scholarly journals Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Malin Bomberg ◽  
Mari Nyyssönen ◽  
Petteri Pitkänen ◽  
Anne Lehtinen ◽  
Merja Itävaara
Keyword(s):  
Microbial Communities ◽  
Salinity Gradient ◽  
Ground Surface ◽  
Gene Transcript ◽  
Depth Range ◽  
Transition Zones ◽  
Indicator Microorganisms ◽  
Crystalline Bedrock ◽  
Below Ground ◽  
Archaeal Communities

Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA,dsrB, andmcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizingε-proteobacteria (Sulfurimonassp.) dominated in the SMMZ andγ-proteobacteria (Pseudomonasspp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea,α-,β- andδ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths.DsrB genes were most numerous and most actively transcribed in the SMMZ while themcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems.

scholarly journals Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland

2015 ◽  
Vol 12 (16) ◽  
pp. 13819-13857 ◽  
Author(s):  
M. Bomberg ◽  
T. Lamminmäki ◽  
M. Itävaara
Keyword(s):  
Microbial Communities ◽  
Physicochemical Parameters ◽  
Calvin Cycle ◽  
Acid Oxidation ◽  
Core Microbiome ◽  
Rare Taxa ◽  
The Core ◽  
Crystalline Bedrock ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Abstract. The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is great but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. The great sequencing depth revealed that up to 95 and 99 % of the bacterial and archaeal communities, respectively, were composed of only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3 and 6 fold more bacterial and archaeal taxa. Several clusters of co-occurring rare taxa were identified, which correlated significantly with physicochemical parameters, such as salinity, concentration of inorganic or organic carbon, sulphur, pH and depth. The metabolic properties of the microbial communities were predicted using PICRUSt. The rough prediction showed that the metabolic pathways included commonly fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier conditions on Earth, but could also be induced again if changes in their living conditions occur. In this study only the rare taxa correlated with any physicochemical parameters. Thus these microorganisms can respond to environmental change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock environments.

Seismic solutions utilizing existing in-mine infrastructure for mineral exploration: A case study from Maseve platinum mine, South Africa

2022 ◽  
Vol 41 (1) ◽  
pp. 54-61
Author(s):  
Moyagabo K. Rapetsoa ◽  
Musa S. D. Manzi ◽  
Mpofana Sihoyiya ◽  
Michael Westgate ◽  
Phumlani Kubeka ◽  
...  
Keyword(s):  
South Africa ◽  
Seismic Data ◽  
Mineral Exploration ◽  
Ground Surface ◽  
Seismic Survey ◽  
Noisy Environment ◽  
Borehole Data ◽  
Passive Seismic ◽  
Below Ground

We demonstrate the application of seismic methods using in-mine infrastructure such as exploration tunnels to image platinum deposits and geologic structures using different acquisition configurations. In 2020, seismic experiments were conducted underground at the Maseve platinum mine in the Bushveld Complex of South Africa. These seismic experiments were part of the Advanced Orebody Knowledge project titled “Developing technologies that will be used to obtain information ahead of the mine face.” In these experiments, we recorded active and passive seismic data using surface nodal arrays and an in-mine seismic land streamer. We focus on analyzing only the in-mine active seismic portion of the survey. The tunnel seismic survey consisted of seven 2D profiles in exploration tunnels, located approximately 550 m below ground surface and a few meters above known platinum deposits. A careful data-processing approach was adopted to enhance high-quality reflections and suppress infrastructure-generated noise. Despite challenges presented by the in-mine noisy environment, we successfully imaged the platinum deposits with the aid of borehole data and geologic models. The results open opportunities to adapt surface-based geophysical instruments to address challenging in-mine environments for mineral exploration.

scholarly journals The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

Composition changes of phototrophic microbial communities along the salinity gradient in the solar saltern evaporation ponds of Eilat, Israel

Hydrobiologia ◽  
2009 ◽  
Vol 636 (1) ◽  
pp. 77-88 ◽  
Author(s):  
Klára Řeháková ◽  
Eliška Zapomělová ◽  
Ondřej Prášil ◽  
Jana Veselá ◽  
Hana Medová ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Salinity Gradient ◽  
Solar Saltern ◽  
Evaporation Ponds ◽  
Composition Changes

Nature of Soils and Soil Development

2007 ◽  
Author(s):  
Earl B. Alexander ◽  
Roger G. Coleman ◽  
Todd Keeler-Wolfe ◽  
Susan P. Harrison
Keyword(s):  
Lower Limit ◽  
Total Mass ◽  
Ground Surface ◽  
Root Penetration ◽  
Unconsolidated Material ◽  
Below Ground ◽  
Porous Soil ◽  
Living Organisms ◽  
Bacteria And Fungi ◽  
The Many

We walk on soils frequently, but we seldom observe them. Soils are massive, even though they are porous. Soil 1m (40 inches) deep over an area of 1 hectare (2.5 acres) might weigh 10,000–15,000 metric tons. It is teeming with life. There are trillions, or quadrillions, of living organisms (mostly microorganisms), representing thousands of species, in each square meter of soil (Metting 1993). In fact, species diversity, or number of species, may be greater below ground than above ground. We seldom see these organisms because we seldom look below ground or dig into it. The many worms and insects one finds digging in a garden are a small fraction of the species in soils because the greatest diversity of soil-dwelling species exists among microscopic insects, mites, roundworms (or nematodes), and fungi. Even though individual organisms in soils are mostly very small or microscopic, the total mass of living organisms in a hectare of soil, excluding plant roots, may be 1–5 or 10 metric tons. More than one-half of that biomass is bacteria and fungi. Living microorganism biomass generally accounts for about 1%–5% of the organic carbon and about 2%–6% of the nitrogen in soils (Lavelle and Spain 2001). The upper limit of soil is the ground surface of the earth. The lower limit is bedrock for engineers, or the depth of root penetration for edaphologists. Unconsolidated material that engineers call soil can be called “regolith” (Merrill 1897, Jackson 1997) to distinguish it from the soil of pedologists and edaphologists. Regolith may consist of disintegrated bedrock, gravel, sand, clay, or other materials that have not been consolidated to form rock. Pedologists investigate the upper part of regolith, where changes are effected by exchanges of gases between soil and aboveground atmosphere and by biological activity. This soil of pedologists may coincide with that of edaphologists or include more regolith. In fact, the lower limit of soil that pedologists investigate is arbitrary, unless this limit is a contact with bedrock that is practically impenetrable with pick and shovel.

scholarly journals Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Antoine Bagnaro ◽  
Federico Baltar ◽  
Gretchen Brownstein ◽  
William G. Lee ◽  
Sergio E. Morales ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Fuzzy Clustering ◽  
Water Mass ◽  
Rrna Gene ◽  
Microbial Ecosystem ◽  
Transition Zones ◽  
Ecosystem Boundaries ◽  
Operational Taxonomic Units ◽  
Pelagic Environment ◽  
Environmental Transitions

Abstract Background One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries. Results We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time. Conclusion We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.

scholarly journals Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Forests ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 550 ◽  
Author(s):  
Huili Feng ◽  
Jiahuan Guo ◽  
Weifeng Wang ◽  
Xinzhang Song ◽  
Shuiqiang Yu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Rrna Gene ◽  
Poplar Plantation ◽  
Plantation Forest ◽  
Bacterial And Archaeal Communities ◽  
Different Depths ◽  
Archaeal Communities

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.

scholarly journals Refinement of Alternate Wetting and Drying Irrigation Method for Rice Cultivation

2014 ◽  
Vol 17 (1-2) ◽  
pp. 33-37 ◽  
Author(s):  
Priya Lal Chandra Paul ◽  
MA Rashid ◽  
Mousumi Paul
Keyword(s):  
Grain Yield ◽  
Water Level ◽  
Block Design ◽  
Water Productivity ◽  
Ground Surface ◽  
Soil Surface ◽  
Ground Level ◽  
Wetting And Drying ◽  
Alternate Wetting And Drying ◽  
Below Ground

Experiments were conducted at BRRI farm Gazipur during Boro season 2010-12 to determine maximum depth of water level below ground surface in alternate wetting and drying (AWD) method. The experiment was laid out in a randomized complete block design with four irrigation treatments. The treatments of AWD method were: T1 = continuous standing water, T2 = irrigation when water level reached 15 cm below ground level, T3 = irrigation when water level reached 20 cm below ground level and T4 = irrigation when water level reached 50 cm below ground level. The experiment involved BRRI dhan28 as a test crop. The treatment T2 gave the highest grain yield (5.9 and 6.2 ton/ha) in 2010-11 and 2011-12, respectively. Maximum benefits per hectare were found Tk. 5476 and 4931 for using 807 and 880 mm water during 2010-11 and 2011-12 respectively and thus water productivity was 7.1 kg/ha-mm in T2 for both the seasons. Continuous standing (T1) water (1013 and 1100 mm) gave comparable grain yield 5.7 and 6.0 ton/ha in 2010-11 and 2011-12, respectively. Minimum water productivity was found in treatment T1 (5.6 and 5.4 kg/ha-mm) for both the seasons. Application of irrigation when water was 15 cm below soil surface was found most profitable in AWD system and the grain yield was decreased when water level was below 15 cm depth. Therefore, the recommended AWD technology could increase rice yield and save irrigation water by 25-30 percent.DOI: http://dx.doi.org/10.3329/brj.v17i1-2.20899Bangladesh Rice j. 2013, 17(1&2): 33-37

scholarly journals Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 275 ◽  
Author(s):  
Tiehang Wu ◽  
Ashley Gray ◽  
Gan Liu ◽  
Hilary Kaminski ◽  
Bolanle Osi Efa ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Tree Species ◽  
Ammonia Oxidation ◽  
Soil Microbial Communities ◽  
Amoa Gene ◽  
Groundwater Depth ◽  
Functional Genes ◽  
Nitrification And Denitrification ◽  
Archaeal Communities

Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.

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