CO2concentration and pH alters subsurface microbial ecology at reservoir temperature and pressure

RSC Advances ◽  
2014 ◽  
Vol 4 (34) ◽  
pp. 17443-17453 ◽  
Author(s):  
Djuna M. Gulliver ◽  
Gregory V. Lowry ◽  
Kelvin B. Gregory
Keyword(s):  
Carbon Sequestration ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Molecular Ecology ◽  
Reservoir Temperature ◽  
Geological Carbon Sequestration ◽  
Temperature And Pressure ◽  
The Impact

Molecular ecology techniques are utilized to determine the impact of CO2concentrations on microbial communities under reservoir temperature and pressure simulating geological carbon sequestration.

scholarly journals Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

2021 ◽  
Vol 11 ◽  
Author(s):  
Angel Rain-Franco ◽  
Guilherme Pavan de Moraes ◽  
Sara Beier
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Processing Time ◽  
Handling Time ◽  
Abundant Species ◽  
Inoculum Size ◽  
Growth Media ◽  
Long Term Storage ◽  
Naturally Occurring ◽  
The Impact

Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45–72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.

How Does Fault-Related Alteration of Basalt Affect the Potential for Geological Carbon Sequestration in Basalt Formations?

2018 ◽  
Author(s):  
Montserrat Recasens ◽  
Kitson Lim ◽  
M. Mercedes Maroto-Valer ◽  
Rachael Ellen ◽  
Susana Garcia
Keyword(s):  
Carbon Sequestration ◽  
Geological Carbon Sequestration

scholarly journals Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Verónica Lloréns-Rico ◽  
Sara Vieira-Silva ◽  
Pedro J. Gonçalves ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Microbial Communities ◽  
Quantitative Methods ◽  
Microbial Load ◽  
Metagenomic Sequencing ◽  
Sampling Depth ◽  
Microbiome Research ◽  
Microbiome Data ◽  
The Impact ◽  
Analytical Approaches ◽  
Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

scholarly journals Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alberto Pascual-García
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Environmental Conditions ◽  
The Novel ◽  
Methodological Framework ◽  
Operational Taxonomic Units ◽  
Traditional Classification ◽  
Taxonomical Classification ◽  
Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

Earth's energy “Golden Zone”: a synthesis from mineralogical research

Clay Minerals ◽  
2011 ◽  
Vol 46 (1) ◽  
pp. 1-24 ◽  
Author(s):  
P. H. Nadeau
Keyword(s):  
Oil And Gas ◽  
Gulf Coast ◽  
Clay Mineralogy ◽  
Sedimentary Basins ◽  
Entrapment Efficiency ◽  
Permeability Evolution ◽  
Reservoir Temperature ◽  
Fundamental Particle ◽  
Geological Processes ◽  
The Impact

AbstractThe impact of diagenetic processes on petroleum entrapment and recovery efficiency has focused the vast majority of the world's conventional oil and gas resources into relatively narrow thermal intervals, which we call Earth's energy “Golden Zone”. Two key mineralogical research breakthroughs, mainly from the North Sea, underpinned this discovery. The first is the fundamental particle theory of clay mineralogy, which showed the importance of dissolution/precipitation mechanisms in the formation of diagenetic illitic clays with increasing depth and temperature. The second is the surface area precipitation-rate-controlled models for the formation of diagenetic cements, primarily quartz, in reservoirs. Understanding the impacts of these geological processes on permeability evolution, porosity loss, overpressure development, and fluid migration in the subsurface, lead to the realization that exploration and production risks are exponential functions of reservoir temperature. Global compilations of oil/gas reserves relative to reservoir temperature, including the US Gulf Coast, have verified the “Golden Zone” concept, as well as stimulated further research to determine in greater detail the geological/mineralogical controls on petroleum migration and entrapment efficiency within the Earth's sedimentary basins.

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