scholarly journals Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
George Westmeijer ◽  
Maliheh Mehrshad ◽  
Stephanie Turner ◽  
Linda Alakangas ◽  
Varvara Sachpazidou ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Hard Rock ◽  
Fennoscandian Shield ◽  
Indigenous Populations ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Soil ◽  
Energy Constrained ◽  
The Baltic ◽  
Autochthonous Species

AbstractThe deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

scholarly journals Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

2021 ◽  
Author(s):  
Patrick H. Thieringer ◽  
Alexander S. Honeyman ◽  
John R. Spear
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Surface Hydrology ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
High Concentrations ◽  
Recharge Rates

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular biological and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (~150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

scholarly journals Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka

2020 ◽  
Vol 8 (11) ◽  
pp. 1736
Author(s):  
Camille Thomas ◽  
Alexander Francke ◽  
Hendrik Vogel ◽  
Bernd Wagner ◽  
Daniel Ariztegui
Keyword(s):  
Microbial Communities ◽  
Lacustrine Sediments ◽  
Environmental Parameters ◽  
Strong Relationship ◽  
Low Energy ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Lake Ohrid ◽  
Metabolic Versatility ◽  
The Impact

Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.

scholarly journals Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Margarita Lopez-Fernandez ◽  
Domenico Simone ◽  
Xiaofen Wu ◽  
Lucile Soler ◽  
Emelie Nilsson ◽  
...  
Keyword(s):  
Residence Time ◽  
Hard Rock ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Rock Laboratory ◽  
Mrna Transcripts ◽  
Domains Of Life

ABSTRACT The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as “modern marine,” and an “old saline” groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available. IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Äspö Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.

scholarly journals Biosignatures of ancient microbial life are present across the igneous crust of the Fennoscandian shield

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Henrik Drake ◽  
Nick M. W. Roberts ◽  
Manuel Reinhardt ◽  
Martin Whitehouse ◽  
Magnus Ivarsson ◽  
...  
Keyword(s):  
Fennoscandian Shield ◽  
Stable Carbon ◽  
Deep Biosphere ◽  
Isotopic Signatures ◽  
Microbial Life ◽  
Carbon Isotopic ◽  
Terrestrial Life ◽  
Vein Mineral ◽  
Methyl Branched Fatty Acids

AbstractEarth’s crust contains a substantial proportion of global biomass, hosting microbial life up to several kilometers depth. Yet, knowledge of the evolution and extent of life in this environment remains elusive and patchy. Here we present isotopic, molecular and morphological signatures for deep ancient life in vein mineral specimens from mines distributed across the Precambrian Fennoscandian shield. Stable carbon isotopic signatures of calcite indicate microbial methanogenesis. In addition, sulfur isotope variability in pyrite, supported by stable carbon isotopic signatures of methyl-branched fatty acids, suggest subsequent bacterial sulfate reduction. Carbonate geochronology constrains the timing of these processes to the Cenozoic. We suggest that signatures of an ancient deep biosphere and long-term microbial activity are present throughout this shield. We suggest that microbes may have been active in the continental igneous crust over geological timescales, and that subsurface investigations may be valuable in the search for extra-terrestrial life.

scholarly journals A Comparative Study on the Microbial Communities of Rhynchophorus ferrugineus (Red Palm Weevil)-Infected and Healthy Palm Trees

2021 ◽  
Author(s):  
N. Alshammari ◽  
Meshari Alazmi ◽  
Naimah A. Alanazi ◽  
Abdel Moneim E. Sulieman ◽  
Vajid N. Veettil ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rhynchophorus Ferrugineus ◽  
Tree Trunk ◽  
Red Palm Weevil ◽  
Healthy Tree ◽  
Palm Trees ◽  
Infected Tree ◽  
Palm Weevil

AbstractSeveral studies have investigated palm trees’ microbiota infected with red palm weevil (RPW) (Rhynchophorus ferrugineus), the major pest of palm trees. This study compared the microbial communities of infected and uninfected palm trees in the Hail region, Northern Saudi Arabia, determined by high-throughput 16S rRNA gene sequencing by Illumina MiSeq. The results indicated that taxonomic diversity variation was higher for infected tree trunk than the healthy tree trunk. Soil samples from the vicinity of healthy and infected trees did not have a significant variation in bacterial diversity. Myxococcota, Acidobacteriota, and Firmicutes were the dominant phyla in RPW-infected tree trunk, and Pseudomonadaceae was the most prominent family. This study is the first report on the characterization of RPW-infected and healthy palm trees’ microbiome.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

scholarly journals 2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

2021 ◽  
Author(s):  
Gunther Brucha ◽  
Andrea Aldas-Vargas ◽  
Zacchariah Ross ◽  
Peng Peng ◽  
Siavash Atashgahi ◽  
...  
Keyword(s):  
Microbial Community Composition ◽  
High Mobility ◽  
16S Rrna Gene Sequencing ◽  
Dichlorophenoxyacetic Acid ◽  
Rrna Gene ◽  
Deep Soil ◽  
Anoxic Environments ◽  
Top Soil ◽  
Significant Enrichment ◽  
2,4 Dichlorophenoxyacetic Acid

Abstract2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D’s high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0—40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

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