Microbial processing of fresh carbon inputs is recognized as a key step in the formation of mineral-associated organic matter. Low molecular weight (LMW) compounds comprise a notable fraction of these inputs and are rapidly assimilated and metabolized by the microbial community. In this work, we employ ecophysiological studies of microbial isolates to better understand the role of substrate identity as a control on preferences, uptake kinetics, and carbon use efficiencies (CUE) across a gradient of phylogenetic differences (gram negative, gram positive, and fungal). Soil-extracted, solubilized organic matter (SESOM) derived from the Oa horizon of a hemlock-hardwood forest stand and synthetic media based off of this extract were chosen as liquid media for batch growth studies. A combination of exometabolomic techniques (1H NMR, UHPLC-MS) were used to quantify 35 LMW substrates in the original extract (0.4 – 195 μM), comprising 19.5% of total C and 39.9% of total N. Consumption of these substrates by microbial isolates accounted for a substantial amount of total C and N assimilated during growth, representing 43-75% and 58-74%, respectively. Time resolved sampling allowed modeling of sigmoidal uptake curves and the comparison of the midpoint of consumption (Th, hr) and 90% usage windows (ranging from 0.18 – 2.29 hr). Complementary experiments were conducted using synthetic media with all substrates at equimolar concentrations (25 μM) to better constrain the impact of initial concentration. We use stable isotope probing to determine CUE for five different LMW substrates of interest (glucose, acetate, formate, glycine, and valine). Ultimately, we are interested in whether unifying trends can be observed across the physiological gradient and how the metabolic transformations of these inputs may impact the organo-mineral formation process.
Pesticide seed treatments (PST) which contain fungicides and insecticides are commonly used in agriculture; however, little is known about their effect on soil microbial communities and soil health. Neonicotinoids – controversial insecticides which are common in PST – have received criticism due to potential non-target effects. While fungal pathogens need to be moderated, PST have the potential to disturb broader fungal communities which could lead to reduced nutrient cycling and poor soil health. Given the broad use of PST, their effect on soil fungi needs to be studied within the context of other agricultural management practices. For example, tillage regimes can result in distinct fungal communities which may respond differently to PST. An experimental site was established in 2013 with a corn-soy rotation under three tillage treatments: Full-till, Strip-till, and No-till. Since 2016, seeds with or without PST (fungicides and insecticides) were planted under each tillage regime in a fully factorial design. In 2018, bulk soil was collected from within rows while soy was growing. A range of soil physicochemical variables were measured, and soil function was determined with substrate-induced respiration and enzyme assays. DNA was extracted from soil and the ITS region was sequenced to determine fungal community structure and diversity. While tillage significantly affected fungal community structure (p < 0.01), there was no effect of PST on either community structure (p = 0.59) or diversity (p = 0.52). This indicates that PST does not affect bulk soil fungal communities; however, they may have an impact at different temporal or spatial scales than those studied here. Across all treatments, fungal community structure correlated with soil water holding capacity (rs = 0.23, p = 0.04) and electrical conductivity (rs = 0.26, p = 0.01). Despite not finding an effect of PST on fungal communities, we did find that PST increased potentially mineralizable nitrogen under no-till and shifted community level physiological profiles determined by substrate-induced respiration. These results suggest that while PST can affect certain aspects of soil health, there are no clear effects on the soil fungal community.
Lava tubes on Mars hold exciting potential for the preservation of biosignatures, which may survive on geological timescales in these isolated, stable environments. To support the development of future astrobiological mission concepts, we turn to terrestrial lava tubes, host to a variety of microbial communities and secondary minerals. Following a multidisciplinary sampling protocol, we retrieved biological, molecular, and mineralogical data from several lava tubes in Iceland. We report on blue-colored copper-rich secondary minerals and their associated bacterial communities using a multi-method approach, and an amalgam of 16S rRNA gene sequencing, Raman spectroscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy data sets. We found numerous bacterial genera known for their high metal resistance and ability to survive in low-nutrient environments, both characteristics to be expected for any potential life in Martian lava tubes. Associated with them, we identified several types of copper-rich secondary minerals as well as carotenoid signals. If found in Martian lava tubes, blue copper-rich mineral precipitates would be deserving of astrobiological investigation, as they have potential to preserve biosignatures and harbor life.
To clarify horizontal variability and regulation of bacterial production (BP), we investigated BP and environmental variables along three east-west transects (Lines 12, 15, and 17) covering inshore/offshore stations in Lake Biwa, Japan, during four seasons. In winter, surface BP along Line 12 (southern transect) was higher than Lines 15 and 17 (central and northern transects) and reflected the water-temperature distribution. Additionally, any nutrients and dissolved organic carbon did not correlate to BP, suggesting water temperature regulated BP in winter. In spring, BP was higher at eastern inshore stations, near large agricultural fields, and was correlated with phosphorus concentration rather than water temperature, suggesting that the limitation shifted to nutrient availability. As well as spring, surface BP in autumn was correlated with phosphorus. Additionally, a negative correlation with water temperature in autumn suggested that nutrient loadings through river and groundwater contributed to enhancing BP. In summer, surface BP at offshore stations along Lines 15 and 17 was notably lower than the other stations. Summer BP was correlated with phosphorus concentration, suggesting that allochthonous nutrient loading determines horizontal BP variations. Moreover, summer depth-integrated BP (DBP) at offshore stations was lower (32-52 mgC m-2 d-1) than inshore stations (43-110 mgC m-2 d-1) regardless of water depth. The average DBP at inshore stations in summer was 2.1 times that offshore stations, and the inshore/offshore DBP ratio was higher than the other seasons (0.58-1.0). The results suggest that inshore BP significantly contributes to whole-lake BP in productive seasons.
Organisms leave traces of DNA as they move through their environments. The extraction of these DNA traces is known as environmental DNA (eDNA). eDNA provides scientists and researchers a non-invasive, rapid, cost-effective and sensitive way to detect and quantify species. Traditional eDNA sampling consists of manually filtering water, which is labor and cost-intensive for remote locations. Furthermore, commercialized solutions are expensive and require a field operator. This eDNA sampler project aims to provide an affordable, open-sourced, remotely deployable, fully automated, and customizable alternative. The PolyWAG (Water Acquired Genomics) system can run up to 24 inline filter units with support for different conditions including pressure, time and volume limit. The pumps deliver maximum 400mL/min with solenoid valves separating each inline filter to minimize cross-contamination. At the end of each sample, the desired stabilizing solution can be injected to fully submerge the filter for preservation. An optional river depth sensor can provide a proxy for flow to correct eDNA concentrations to allow for improved quantification of organisms. Data acquired during operation including water depth, pressure, temperature, and flow rate will be stored on microSD card in CSV format, which allows easier data export and analysis. A web application provides an intuitive UI for in-field programming, real-time sensor updates, scheduling tasks, and manual operations. We present data from multiple tests showing the length of the preservation period and the contamination level between samples. The PolyWAG system is estimated to be $3000 each, with add-on river depth sensor and 10ah 12V battery.
An engaged community of scientific programmers is an invaluable asset to any open data provider. The National Ecological Observatory Network (NEON) is a long-term observatory focused on collecting and providing open, continental-scale data that characterize and quantify complex and rapidly changing ecological patterns and processes. The observatory provides over 180 different data products that cover a wide range of variables of interest to researchers across the earth and life sciences. NEON creates and provides code and tools to enhance researchers’ ability to work with these data. In addition, NEON provides several platforms to help connect researchers sharing open code related to NEON data products with those who are also interested in using them. Code and tools created by NEON scientists are distributed through the NEONScience GitHub organization (https://github.com/NEONScience). Current tools include the neonUtilities R package that provides basic tools for accessing and working with most NEON data products, as well as the geoNEON package that facilitates access to NEON spatial data. Other code packages contain the algorithms used to produce specific data products, including the eddy4R package, used to create the bundled eddy-covariance data product. Finally, some code packages are designed to build upon published NEON data to create value-added, derived products. Members of NEON’s user community have contributed to some of the packages described above, and others are creating their own open code resources for using NEON data. Use of NEON code packages and development of open code are highly variable within the NEON user community, and NEON has explored several approaches to engage users in this aspect of the observatory, including online tutorials, webinars, workshops, and hackathons. Developing and expanding an engaged community of open code users around NEON data is a continuing and evolving effort for the NEON project.
Phosphorus (P) is hypothesised to be the main nutrient limiting forest productivity in tropical forests, but more recent evidence suggests that multiple nutrients could regulate forest functioning. Root functional trait expression represents a trade-off between maximising the acquisition of limiting resources and minimising root tissue construction and maintenance. Therefore, if the limiting soil nutrient supply is increased, plant investment in root biomass and nutrient uptake strategies should decrease. To test this hypothesis we investigated how fine root traits associated with nutrient acquisition responded to large-scale nutrient additions of nitrogen, phosphorus and cations in a slow-growing mature tropical forest established on low fertility soils in the Central Amazon. To evaluate short-term responses to nutrient addition 6 months after fertilisation commenced, we sampled young fine roots (<2mm diameter), measuring root biomass and productivity, root morphological traits (root diameter, specific root length, specific root area and root tissue density) and root phosphatase enzyme activity. We hypothesised that if tropical forests are P limited, responses to P addition would be strongest, resulting in i) a decrease in root production; ii) a shift in root morphology from acquisitive to more conservative traits by increased root diameter and decreased specific length and area and iii) decrease in the investment in phosphatase enzyme. As expected, root phosphatase activity decreased by ~13% with P addition. Among the root morphological traits, root diameter increased, mainly for the 0-10 cm soil layer, with the addition of cations and P, but there were no significant effects on other root morphological traits. Contrary to expectations, root productivity was >50% higher in plots where cations were added, with no effects of P addition. Although we found support for the hypothesis that P limits some aspects of plant functioning in this Central Amazon forest, the results also suggest that cations could play an important role in controlling the expression of root traits. We conclude that multiple nutrients may limit belowground process in Central Amazon forests and that even slow-growing tropical forest can respond very rapidly to changes in soil nutrient availability.
Laboratory studies have shown that rhizodeposits could lead to either soil structural formation or dispersion depending on plant species, soil conditions, and microbial activity. However, these studies have usually been conducted in dry soils and rarely considered the combined effect of rhizodeposit and organic residues on soil structure. This study hypothesizes that root exudates promote soil dispersion initially, but over time decomposition of root exudates produce binding agents that promote stable soil structure in the rhizosphere. To test this hypothesis, a sandy loam soil sieved to < 500 µm particle size was first amended with root exudate compounds (14.4 mg C g-1), δ13C-barley residue (0.44 mg C g-1 soil), or both. Six replicate samples per treatment were packed in cores to a bulk density of 1.27 g cm-3 and then equilibrated on a tension table at -2 kPa matric potential. Rheological measurements of flow characteristics (dynamic viscosity) and strength (storage modulus, loss modulus, tan δ, and yield stress) of the control and amended soils were obtained immediately after amendment and after twelve days of incubation at 20 oC. Only root exudate compounds initially decreased the capacity of soil to retain water at -2 kPa by 21% and by 49% after incubation. Likewise, the yield stress of root exudate amended soil was significantly (P < 0.05) lower than that of the unamended soil, reflecting dispersion of soil. However, microbial decomposition/activities significantly (P < 0.05) increased yield stress over the corresponding pre-incubation values for these treatments by 200% (root exudate) and 230% (root exudate + δ13C-barley residue). These results confirmed the hypothesized dual effect of root exudates on rhizosphere structure. The initial soil dispersion may facilitate root growth by augmenting soil penetrability and releasing nutrients that were occluded in soil aggregates, whereas stable soil structure is achieved upon decomposition of root exudates.
Drilling by the Oman Drilling Project provided a unique opportunity to access partially-serpentinized harzburgite and dunite. These are in contact with alkaline fluids in a subsurface environment that support a microbial ecosystem. In concert with studies of the rock-hosted microbial community, we are characterizing the mineralogy and petrology of the serpentinized mantle rocks that host this ecosystem. Samples of whole-round core were collected and preserved every 10 m from 3 boreholes and split into paired subsamples for microbiology and mineral characterization. Thin sections were analyzed with a petrographic microscope to complete mineral abundance estimations and interpret textural relationships. Raman spectroscopy was conducted on the thin sections to reveal structural/compositional data about mineral phases. Powders were prepared for XRD analysis for quantitative phase identification. The main rock types are altered harzburgite and dunite, and altered veins of gabbro or pyroxenite occur at certain depths. All of the cores have experienced multiple episodes of serpentinization. The observed mineral assemblages include relict olivine, pyroxene and abundant secondary serpentine, brucite, iron sulfide and andradite-grossular garnet. The assemblages are generally expected from partial serpentinization of peridotite, but the widespread distribution of garnet was particularly surprising. Over 50% of the samples contained sufficient garnet to be detected by XRD. Optical and Raman analyses show that garnet occurs in many textural contexts, notably inside mm-scale, late-stage serpentine veins. Andradite garnet in serpentine veins similar to those found here are likely to have formed during serpentinization at temperatures below ~200°C [1,2]. Incorporating Fe3+ into the andradite component could facilitate H2 production, a potent energy source for microbial metabolisms . Its high abundance may provide key insights into H2 production and habitability during late-stage serpentinization of the Oman ophiolite.  Ménez et al. (2018) LITHOS DOI: 10.1016/j.lithos.2018.07.022  Plümper et al. (2014) Geochimica et Cosmochimica Acta 141 (454-471).
Many drinking water utilities drawing from waters susceptible to harmful algal blooms (HABs) are implementing monitoring tools that can alert them of the onset of potential blooms. Some have invested in fluorescence-based online monitoring probes to measure chlorophyll a and phycocyanin, two pigments found in cyanobacteria, but it is not clear how to best use the data generated this way. Previous studies have focused on correlating phycocyanin fluorescence and cyanobacteria cell counts. However, not all utilities collect cell count data, making this method impossible to apply in some cases. Instead, this paper proposes a novel approach to determine when a utility needs to respond to an HAB based on machine learning by identifying outliers in chlorophyll a and phycocyanin fluorescence data without the need for corresponding cell counts or biovolume. Four existing algorithms are evaluated on data collected at four buoys in Lake Erie from 2014-2019: k-means clustering, One-Class Support Vector Machine (SVM), elliptic envelope, and Isolation Forest (iForest). When trained and tested on data collected at different buoys, the iForest algorithm performed the best in terms of computation time for training and true positive rate, and second best for false positive rate. In a more realistic application where the algorithms are trained on historical phycocyanin data collected at the same location as the testing data, all the algorithms, except k-means, accurately identified anomalies in phycocyanin data coinciding with real cyanobacteria bloom events. Therefore, One-Class SVM, elliptic envelope, and iForest are promising algorithms for detecting potential HABs using fluorescence data.
Extremely halophilic archaea are microbes that thrive under very high salinities (>20% NaCl) and are almost exclusively placed in the class Halobacteria. In addition to their characteristic preference for high salinity and moderately high temperatures, many species of this class are resistant to desiccation, vacuum, and radiation, making them interesting targets for Astrobiological studies as model organisms and particularly relevant for the study of Mars, as highlighted by several authors. This class has a wide environmental range and includes species that live in salty biotopes such as salterns, salted foods, subterranean halite, lakes, or even in deep-sea brines in a list that includes several analogue sites. One current bottleneck of research with this group is the dispersed nature of data associated with its species. Our study partly addresses this by compiling phenotypic information and records of astrobiological experiments for all Halobacteria. We have established a database (HAPIE- Halophilic Archaea Phenotypic Information Explorer) that allows us to quickly compare different species as well as analyse trends and identify knowledge gaps and research opportunities. Our study identified gaps in coverage and knowledge (both at the level of taxonomy and range of tested parameters) and assisted us in defining new testing priorities.
Oxygen first arose in Earth’s atmosphere 2.3 billion years ago, but geochemical evidence suggests that small pockets of oxygen may have arisen earlier than the atmospheric rise in oxygen. Cyanobacteria, a modern phylum of bacteria, are believed to have been the driving force behind the oxygenation of Earth’s atmosphere, and there are two basic hypotheses about how they caused this major geologic event. There is a hypothesis, called the ‘ecological’ hypothesis, that suggests cyanobacteria were unable to live in most environments initially, and thus we see the evidence for pockets of oxygen earlier than the atmospheric rise in oxygen. Specifically, the ‘ecological’ hypothesis says that cyanobacteria originally were unable to swim and couldn’t live in saline water, meaning seawater. However, the data for this only considers two possible states for the levels of salinity: freshwater and seawater. We used data from the literature and from experiments to show that the gradient of salinity matters to the ability of cyanobacteria to live in environments, and that we cannot say what salinity levels a cyanobacteria can tolerate based on where they were found alone. See supplemental file for full abstract.
For years the debate about the possible contamination of space and other planets with microbes from Earth has been a hot topic. Furthermore, the discovery of sulfate minerals on the Martian surface make this planet suitable to colonization by microorganisms adapted to survive and grow under earthly extreme conditions. One of these microorganisms is Desulfotalea psychrophila, a microbe able to generate cellular energy by means of an enzyme known as the dissimilatory sulfate reductase. As all bacterial enzymes are encoded within the bacterium nucleic acids, we have designed experiments to study the ability of this microbe to survive, grow and metabolize under simulated Martian conditions of pressure, temperature and different concentrations of sulfate compounds.
Microbial-induced calcium carbonate precipitation (MICP) is an innovative technique used for soil improvement, for controlled reduction of permeability in porous media or immobilization of soil contaminants. The application of MICP in the field is influenced by the environmental factors. In the present study, the main purpose is to explore the effectiveness of MICP in treating porous media at different environmental temperatures and reveal the underlying mechanisms. The microstructure characteristics were investigated via SEM imaging, EDS and XRD analyses and consolidated drained triaxial compression tests were performed to examine the performance of MICP-treated samples. Results indicate that the shear strength depends heavily on the treatment temperature, which was mainly due to the different content, size and distribution of CaCO3 in samples at different conditions. The observations of pore-scale characteristics revealed that low temperature (4℃) and high temperature (50℃) produced less CaCO3 precipitation, resulted in smaller carbonate crystals precipitation and thus lower strength. In contrast, samples treated at room temperature and 35 ℃ show more CaCO3 precipitation and greater strength. The crystal forms, though, were not influenced by the temperature. The climate conditions are a very important parameter that needs to be tuned specifically for the purposes of each MICP application (whether controlled alteration of permeability or for soil stabilization). However, in most MICP field applications, temperature is nearly impossible to control, and in such conditions where bacterial activity is reduced, the alteration of the MICP recipe is required, and specifically the number of bacterial solution injections are worth to be considered.
Astrobiology as a field is not well known by the public, and is a difficult topic to introduce to the those who have never heard of it before. This presentation will showcase projects and experiences from a museum setting to explore how to best bring up such a complex field of science, and how astrobiologists can make their work as digestible as possible to the general public.
New bioavailable nitrogen (N) from biological nitrogen fixation (BNF) is critical for the N budget and productivity of marine ecosystems. Nitrogen-fixing organisms typically inactivate BNF when less metabolically costly N sources, like ammonium (NH4+), are available. Yet, several studies observed BNF in benthic marine sediments linked to anaerobic sulfate-reducing bacteria (SRB) and fermenting firmicutes despite high porewater NH4+;concentrations (10-1,500 μM), making the importance of and regulating controls on benthic BNF unclear. Here, we evaluate BNF sensitivity to NH4+ in model anaerobic diazotrophs, the sulfate-reducer Desulfovibrio vulgaris var. Hildenborough and fermenter Clostridium pasteurianum strain W5; in sulfate-reducing sediment enrichment cultures, and in sediment slurry incubations from three Northeastern salt marshes (USA). BNF in sulfate-reducing cultures and sediments is highly sensitive to external NH4+, with a threshold for BNF inhibition of [NH4+] < 2 μM in cultures and < 9 μM in sediment slurries. The prevalence of SRB-like sequences in sediment-derived nitrogenase (nifH) genes and transcripts in this and other studies of benthic BNF along with an analysis of benthic NH4+ porewater data suggests a broad applicability of the inhibition thresholds measured here and the confinement of benthic BNF to surficial sediments. The timing of inhibition, fast NH4+ drawdown, and sediment heterogeneity are factors that can complicate studies of benthic BNF sensitivity to NH4+. We propose a simple theoretical framework based on the affinity of the NH4+ transporter to explain NH4+ control of BNF and improve biogeochemical models of N cycling.
Dinitrogen (N2) fixers (diazotrophs) fuel primary productivity by providing reactive nitrogen into the ocean ecosystem and promoting CO2 sequestration. N2 fixation has been extensively studied in the low latitudes of the Atlantic and Pacific Oceans. By comparison, the Indian Ocean remains the least explored and most enigmatic ocean basin. This is particularly the case for the Southern Indian Ocean (SIO). Here we explore N2 fixation activity and diazotroph community composition, diversity, and abundance from 20 to 60ºS in the SIO. While this region plays a key biogeochemical role serving as a link between the Atlantic and South Pacific Ocean waters, its N2 fixation potential remains unknown. Our results provide new insights into diazotrophy in a poorly studied region and expand the range of biomes where diazotrophy may be observed.
Earth’s atmosphere underwent an irreversible, and geologically sudden, change approximately 2.5 billion years ago from oxygen free, to oxygenated, called the Great Oxidation Event (GOE). This change was driven by the evolution of a new form of photosynthesis which produced molecular oxygen as a byproduct. The group of bacteria in which this evolved, Cyanobacteria, are the only organisms to independently harness this form of photosynthesis. While we know that by the time of the GOE, Cyanobacteria were present, we do not know if they were present before the GOE. It has been proposed that Cyanobacteria were restricted to freshwater environments for hundreds of millions of years before the GOE, and only when they were able to inhabit the oceans did the GOE occur. We address this hypothesis by surveying the literature to understand how modern cyanobacteria respond to changes in salinity, as well as running a 1000 generation evolution experiment. We find evidence that just because a cyanobacterial species is found in freshwater does not mean it cannot live in marine salinities, and vice versa. Additionally, we find that prolonged exposure to a different salinity does not result in loss of ability to grow in the ancestral salinity.