Initial Investigations into Microbial Dynamics and Biogeochemical Cycling in the Bedretto Tunnel

2021 ◽  
Author(s):  
Andrew Acciardo ◽  
Moira Arnet ◽  
Bernard Brixel ◽  
Nima Gholizadeh Doonechaly ◽  
Quinn Wenning ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Chemical Properties ◽  
Swiss Alps ◽  
Epifluorescence Microscopy ◽  
Microbial Dynamics ◽  
Flow Paths ◽  
Subsurface Environments ◽  
Holistic Understanding ◽  
Terrestrial Subsurface

<p>Over 70% of Earth’s bacteria and archaea live in the subsurface. These rock-dwelling microorganisms are capable of exerting considerable influence on their environment by altering and recycling nutrients, as well as inducing changes to fluid flow paths through bioclogging. Subsurface life, therefore, has considerable implications for both natural and engineered subsurface environments. The Bedretto tunnel, located within the Swiss Alps, is 5,218 meters long and is host to the Bedretto Underground Laboratory for Geosciences and Geoenergies (BULGG), which was built to study the feasibility of large-scale geothermal energy storage and extraction. The tunnel, with a maximum overburden of approximately 1,650m, is embedded within both gneiss and Rotondo granite and offers an ideal location to investigate the biogeochemical feedbacks associated with natural fluids as well as the effect that stimulation has on the biological and chemical properties of subsurface fluids. For these reasons, a multi-year, monthly survey of fracture fluids at over 20 locations across the entire length of the tunnel has been carried out since August 2020 with the goal of performing 16S rRNA sequencing of cells captured by 0.22µm Millipore Sterivex filters and cell enumeration by epifluorescence microscopy of cells fixed with ethanol. By studying the microorganisms inhabiting BULG, we will be able to understand how the physical-chemical heterogeneities of the subsurface influence microbial physiology and community structure. Preliminary results of DNA extractions from the cells concentrated on Sterivex filters show that there is a measurable amount of DNA found in the fluids of the Bedretto tunnel that correlates with pH, indicating the presence of microbial communities which may vary with changes in fluid chemistry. With continued monitoring through 2021, we will determine whether there is significant variability of microbial taxa at different locations within the tunnel and the relationship between the hydrochemical properties of the fluids and the microbial communities. Alongside the profiling survey, whole genome sequencing as well as targeted virome sequencing procedures will be developed and used to learn more about the genetic and metabolic capacity of the microbial communities and to better understand how viruses can influence their hosts in such an environment. These results will be compared to other subsurface environments around the globe to gain a more holistic understanding of microbial dynamics in the terrestrial subsurface. Together, these results provide a new and important tool for tracking subsurface processes.</p>

scholarly journals Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin

2002 ◽  
Vol 68 (8) ◽  
pp. 3759-3770 ◽  
Author(s):  
David W. Reed ◽  
Yoshiko Fujita ◽  
Mark E. Delwiche ◽  
D. Brad Blackwelder ◽  
Peter P. Sheridan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Marine Sediments ◽  
Methane Hydrate ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Forearc Basin ◽  
Subsurface Environments ◽  
Lipid Biomarker ◽  
Archaeal Lipids ◽  
Terrestrial Subsurface

ABSTRACT Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacterial lipids. Methane was produced from both acetate and hydrogen in enrichments inoculated with sediment from all depths evaluated, at both 10 and 35°C. Characterization of 16S rRNA genes amplified from the sediments indicated that archaeal clones could be discretely grouped within the Euryarchaeota and Crenarchaeota domains. The bacterial clones exhibited greater overall diversity than the archaeal clones, with sequences related to the Bacteroidetes, Planctomycetes, Actinobacteria, Proteobacteria, and green nonsulfur groups. The majority of the bacterial clones were either members of a novel lineage or most closely related to uncultured clones. The results of these analyses suggest that the microbial community in this environment is distinct from those in previously characterized methane hydrate-bearing sediments.

Species Responses to Grazing and Environmental-Factors in an Arid Halophytic Shrubland Community

1987 ◽  
Vol 35 (2) ◽  
pp. 135 ◽  
Author(s):  
RB Hacker
Keyword(s):  
Environmental Factors ◽  
Soil Salinity ◽  
Large Scale ◽  
Chemical Properties ◽  
Grazing Pressure ◽  
Aerial Photographs ◽  
Small Scale ◽  
Factors Affecting ◽  
Species Responses

Species responses to grazing and environmental factors were studied in an arid halophytic shrubland community in Western Australia. The grazing responses of major shrub species were defined by using reciprocal averaging ordination of botanical data, interpreted in conjunction with a similar ordination of soil chemical properties and measures of soil erosion derived from large-scale aerial photographs. An apparent small-scale interaction between grazing and soil salinity was also defined. Long-term grazing pressure is apparently reduced on localised areas of high salinity. Environmental factors affecting species distribution are complex and appear to include soil salinity, soil cationic balance, geomorphological variation and the influence of cryptogamic crusts on seedling establishment.

Islamic Glass in the Making

2022 ◽  
Author(s):  
Nadine Schibille
Keyword(s):  
Glass Industry ◽  
Large Scale ◽  
Interdisciplinary Approach ◽  
Islamic Period ◽  
Holistic Understanding ◽  
History Of ◽  
Early Islamic Period ◽  
Early Islamic ◽  
Plant Ash ◽  
Islamic Glass

The ancient glass industry changed dramatically towards the end of the first millennium. The Roman glassmaking tradition of mineral soda glass was increasingly supplanted by the use of plant ash as the main fluxing agent at the turn of the ninth century CE. Defining primary production groups of plant ash glass has been a challenge due to the high variability of raw materials and the smaller scale of production. Islamic Glass in the Making advocates a large-scale archaeometric approach to the history of Islamic glassmaking to trace the developments in the production, trade and consumption of vitreous materials between the eighth and twelfth centuries and to separate the norm from the exception. It proposes compositional discriminants to distinguish regional production groups, and provides insights into the organisation of the glass industry and commerce during the early Islamic period. The interdisciplinary approach leads to a holistic understanding of the development of Islamic glass; assemblages from the early Islamic period in Mesopotamia, Central Asia, Egypt, Greater Syria and Iberia are evaluated, and placed in the larger geopolitical context. In doing so, this book fills a gap in the present literature and advances a large-scale approach to the history of Islamic glass.

scholarly journals Semi-automated calibration method for modelling of mountain permafrost evolution in Switzerland

2016 ◽  
Vol 10 (6) ◽  
pp. 2693-2719 ◽  
Author(s):  
Antoine Marmy ◽  
Jan Rajczak ◽  
Reynald Delaloye ◽  
Christin Hilbich ◽  
Martin Hoelzle ◽  
...  
Keyword(s):  
Large Scale ◽  
Calibration Method ◽  
Swiss Alps ◽  
Climate Projections ◽  
European Alps ◽  
Permafrost Degradation ◽  
Future Evolution ◽  
Mountainous Regions ◽  
Automated Calibration ◽  
The Future

Abstract. Permafrost is a widespread phenomenon in mountainous regions of the world such as the European Alps. Many important topics such as the future evolution of permafrost related to climate change and the detection of permafrost related to potential natural hazards sites are of major concern to our society. Numerical permafrost models are the only tools which allow for the projection of the future evolution of permafrost. Due to the complexity of the processes involved and the heterogeneity of Alpine terrain, models must be carefully calibrated, and results should be compared with observations at the site (borehole) scale. However, for large-scale applications, a site-specific model calibration for a multitude of grid points would be very time-consuming. To tackle this issue, this study presents a semi-automated calibration method using the Generalized Likelihood Uncertainty Estimation (GLUE) as implemented in a 1-D soil model (CoupModel) and applies it to six permafrost sites in the Swiss Alps. We show that this semi-automated calibration method is able to accurately reproduce the main thermal condition characteristics with some limitations at sites with unique conditions such as 3-D air or water circulation, which have to be calibrated manually. The calibration obtained was used for global and regional climate model (GCM/RCM)-based long-term climate projections under the A1B climate scenario (EU-ENSEMBLES project) specifically downscaled at each borehole site. The projection shows general permafrost degradation with thawing at 10 m, even partially reaching 20 m depth by the end of the century, but with different timing among the sites and with partly considerable uncertainties due to the spread of the applied climatic forcing.

scholarly journals Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pengshuo Yang ◽  
Chongyang Tan ◽  
Maozhen Han ◽  
Lin Cheng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Network Connectivity ◽  
Small Range ◽  
Environmental Disturbance ◽  
Target Species ◽  
Important Species ◽  
Metagenome Analysis ◽  
Occurrence Patterns ◽  
Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

scholarly journals Effect of three different agronomic conditions on biochemical profile and diversity in the rhizosphere of banana plantations infected with Fusarium oxysporum Race 1

2021 ◽  
Vol 27 (2) ◽  
Author(s):  
Katherine Sánchez-Zúñiga ◽  
◽  
Ana Tapia-Fernández ◽  
William Eduardo Rivera-Méndez ◽  
◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Soil Health ◽  
Chemical Properties ◽  
Principal Component ◽  
Exchange Capacity ◽  
High Fertility ◽  
Fertility Level ◽  
Biochemical Profile ◽  
Agronomic Conditions

Soil microorganisms play an important role as a link in the transfer of nutrients from the rhizosphere. The physical and chemical properties of soil, the metabolic profiles of microbial communities and different crop management practices can enhance our understanding of hizospheric interactions. This study aimed to establish differences in microbial communities associated with banana crops and the biochemical profile in farms under different agronomic conditions. Seven farms with different levels of intervention, management, and fusariosis severity were analyzed. The biochemical profile of the microbial community was determined using EcoPlates and the main substrates consumed by the microbial communities were identified through multivariate principal component analysis (PCA). Seven microorganisms were selected as indicators of nutrient cycles, pathogenicity and soil health. Also, soil chemical indicators were determined through a complete mineral analysis. For the physiological profile of soil microbial populations, it was observed that farms with the same management tend to be metabolically very similar. In the PCA, two principal components explained 90 % of the variance in the data. It was also determined that the genus Bacillus is predominant in all farms and that farm 4 (medium intervention) presented the most favorable values in all factors analyzed. The effective cation exchange capacity values are highlighted in the chemical analyses, which determined that all farms have a high fertility level. The metabolic profile, diversity and richness of each of the different farms were affected by the type of agronomic management used.

scholarly journals Pratiques de production et caracteristiques physiques et chimiques du shô basi, un couscous de niebe (Vigna unguiculata) produit au Mali

2021 ◽  
Vol 21 (02) ◽  
pp. 17509-17528
Author(s):  
A Timitey ◽  
◽  
L Adinsi ◽  
YE Madodé ◽  
F Cissé ◽  
...  
Keyword(s):  
Vigna Unguiculata ◽  
Large Scale ◽  
Chemical Properties ◽  
Quality Criteria ◽  
Scale Production ◽  
Production Flow ◽  
Cowpea Seeds ◽  
Steam Cooking ◽  
End Products ◽  
Cowpea Varieties

In West Africa, cowpea is processed into several end-products among which the most consumed in Mali is a steamed granulated product known as cowpea couscous or Shô basi, in Bambara. Organoleptic properties ofShô basi are variable, probably as a consequence of the diversity of the practices of production. This study aims at determining these practices, their constraints and the physico-chemical characteristics of Shô basi as sold on Malian markets. A survey using focus group discussions, and involving eighteen (18) Shô basi production cooperatives, each gathering 8 to 32 members, was conducted in South Mali. The information collected was related to cowpea varieties used for production, flow diagrams, constraints of production, and quality criteria of the end-products. Eighteen (18) Shô basi samples were collected from the interviewed groups and used for the determination of the physical and chemical properties of Shô basi. Results showed that most of the processors were married, non or moderately literate and aged between 20 and 59 years women. The main cowpea varieties used for the production are sangaraka and wilibali, both from the species Vigna unguiculata. Both varieties of cowpea are characterized by a white or cream color. Shô basi is produced using a single process with two major technological variants. One involves a wet total dehulling (VDT), whereas the second involves a dry partial dehulling (VDP) of cowpea seeds. Regardless of the technological variant and cowpea variety used, interviewees indicated that a good qualityShô basi must have a light color, a soft mouthfeel texture, a homogeneous granule size and lacking beany flavor. Protein(25,0g/100g) and polyphenol (24,3mg/100g)contents as well as swelling level were similar for Shô basi from both variants. However, Shô basi from technology involving partial dehulling (VDP) was less bright, richer in fiber and minerals, and contained more fine granules thanShô basi involving whole dehulling(VDT). Cowpea dehulling, flour granulation, steam cooking and drying are the mean constraints for quality standardization and large-scale production of Shô basi in Mali.

Characterization of microbial communities in exhaust air treatment systems of large-scale pig housing facilities

2010 ◽  
Vol 62 (7) ◽  
pp. 1551-1559 ◽  
Author(s):  
J. Haneke ◽  
N. M. Lee ◽  
T. W. Gaul ◽  
H. F. A. Van den Weghe
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Dust Particles ◽  
Nitrifying Bacteria ◽  
Ammonium Concentration ◽  
Nitrogen Compounds ◽  
Air Treatment ◽  
Fattening Period ◽  
Washing Water ◽  
Housing Facilities

Exhaust air treatment has gained importance as an essential factor in intensive livestock areas due to the rising emissions in the environment. Wet filter walls of multi-stage exhaust air treatment systems precipitate gaseous ammonia and dust particles from exhaust air in washing water. Microbial communities in the biomass developed in the washing water of five large-scale exhaust air treatment units of pig housing facilities, were investigated by fluorescence in situ hybridization (FISH) and 16S rDNA sequence analyses. No “standard” nitrifying bacteria were found in the washing water. Instead mainly α-Proteobacteria, aggregating β- and χ-Proteobacteria, a large number of Actinobacteria, as well as individual Planctomycetales and Crenarchaeota were detected after more than twelve months' operation. The main Proteobacteria species present were affiliated to the families Alcaligenaceae, Comamonadaceae and Xanthomonadaceae. Furthermore, we investigated the consumption of inorganic nitrogen compounds in the washing water of one exhaust air treatment unit during a fattening period with and without pH control. Maintaining the pH at 6.0 resulted in a ca. fivefold higher ammonium concentration and a ca. fourfold lower concentration of oxidized nitrogen compounds after the fattening period was finished.

scholarly journals Development of a Vital Fluorescent Staining Method for Monitoring Bacterial Transport in Subsurface Environments

2000 ◽  
Vol 66 (10) ◽  
pp. 4486-4496 ◽  
Author(s):  
Mark E. Fuller ◽  
Sheryl H. Streger ◽  
Randi K. Rothmel ◽  
Brian J. Mailloux ◽  
James A. Hall ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Detection Limit ◽  
Sediment Cores ◽  
Growth Conditions ◽  
Bacterial Transport ◽  
Epifluorescence Microscopy ◽  
Transport Studies ◽  
Subsurface Environments ◽  
High Throughput Method ◽  
Initial Work

ABSTRACT Previous bacterial transport studies have utilized fluorophores which have been shown to adversely affect the physiology of stained cells. This research was undertaken to identify alternative fluorescent stains that do not adversely affect the transport or viability of bacteria. Initial work was performed with a groundwater isolate,Comamonas sp. strain DA001. Potential compounds were first screened to determine staining efficiencies and adverse side effects. 5-(And 6-)-carboxyfluorescein diacetate, succinimidyl ester (CFDA/SE) efficiently stained DA001 without causing undesirable effects on cell adhesion or viability. Members of many other gram-negative and gram-positive bacterial genera were also effectively stained with CFDA/SE. More than 95% of CFDA/SE-stained Comamonas sp. strain DA001 cells incubated in artificial groundwater (under no-growth conditions) remained fluorescent for at least 28 days as determined by epifluorescent microscopy and flow cytometry. No differences in the survival and culturability of CFDA/SE-stained and unstained DA001 cells in groundwater or saturated sediment microcosms were detected. The bright, yellow-green cells were readily distinguished from autofluorescing sediment particles by epifluorescence microscopy. A high throughput method using microplate spectrofluorometry was developed, which had a detection limit of mid-105CFDA-stained cells/ml; the detection limit for flow cytometry was on the order of 1,000 cells/ml. The results of laboratory-scale bacterial transport experiments performed with intact sediment cores and nondividing DA001 cells revealed good agreement between the aqueous cell concentrations determined by the microplate assay and those determined by other enumeration methods. This research indicates that CFDA/SE is very efficient for labeling cells for bacterial transport experiments and that it may be useful for other microbial ecology research as well.

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