascertaining the spatial resolution and sampling scheme is important. However, current knowledge about this is still limited. Here we proposed a simulation method for the MERO-measured Earth top of atmosphere (TOA) outgoing shortwave radiation (OSR) and outgoing longwave radiation (OLR) fluxes and constructed the “true” Earth TOA OSR and OLR fluxes based on the Clouds and Earth’s Radiant Energy System (CERES) data. Then we used them to reveal the effects of spatial resolution and temporal scheme (sampling interval and the temporal sampling sequence) on the measurement error of a MERO. Our results indicate that the spatial sampling error in the unit of percentage reduces linearly as the spatial resolution varies from 1000 km to 100 km; the rate is 2.5%/100 km for the Earth TOA OSR flux, which is higher than that (1%/100 km) of the TOA OLR flux. Besides, this rate becomes larger when the spatial resolution is finer than 40 km. It is also demonstrated that a sampling temporal sequence of starting time of 64 min with a sampling interval of 90 min is the optimal sampling scheme that results in the least temporal sampling error for the MERO system with a 40 km spatial resolution, note that this conclusion depends on the temporal resolution and quality of the data used to construct the “true” Earth TOA OSR and OLR fluxes. The proposed method and derived results in this study could facilitate the ascertainment of the optimal spatial resolution and sampling scheme of a MERO system under certain manufacturing budget and measurement error limit.