Groundwater contamination with geogenic arsenic poses a major health risk to millions of people throughout the world. Among various group of microbes, dissimilatory arsenate reducing bacteria (DARB) are considered to be primarily responsible for arsenic mobilization in anaerobic environments of deep underground aquifer sediments. This group of microbes carries out enzyme catalyzed conversion of more immobilized and less toxic arsenate [As (V)] to more soluble and more toxic arsenite [As (III)]. Aquifers are deep subsurface layers of rocks, sand or soil capable of storing and transmitting water. These are potential environments for arsenic mobilization by anaerobic dissimilatory arsenate reducing bacteria (DARB). Study of these bacteria has been restricted to culture based microcosm studies, which suffers from several drawbacks like inappropriate simulation of ecological factors, exclusion of unculturable members, inappropriate elucidation of community behavior etc. With the recent advent of culture independent molecular analysis, more wholesome analysis of microbial community in diverse ecological habitats has become possible. Anaerobic dissimilatory As(V) reduction is catalyzed by the periplasmic arsenate respiratory reductase (Arr) complex, which consists of a large catalytic subunit (ArrA) and a small subunit (ArrB). arrA gene encoding large subunit of the reductase can be used as a reliable marker for arsenate respiration. Our study is a preliminary attempt to isolate community DNA from aquifer sediments collected from various depths and study the differential distribution of arrA in community genome at various depths. We had successfully isolated humic contaminant free community DNA from aquifer sediments and subjected them to PCR amplification with arrA gene specific primers. The amplicons obtained from community DNA of various depths were subsequently sublected to RFLP analysis by HaeIII and the restriction patterns was compared. The study revealed differential distribution of arrA containing DARB population at various depths of aquifer sediments.
As phytoplankton form the base of the marine food web, understanding the controls on their abundance is fundamental to understanding marine ecology and how it might be altered by global climate change. While many Earth System Models (ESMs) predict phytoplankton biomass, it is unclear whether they properly capture the mechanistic relationships that control this quantity in the real ocean. In this paper, we used Random Forest (RF) analysis to analyze the output of ESMs and observational datasets. We gathered information from 13 ESMs and two observational datasets. The target variable was phytoplankton carbon and the predictors included environmental parameters known to influence phytoplankton, such as nutrients, light, mixed layer depth, salinity, temperature, and upwelling. We examined three questions: (1) What fractions of variability in ESMs and observations can be linked to the large-scale environmental variables simulated by ESMs? (2) What are the dominant predictors and relationships affecting phytoplankton biomass? (3) How well do ESMs simulate phytoplankton carbon and do they simulate the relationships we see in observations? We show that about 88% to 96% of the variability in observational datasets and greater than 98% in the ESMs was accounted for by variables known to influence phytoplankton biomass from large-scale environmental variables. The dominant predictors in the observational datasets were dissolved iron and shortwave radiation. The dominant predictors in the ESMs were dissolved iron, shortwave radiation, and mixed layer depth. While relationships in most of the ESMs matched the general trends seen in the observations, significant quantitative differences were seen. While the assumption made by ESMs that large-scale environmental conditions control phytoplankton biomass appears to hold in the real world, much work remains to be done to ensure that ESMs properly represent these controls.
The complexity of organic matter (OM) degradation mechanisms represents a significant challenge for developing biogeochemical models to quantify the role of aquatic sediments in the climate system. The common representation of OM by carbohydrates formulated as CHO in models comes with the assumption that its degradation by fermentation produces equimolar amounts of methane (CH) and dissolved inorganic carbon (DIC). To test the validity of this assumption, we modeled using reaction-transport equations vertical profiles of the concentration and isotopic composition (δC) of CH and DIC in the top 25 cm of the sediment column from two lake basins, one whose hypolimnion is perennially oxygenated and one with seasonal anoxia. Our results reveal that methanogenesis only occurs via hydrogenotrophy in both basins. Furthermore, we calculate, from CH and DIC production rates associated with methanogenesis, that the fermenting OM has an average carbon oxidation state (COS) below −0.9. Modeling solute porewater profiles reported in the literature for four other seasonally anoxic lake basins also yields negative COS values. Collectively, the mean (±SD) COS value of −1.4 ± 0.3 for all the seasonally anoxic sites is much lower than the value of zero expected from carbohydrates fermentation. We conclude that carbohydrates do not adequately represent the fermenting OM and that the COS should be included in the formulation of OM fermentation in models applied to lake sediments. This study highlights the need to better characterize the labile OM undergoing mineralization to interpret present-day greenhouse gases cycling and predict its alteration under environmental changes.
Marine free-living bacteria play a key role in the cycling of essential biogeochemical elements, including iron (Fe), during their uptake, transformation and release of organic matter. Similar to phytoplankton, the growth of free-living bacteria is regulated by resources such as Fe, and the low availability of these resources may influence bacterial interactions with phytoplankton, causing knock-on effects for biogeochemical cycling. Yet, knowledge of the factors limiting free-living bacterial growth and their role within the Fe cycle is poorly constrained. Here, we explicitly represent free-living bacteria in a global ocean biogeochemistry model to address these questions. We find that although Fe can emerge as proximally limiting in the tropical Pacific and in high-latitude regions during summer, the growth of free-living bacteria is ultimately controlled by the availability of labile dissolved organic carbon. In Fe-limited regions, free-living bacterial biomass is sensitive to their Fe uptake capability in seasonally Fe-limitation regions and to their minimum Fe requirements in regions perennially Fe-limited. Fe consumption by free-living bacteria is significant in the upper ocean in our model, and their competition with phytoplankton for Fe affects phytoplankton growth dynamics. The impact of free-living bacteria on the Fe distribution in the ocean interior is small due to a tight coupling between Fe uptake and release. Moving forward, future work that considers particle-attached bacteria and different bacterial metabolisms is needed to explore the broader role of bacteria in ocean Fe cycling. In this context, the global growing ’omics data from ocean observing programs can play a crucial role.
Chaotropicity (order-destroying) describes the entropic disordering of lipid bilayers and other biomacromolecules which is caused by substances dissolved in water. Solvents in water are defined as kosmotropic (order-making) if they contribute to the stability and structure of water-water interactions. These interactions between brine solutions (water and salt) and ancestral proteins (AncC ribonuclease) induce varying changes in the protein’s structure. Understanding how these brine solutions and early protein structures interact provides insight into the origins of life and zones of habitability across the solar system. Here, we used a molecular dynamics simulator to assess the reaction of an ancient protein (ribonuclease sequence) when exposed to .15M and 1.5M concentrations of MgCl2 and NaCl. The ancient ribonuclease structure responded uniquely to .15M NaCl and both concentrations of MgCl2. Both the nature of the cation and concentration of the salt promote different responses and effects in the secondary structures of the AncC protein. According to the Hoffmeister Series scale, sodium is more kosmotropic and magnesium is more chaotropic. These two different salts with two different chao-kosmo properties create two different responses within the protein structure in that particular brine. This observation speaks highly to the significance of chao-kosmo influences on molecular level outcomes.
Reducing nitrous oxide (N2O) emissions from agriculture is critical to limiting future global warming. In response, a growing number of food retailers and manufacturers have committed to reducing N2O emissions from their vast networks of farmer suppliers by providing technical assistance and financial incentives. A key challenge for such companies is demonstrating that their efforts are leading to meaningful progress towards their climate mitigation commitments. We show that a simplified version of soil surface nitrogen (N) balance, the difference between N inputs to and outputs from a farm field (e.g., fertilizer N minus crop N), is a robust indicator of N2O emissions. Furthermore, we present a generalized environmental model which will allow food-supply-chain companies to translate aggregated and anonymized changes in average N balance across their supplying farms into aggregated changes in N2O emissions. This research is an important first step, based on currently available science, in helping companies demonstrate the impact of their sustainability efforts.
The seasonal variation in concentration of transparent exopolymer particles (TEP), particulate organic carbon (POC) and nitrogen (PON) were investigated together with floc size and the concentration of suspended particulate matter (SPM) along the cross-shore gradient, from the high turbid nearshore towards the low-turbid offshore waters in the southern Bight of the North Sea. The analyses of TEP, POC and PON result in a set of parameters that incorporate labile and refractory organic matter (OM) fractions. Our data demonstrate that biophysical flocculation cannot be explained by these heterogeneous parameters, but requires a distinction between a more reactive labile (“fresh”) and a less reactive refractory (“mineral-associated”) fraction. Based on all data we separated the labile and mineral-associated POC, PON and TEP using a semi-empirical model approach. The model’s estimates of fresh and mineral-associated OM show that great parts of the POC, PON and TEP are associated with suspended minerals, which are present in the water column throughout the year, whereas the occurrence of fresh TEP, POC and PON is restricted to spring and summer months. In spite of a constantly high abundance of total TEP throughout the entire year, it is its fresh fraction that promotes the formation of larger and faster sinking biomineral flocs, thereby contributing to reduce the SPM concentration in the water column over spring and summer. Our results show that the different components of the SPM, such as minerals, extracellular OM and living organisms, form an integrated dynamic system with direct interactions and feedback controls.
Mosquitoes in recent years have increased greatly in numbers due to the rapidly changing climate and rising temperatures. With this change comes suitable habitats for mosquitoes which are the most efficient killers in all of the animal kingdom due to the number of death from mosquito-borne diseases. If we were able to pinpoint the certain areas that mosquitoes are most attracted to we could in theory slow or even prevent the spread of mosquitoes. In our project, the research was conducted to find a correlation between the color and size of the traps to the amount of mosquitos that are present. With our findings, we were able to conclude that the bigger the traps, the faster the mosquitoes would be attracted to that area. We also found that the different traps would hold similar densities of mosquito larvae per square inch.
The Yeongsan River in southwestern Korea is 150 km long and has a basin area of 3,551 km2. A number of hydraulic structures have been installed along the river, including an estuary dam and two weirs (Seungchon and Juksan). While these structures aid in regional water security and reduced flooding, they stagnate water flow and frequently cause algal blooms during the summer. This study simulated the algal bloom and water quality characteristics in the middle and downstream sections of the Yeongsan River under different weir and estuary dam operating conditions using the Environmental Fluid Dynamics Code-National Institute of Environment Research (EFDC-NIER) model. Results showed that when the management levels of the Juksan Weir and estuary dam were maintained, the simulated water levels were 3.7 and -1.2 m in the Juksan Weir and estuary dam sections, respectively. When both the Juksan Weir and estuary dam were open, the water levels varied with the tide and were maintained at an average of 0.2-0.6 m in contrast, when the Juksan Weir alone was open, the water level was between -1.2 and -0.9 m in line with the management level of the estuary dam. Opening the Juksan Weir alone reduced the algal blooms by 72-84% in the Juksan Weir section, and opening the estuary dam alone reduced the algal blooms by 83% in the estuary dam. This improvement was attributed to the reduced water retention time and dilution due to seawater inflows.
The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological and microbial oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics. However, the main modelling currencies continue to be biological rates and biogeochemical fluxes. Here we ask: how do we translate the wealth of information on physiological potential from omics-based studies to quantifiable physiological rates and, ultimately, to biogeochemical fluxes? Based on the trajectory of the state-of-the-art in biomedical sciences, along with case-studies from ocean sciences, we conclude that it is unlikely that omics can provide such rates in the coming decade. Thus, while physiological rates will continue to be central to providing projections of global change biology, we must revisit the metrics we rely upon. We advocate for the co-design of a new generation of rate measurements that better link the benefits of omics and physiology.
Background/Question/Methods This project attempts to quantify the resilience of prairie ecosystems to climate change in the Pacific Northwest (PNW). In this region, prairie ecosystems currently sustain ~1.3 million beef cows and calf production costs are expected to increase to offset drought-induced plant productivity loss. Here, we investigate patterns of asymbiotic nitrogen fixation (ANF) and biogeochemical controls, that also influence plant community composition and prairie productivity, under experimental drought to address a major challenge for sustainable agriculture in the region. We hypothesize that the effect of drought on prairie vegetation cover increases soil asymbiotic N inputs by diminishing the dominance of symbiotic root-fungal networks. To test this hypothesis, we quantified the impacts of decadal drought stress on soil ANF using 15N-labeled dinitrogen (15N2) incubations of soils from high- and low-diversity prairies across a 520-km latitudinal gradient (i.e., southern Oregon-SOR, central Oregon-COR, and central Washington-CWA) representing increasingly severe Mediterranean conditions. We also quantified total soil organic carbon-C, total, and available N, and available phosphorus-P and iron-Fe pools to better understand underlying mechanisms governing drought-induced changes in ANF. At each site, composite soil samples (n = 3) were collected from five co-located high- and low-diversity prairie plots under control (ambient) and drought (-40% precipitation) conditions. Results/Conclusions We found that soil ANF response to drought increased with the PNW Mediterranean drought intensity gradient; while ANF rates increased nearly two-fold in the southernmost site (SOR), a significant decrease in ANF was verified in the northernmost site (CWA). ANF response to drought also varied depending on plant diversity, where low-diversity prairies had a more predictable response to drought than high-diversity prairies. For instance, ANF in SOR high-diversity prairies was suppressed but no change was verified in COR high diversity prairies. Soil C and N contents were generally higher in high-diversity prairies whereas treatment had no significant effect across sites. Soil P availability, also affected by drought, and pH were the most important variables explaining ANF variability across vegetation types and sites. Based on our findings, low-diversity prairies in central WA may be those most severely impacted by increased climate change-induced drought stress. Our study highlights the importance of using soil-plant-atmosphere interactions to assess prairie ecosystem resilience to drought in the PNW.
Haptophytes and Dinoflagellates are two cosmopolitan algae associated with dimethylsulfoniopropionate (DMSP) synthesis, which regulates the marine biogenic flux of dimethylsulfide (DMS) to the atmosphere and subsequently affects marine aerosols. Attempting to reveal the potential impact of atmospheric deposition on the growth of main DMSP producers, four bioassay experiments were conducted in the western North Pacific (WNP) by adding aerosols, nutrients and trace metals. Our results showed that the percentage of main DMSP producers increased substantially from coastal regions (<1%) to the open ocean (~17%) with the dominance of Dinophyceae and Haptophyceae, respectively. Aerosol additions largely increased the percentage of DMSP species in the open WNP. Specifically, atmospheric DIN and soluble Cu, and Fe promoted Chrysochromulina, and Phaeocystis and E. huxleyi, respectively. It is very likely that atmospheric deposition could lift the relative abundance of main DMSP producers in the vast oligotrophic oceans and contribute to the climate change.
To understand an integral environmental health dynamic a symbiotic observation of water and its socio-environmental interactions should be knitted. Assuming circularity of water can provide related knowledge. A robust scientific evidence baseline is essential to allow health impact evaluation, in order to inform collective decisions on infrastructure development. Mixed methods are used to elaborate an analytical process to combine different heterogeneous data sources. Three analytical levels were defined: Population health, socioeconomic status infrastructure and natural resources specifically river basin. In 2017, water quality perception was surveyed in Drake, Osa Peninsula, Southern of Costa Rica. Then in 2018, a socioeconomic and general health census strategy was undertaken. A water microbiology survey was applied to assess river basin quality. Interaction between population health economics and river basin was observed on aqueducts. This technology play an essential role enabling communities for health improvement and address reduction of socio-economic inequalities by means of community-specific tools for social learning. Since water filtering was identified missing in overall water systems, a water bio-sand filter was designed and tested as a novel conservation technology to cultivate drinkable water at a very low cost. Drake’s inhabitants perceived the need for technologies to treat drinkable water. Conservation culture should be considered for the design of new aqueduct communal systems. An integral ecosystem health assessment index (IEHAI) is proposed as a baseline specification model to improved water resources research.
Transition metal cofactors are crucial for many biological processes. Despite being primarily considered to be toxic, the transition metal cadmium (Cd) was discovered to be a substitute for zinc (Zn) in photosynthetic carbon fixation pathways in marine diatoms. However, it is not known how conditions in the geosphere impacted Cd availability and its incorporation as an alternative metal cofactor for phytoplankton. We employed mineral chemistry network analysis to investigate which geochemical factors may have influenced the availability of Cd and Zn during the putative time period that alternative Cd-based pathway evolved. Our results show that Zn minerals are more chemically diverse than are Cd minerals, but Zn- and Cd-containing minerals have similar mean electronegativities when specifically considering sulfur (S)-containing species. Cadmium and zinc sulfides are the most common Cd- and Zn-containing mineral species over the past 500 million years. In particular, the Cd and Zn sulfides, respectively greenockite and sphalerite, are highly abundant during this time period. Furthermore, S-containing Cd- and Zn minerals are commonly co-located in geologic time, allowing them to be weathered and transported to the ocean in tandem, rather than occurring from separate sources. We suggest that the simultaneous weathering of Cd and Zn sulfides allowed for Cd to be a bioavailable direct substitute for Zn in protein complexes during periods of Zn depletion. The biogeochemical cycles of Zn and Cd exemplify the importance of the coevolution of the geosphere and biosphere in shaping primary production in the modern ocean.
Recently, Fisher et al. (2016) found that tree-mycorrhizal associations can be detected remotely using spaceborne multi-spectral measurements of canopy spectral and phenological signals. However, hyper-spectral data have enormous potential to refine this detection, and possibly connect mycorrhizal association directly to canopy nutrient concentrations. Here, we evaluate airborne AVIRIS data flown over mycorrhizal gradients in the US to detect mycorrhizal association. As spaceborne spectroscopic instruments are imminent, and the impact of mycorrhizae on global biogeochemical cycling and CO2 fertilization responses continue to emerge, we may soon have the ability to produce global coverage of fine scale mycorrhizal detection.
The majority of marine plastic pollution originates from land-based sources with the dominant transport agent being riverine. Despite the widespread recognition that rivers dominate the global flux of plastics to the ocean, there is a key knowledge gap regarding the nature of the flux, the behaviour of microplastics (<5mm) in transport and its pathways from rivers into the ocean. To predict transport, fate and biological interactions of microplastics in aquatic environments at a global scale, the factors that control these processes must be identified and understood. Currently, there remains a large knowledge gap around prediction of microplastic transport in rivers, especially in regards to how biofilm formation influence particle settling velocities. This prevents progress in understanding microplastic fate and hotspot formation, as well as curtailing the evolution of effective mitigation and policy measures. A settling experiment was therefore undertaken to understand how different factors, including salinity, suspended sediment concentration and biofilm formation influence microplastic particle settling velocity. The results presented herein explore the role of biofilms on the generation of microplastic flocs and the impact on buoyancy and settling velocities. Five different polymers were tested and compared including fragments and fibres. Settling velocities were then combined with observed flow velocity data from the Mekong River, one of the top global contributors to marine plastic pollution, allowing predictions of areas of microplastic fallout and hotspots. The results highlight potential areas of highest ecological risk related to the dispersal and distribution of microplastics across the river-delta-coast system including the Tonle Sap Lake. Future work involves supporting predicted hotspots with aligned fieldwork from the Mekong River that details the particulate flux and transport of microplastic, throughout the vertical velocity profile.
Given the increasing global demand for rare earth elements (REE), prospects for REE recovery from both traditional and non-traditional sources have been a focus of intense interest. Many have noted the need for ecologically sustainable alternatives to conventional pyrometallurgical and hydrometallurgical methods to recover REE. Among the newer approaches that have garnered recent interest are those that rely on microbiological processes or microbiologically produced reagents to recover the rare earths. Biological approaches can often avoid many of the environmental and or safety hazards associated with the corrosive (e.g., strong acids) or toxic chemicals (e.g., organic solvents) often used in hydrometallurgy as well as costs related to the high energy, reagent and capital requirements and potential air emissions associated with pyrometallurgy. Microbial processes are considered environmentally friendly because they are “natural”, although opportunities also exist to improve on native capabilities by the application of synthetic biology. In this chapter we will focus on some important factors that have not been as widely discussed but which should be considered in planning actual deployment of biological approaches for recovery and purification of rare earths, drawing on some of our own experience for examples. In particular we will focus on geochemical and biogeochemical constraints posed by the feedstocks from which REE may be extracted, for both bioleaching and biosorption, and point out the importance of aqueous equilibrium modeling as a tool for interpreting results and supporting design of biological recovery methods. We will also discuss some important cost factors for REE recovery that are specific to biological processes.
From inside the stemflow research community, the past decade’s progress might look great: 1) the number of papers published on stemflow per year has doubled; 2) citations of stemflow publications have more than doubled; and 3) the number of research sites monitoring stemflow is on the rise. However, from a broader perspective, a brief Web of Science bibliometric analysis of the past decade reveals issues with these trends: 1) annual publication numbers have increased year-to-year for most topics in natural science, but stemflow publication trends are lower than related and broader disciplines; 2) self-citation is significantly higher for stemflow research than other disciplines (e.g., 26% compared to 2% for all hydrology); and, most importantly, 3) we may have more stemflow data, but we still lack a clear understanding of stemflow’s mechanistic importance. This creates ambiguities as to whether and how stemflow processes can be incorporated into hydrological models and concepts. In this presentation, I argue that we should progress from using metrics that are exclusively used by those who work on stemflow (e.g., unitless metrics such as funneling and enrichment ratios) towards using scaled flux-per-unit-area metrics that may support better integration into hydrological and ecological models (e.g., water or chemical yield per unit canopy area). While the magnitudes of funneling and enrichment ratios from individual plants have effectively conveyed to broader audiences the possibility for stemflow to play important roles in ecosystem functioning, I argue that we need to now move onto mechanistic investigations of stemflow’s impact on specific processes at ecohydrologically relevant scales. Dimensionless (often individual plant-scale) funneling-type metrics may not be useful in this regard, as they tell us nothing about where stemflow goes or what roles stemflow may play in the ecosystem. They also rely on an estimate of infiltration area, which has rarely been observed to date. Their use is further limited to falling liquid-phase rain, which prevents comparison of stemflow observations/processes under occult precipitation (fog, condensation) or mixed and solid-phase precipitation (snow, rime, etc). Please view the “Make Stemflow Unit-ed Again” companion video on YouTube: https://youtu.be/4vPk9m45V0c