scholarly journals Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment

2017 ◽  
Author(s):  
Xabier Vázquez-Campos ◽  
Andrew S. Kinsela ◽  
Mark W. Bligh ◽  
Jennifer J. Harrison ◽  
Timothy E. Payne ◽  
...  
Keyword(s):  
Microbial Community ◽  
Redox Balance ◽  
Water Levels ◽  
Functional Metagenomics ◽  
Shotgun Metagenomics ◽  
Near Surface ◽  
Reducing Conditions ◽  
Contaminant Mobility ◽  
The 1960S ◽  
Associated Species

AbstractDuring the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically-diverse microbial community played in this transition. In particular, aerobes dominated in the first day followed by an increase of facultative anaerobes/denitrifiers at day four. Towards the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.ImportanceThe role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility.Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solidiron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically-diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

scholarly journals Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Xabier Vázquez-Campos ◽  
Andrew S. Kinsela ◽  
Mark W. Bligh ◽  
Jennifer J. Harrison ◽  
Timothy E. Payne ◽  
...  
Keyword(s):  
Microbial Community ◽  
Redox Balance ◽  
Water Levels ◽  
Shotgun Metagenomics ◽  
Near Surface ◽  
Reducing Conditions ◽  
Contaminant Mobility ◽  
Solid Iron ◽  
The 1960S ◽  
Associated Species

ABSTRACT During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

Geochemical Behaviour of Uranium in Sedimentary Formations: Insights From a Natural Analogue Study

2009 ◽  
Author(s):  
Ulrich Noseck ◽  
Vaclava Havlova ◽  
Juhani Suksi ◽  
Thomas Brasser ◽  
Radek Cervinka
Keyword(s):  
Current Knowledge ◽  
Natural Analogue ◽  
Near Surface ◽  
Co2 Partial Pressure ◽  
Long Term Stability ◽  
Reducing Conditions ◽  
Phosphate Mineral ◽  
Sedimentary System ◽  
The Impact

Groundwater data from the natural analogue site Ruprechtov have been evaluated with special emphasis on the uranium behaviour in the so-called uranium-rich clay/lignite horizon. In this horizon in-situ Eh-values in the range of −160 to −280 mV seem to be determined by the SO42−/HS− couple. Under these conditions U(IV) is expected to be the preferential redox state in solution. However, on-site measurements in groundwater from the clay/lignite horizon show only a fraction of about 20% occurring in the reduced state U(IV). Thermodynamic calculations reveal that the high CO2 partial pressure in the clay/lignite horizon can stabilise hexavalent uranium, which explains the occurrence of U(VI). The calculations also indicate that the low uranium concentrations in the range between 0.2 and 2.1μg/l are controlled by amorphous UO2 and/or the U(IV) phosphate mineral ningyoite. This confirms the findings from previous work that the uranium (IV) mineral phases are long-term stable under the reducing conditions in the clay/lignite horizon without any signatures for uranium mobilisation. It supports the current knowledge of the geological development of the site and is also another important indication for the long-term stability of the sedimentary system itself, namely of the reducing geochemical conditions in the near-surface (30m to 60 m deep) clay/lignite horizon. Further work with respect to the impact of changes in redox conditions on the uranium speciation is on the way.

scholarly journals Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmad Nuruddin Khoiri ◽  
Supapon Cheevadhanarak ◽  
Jiraporn Jirakkakul ◽  
Sudarat Dulsawat ◽  
Peerada Prommeenate ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Farming ◽  
Keystone Species ◽  
Taxonomic Diversity ◽  
Plant Growth Promoting Bacteria ◽  
Shotgun Metagenomics ◽  
Mesorhizobium Loti ◽  
Metagenome Analysis ◽  
Microbial Network ◽  
Plant Growth Promoting

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

scholarly journals Anthropogenic Influences on Environmental Changes of Lake Bosten, the Largest Inland Freshwater Lake in China

2020 ◽  
Vol 12 (2) ◽  
pp. 711 ◽  
Author(s):  
Wen Liu ◽  
Long Ma ◽  
Jilili Abuduwaili
Keyword(s):  
Central Asia ◽  
Lake Sediments ◽  
Human Activities ◽  
Environmental Changes ◽  
Living Environment ◽  
Water Levels ◽  
Aral Sea ◽  
Anthropogenic Factors ◽  
Large Spatial Scale ◽  
The 1960S

A short lacustrine sediment core (41 cm) from Lake Bosten in arid central Asia was used to investigate the environmental changes that occurred in the past ≈150 years based on the superposition of climate and anthropogenic factors. Geochemical elements, total organic carbon (TOC) and nitrogen (TN), and stable isotope data (δ13Corg and δ15N) were used to identify abnormal environmental changes. The average C/N ratio in the sediments of Lake Bosten suggested that the organic matter in lake sediments was mainly from aquatic plants. The δ13Corg and δ15N in the lake sediments mainly reflect changes in the structure of the lake’s ecosystem. Before the 1960s, the primary productivity of the lake was relatively low with a relatively stable lake water environment. From the 1960s to the mid-1980s, the lake’s ecosystem was closely related to a significant decline in water levels caused by human activities and an increase in salinity. From the late 1980s to ≈2000, the aquatic plant structure of Lake Bosten did not change significantly. After 2000, the upper part of the sedimentary record suggested enhanced productivity due to urban and industrial development in the catchment area. However, sedimentary perspectives of the responses of different environmental proxies in sediments to human activities were anisochronous, and the increasing heavy metal (Pb and Cu) and P accumulations appeared in 1970, reflecting heightened human impacts. Through the comparison between the Aral Sea and Lake Bosten, it was inferred that, under the intervention of human activities, the lake experienced a completely different evolution trend. Humans, as geological agents, should protect our living environment while satisfying social development. The results will provide an important supplement to a large spatial scale study of the influences of human activities on the environment in Central Asia, which also has some significant implications for the protection of the ecological environment and the realization of sustainable development in arid regions.

Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Madangchanok Imchen ◽  
Ranjith Kumavath
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Community ◽  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Mangrove Ecosystem ◽  
Mangrove Sediment ◽  
Mangrove Forests ◽  
Human Intervention ◽  
Shotgun Metagenomics

ABSTRACT Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P &lt; 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering &gt;90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.

Assessment of the Effect of Increasing Temperature On the Ecology and Assemblage Structure of Modern Planktic Foraminifers in the Caribbean and Surrounding Seas

2018 ◽  
Vol 48 (3) ◽  
pp. 251-272 ◽  
Author(s):  
Anna Jentzen ◽  
Joachim Schönfeld ◽  
Ralf Schiebel
Keyword(s):  
Surface Waters ◽  
Surface Sediments ◽  
Seawater Temperature ◽  
Chlorophyll Concentration ◽  
Caribbean Sea ◽  
Trophic Conditions ◽  
Near Surface ◽  
The Caribbean ◽  
Standing Stocks ◽  
The 1960S

Abstract Habitat patterns of subtropical and tropical planktic foraminifers in the Caribbean Sea were obtained from plankton samples collected in spring 2009 and 2013. The spatial distribution in surface waters (3.5 m water depth) and depth habitat patterns (surface to 400 m) of 33 species were compared with prevailing water-mass conditions (temperature, salinity, and chlorophyll-a concentration) and planktic foraminiferal test assemblages in surface sediments. Distribution patterns indicate a significant relationship with seawater temperature and trophic conditions. A reduction in standing stocks was observed close to the Orinoco River plume and in the Gulf of Paria, associated with high turbidity and concomitant low surface-water salinity. In contrast, a transient mesoscale patch of high chlorophyll concentration in the eastern Caribbean Sea was associated with higher standing stocks in near surface waters, including high abundances of Globigerinita glutinata and Neogloboquadrina dutertrei. Globorotalia truncatulinoides mainly lives close to the seasonal pycnocline and can be linked to winter conditions indicated by lower sea-surface temperatures (SSTs) of ∼20°C. Globigerinoides sacculifer and Globoturborotalita rubescens were associated with oligotrophic conditions in the pelagic Caribbean Sea during early spring and showed a synodic lunar reproduction cycle. The live assemblages in the water column from 2009 and 2013 were similar to those reported in earlier studies from the 1960s and 1990s and to assemblages of tests in the surface sediments. Minor differences in faunal proportions were attributed to seasonal variability and environmental differences at the local scale. An exception was the low relative abundance of Globigerinoides ruber in the Caribbean Sea in 2009 compared to surface sediment samples and plankton net samples collected in the 1960s and 1990s. Decreasing abundance of Gs. ruber white in the Caribbean Sea may be associated with increasing SSTs over past decades and changes in nutrient flux and primary production.

Linking hydrological response to forest dynamics in Mediterranean areas: a new experimental catchment in the Apennine Mountains, Tuscany, Italy

2020 ◽  
Author(s):  
Daniele Penna ◽  
Marco Borga ◽  
Elena Bresci ◽  
Giulio Castelli ◽  
Pietro Castellucci ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Soil Moisture ◽  
Forest Dynamics ◽  
Stream Water ◽  
Water Levels ◽  
Mean Annual Precipitation ◽  
Hydrological Response ◽  
Canopy Interception ◽  
Near Surface ◽  
Mediterranean Areas

&lt;p&gt;The bi-directional ecohydrological interactions between forest dynamics and catchment hydrological response in Mediterranean forest ecosystems remain poorly conceptualized. Understanding the effect of tree water uptake and transpiration patterns on how catchments store and release water and, vice versa, on how catchment water availability affects tree physiological response is of paramount importance for forest and water resource management. This is crucial in the light of the predicted prolonged drought periods that will exacerbate the dry summer spells that characterize Mediterranean areas. In order to address these pressing issues, a new experimental mountain forested catchment for interdisciplinary ecohydrological research has been recently implemented in the Tuscan Apennines (Italy).&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;The catchment size is 2 km&lt;sup&gt;2&lt;/sup&gt; and elevation ranges from 650 to 1280 m a.s.l.. Forest covers more than 95% of the area, and the main tree species are beech and oak trees, with a much smaller proportion of conifers. Mean annual precipitation is around 1180 mm. Instrument installation is currently in progress and supported by two research projects (run in parallel in Italy and Luxembourg). By spring 2020, the catchment is expected to host the following equipment: one weather station plus one additional rain gauge, including a rainfall collector for isotope analysis; four stream gauges at different spatial scales (from a 2-ha headwater subcatchment to the catchment outlet) including continuous electrical conductivity measurements; three groundwater wells (ranging from 2 to 5 m depth) equipped with water level and electrical conductivity loggers; a network of soil moisture sensors at different depths; stemflow collectors; rain totalizers for manual throughfall measurements; a network of innovative multi-parametric sensors mounted on individual beech trees for continuous measurement (logging to cloud) of physiological and micro-meteorological parameters (sap flow, stem radial growth, canopy light transmission, stem wood temperature and humidity, 3D position over time, and air temperature and relative humidity).&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Preliminary data collected in 2019 show a marked seasonality of stream runoff, with low runoff coefficients in summer (&lt;0.1), consistent with the high drainage of forested soils and large evapotranspiration fluxes. Stream electrical conductivity values increase from upstream to downstream sections, showing a consistent spatial variability among seasons and suggesting an increasingly relevance of subsurface flow for sustaining baseflow. Marked diel fluctuations in stream water levels during sunny summer days suggest a dominant control of tree transpiration on streamflow. Near-surface soil moisture spatial patterns at the hillslope scale show strong temporal stability. Future experimental activities will assess water pools used by beech trees along a hillslope. Planned tools and research include water stable isotopes, seasonal variations in canopy interception, stemflow, and throughfall as well as the spatio-temporal variability of soil moisture patterns at the plot, hillslope, and catchment scale.&lt;/p&gt;

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