scholarly journals Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

2018 ◽  
Author(s):  
Alexander J. Probst ◽  
Felix J. Elling ◽  
Cindy J. Castelle ◽  
Qingzeng Zhu ◽  
Marcus Elvert ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Lipid Membranes ◽  
Membrane Lipids ◽  
Lipid Analysis ◽  
Membrane Curvature ◽  
Deep Biosphere ◽  
Community Members ◽  
Deep Subsurface ◽  
Carbon Isotopic

ABSTRACTSediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.

scholarly journals Carbon isotopic composition of branched tetraether membrane lipids in soils suggest a rapid turnover and a heterotrophic life style of their source organism(s)

2010 ◽  
Vol 7 (9) ◽  
pp. 2959-2973 ◽  
Author(s):  
J. W. H. Weijers ◽  
G. L. B. Wiesenberg ◽  
R. Bol ◽  
E. C. Hopmans ◽  
R. D. Pancost
Keyword(s):  
Organic Carbon ◽  
Isotopic Composition ◽  
Life Style ◽  
Membrane Lipids ◽  
Carbon Isotopic Composition ◽  
Turnover Time ◽  
Arable Soils ◽  
Higher Plant ◽  
Δ13c Values ◽  
Carbon Isotopic

Abstract. Branched Glycerol Dialkyl Glycerol Tetraethers (GDGTs) are membrane spanning lipids synthesised by as yet unknown bacteria that thrive in soils and peat. In order to obtain more information on their ecological niche, the stable carbon isotopic composition of branched GDGT-derived alkanes, obtained upon ether bond cleavage, has been determined in a peat and various soils, i.e. forest, grassland and cropland, covered by various vegetation types, i.e., C3- vs. C4-plant type. These δ13C values are compared with those of bulk organic matter and higher plant derived n-alkanes from the same soils. With average δ13C values of −28‰, branched GDGTs in C3 soils are only slightly depleted (ca. 1‰) relative to bulk organic carbon and on average 8.5‰ enriched relative to plant wax-derived long-chain n-alkanes ( nC29–nC33). In an Australian soil dominantly covered with C4 type vegetation, the branched GDGTs have a δ13C value of −18‰, clearly higher than observed in soils with C3 type vegetation. As with C3 vegetated soils, branched GDGT δ13C values are slightly depleted (1‰) relative to bulk organic carbon and enriched (ca. 5‰) relative to n-alkanes in this soil. The δ13C values of branched GDGT lipids being similar to bulk organic carbon and their co-variation with those of bulk organic carbon and plant waxes, suggest a heterotrophic life style and assimilation of relatively heavy and likely labile substrates for the as yet unknown soil bacteria that synthesise the branched GDGT lipids. However, a chemoautotrophic lifestyle, i.e. consuming respired CO2, could not be fully excluded based on these data alone. Based on a natural labelling experiment of a C3/C4 crop change introduced on one of the soils 23 years before sampling and based on a free-air CO2 enrichment experiment with labelled CO2 on another soil, a turnover time of ca. 18 years has been estimated for branched GDGTs in these arable soils.

scholarly journals Carbon isotopic composition of branched tetraether membrane lipids in soils suggest a rapid turnover and a heterotrophic life style of their source organism(s)

2010 ◽  
Vol 7 (3) ◽  
pp. 3691-3734 ◽  
Author(s):  
J. W. H. Weijers ◽  
G. L. B. Wiesenberg ◽  
R. Bol ◽  
E. C. Hopmans ◽  
R. D. Pancost
Keyword(s):  
Organic Carbon ◽  
Isotopic Composition ◽  
Life Style ◽  
Membrane Lipids ◽  
Carbon Isotopic Composition ◽  
Turnover Time ◽  
Arable Soils ◽  
Higher Plant ◽  
Δ13c Values ◽  
Carbon Isotopic

Abstract. Branched Glycerol Dialkyl Glycerol Tetraethers (GDGTs) are membrane spanning lipids synthesised by as yet unknown bacteria that thrive in soils and peat. In order to obtain more information on their ecological niche, the stable carbon isotopic composition of branched GDGT-derived alkanes, obtained upon ether bond cleavage, has been determined in various soils, i.e. peat, forest, grassland and cropland, covered by various vegetation types, i.e., C3- vs. C4-plant type. These δ13C values are compared with those of bulk organic matter and higher plant derived n-alkanes from the same soils. With average δ13C values of −28‰, branched GDGTs in C3 soils are only slightly depleted (ca. 1‰) relative to bulk organic carbon and on average 8.5‰ enriched relative to plant wax-derived long-chain n-alkanes (nC29–nC33). In an Australian soil covered with C4 type vegetation, the branched GDGTs have a δ13C value of −18‰, clearly higher than observed in soils with C3 type vegetation. As with C3 vegetated soils, branched GDGT δ13C values are slightly depleted (1‰) relative to bulk organic carbon and enriched (ca. 5‰) relative to n-alkanes in this soil. The δ13C values of branched GDGT lipids being similar to bulk organic carbon and their co-variation with those of bulk organic carbon and plant waxes, suggest a heterotrophic life style and assimilation of relatively heavy and likely labile substrates for the as yet unknown soil bacteria that synthesise the branched GDGT lipids. However, a chemoautotrophic lifestyle, i.e. consuming respired CO2, could not be fully excluded based on these data alone. Based on a natural labelling experiment of a C3/C4 crop change introduced on one of the soils 23 years before sampling and based on a free air CO2 enrichment experiment with labelled CO2 on another soil, a turnover time of ca. 17 years has been estimated for branched GDGTs in these arable soils.

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.

The Carbon:²³⁴Thorium ratios of sinking particles in the California Current Ecosystem 2: Examination of a thorium sorption, desorption, and particle transport model

2019 ◽  
Author(s):  
Michael Stukel ◽  
Thomas Kelly
Keyword(s):  
Organic Carbon ◽  
Water Column ◽  
Particulate Organic Carbon ◽  
Transport Model ◽  
California Current ◽  
In Situ Measurements ◽  
Power Law Distribution ◽  
Sinking Particles ◽  
Organic Carbon Concentration

Thorium-234 (234Th) is a powerful tracer of particle dynamics and the biological pump in the surface ocean; however, variability in carbon:thorium ratios of sinking particles adds substantial uncertainty to estimates of organic carbon export. We coupled a mechanistic thorium sorption and desorption model to a one-dimensional particle sinking model that uses realistic particle settling velocity spectra. The model generates estimates of 238U-234Th disequilibrium, particulate organic carbon concentration, and the C:234Th ratio of sinking particles, which are then compared to in situ measurements from quasi-Lagrangian studies conducted on six cruises in the California Current Ecosystem. Broad patterns observed in in situ measurements, including decreasing C:234Th ratios with depth and a strong correlation between sinking C:234Th and the ratio of vertically-integrated particulate organic carbon (POC) to vertically-integrated total water column 234Th, were accurately recovered by models assuming either a power law distribution of sinking speeds or a double log normal distribution of sinking speeds. Simulations suggested that the observed decrease in C:234Th with depth may be driven by preferential remineralization of carbon by particle-attached microbes. However, an alternate model structure featuring complete consumption and/or disaggregation of particles by mesozooplankton (e.g. no preferential remineralization of carbon) was also able to simulate decreasing C:234Th with depth (although the decrease was weaker), driven by 234Th adsorption onto slowly sinking particles. Model results also suggest that during bloom decays C:234Th ratios of sinking particles should be higher than expected (based on contemporaneous water column POC), because high settling velocities minimize carbon remineralization during sinking.

scholarly journals Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

2020 ◽  
Vol 9 (1) ◽  
pp. 64
Author(s):  
Maija Nuppunen-Puputti ◽  
Riikka Kietäväinen ◽  
Lotta Purkamo ◽  
Pauliina Rajala ◽  
Merja Itävaara ◽  
...  
Keyword(s):  
Significant Proportion ◽  
Debaryomyces Hansenii ◽  
Fungal Communities ◽  
Fungal Colonization ◽  
Rock Surface ◽  
Mica Schist ◽  
Deep Subsurface ◽  
Bacterial Phyla ◽  
In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

scholarly journals Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein DivIVA

2021 ◽  
Vol 22 (15) ◽  
pp. 8350
Author(s):  
Naďa Labajová ◽  
Natalia Baranova ◽  
Miroslav Jurásek ◽  
Robert Vácha ◽  
Martin Loose ◽  
...  
Keyword(s):  
Cell Division ◽  
Lipid Bilayers ◽  
Bacterial Cell ◽  
Lipid Membranes ◽  
Model Organism ◽  
Active Role ◽  
Membrane Curvature ◽  
Bacterial Cell Division ◽  
Division Site ◽  
Clostridioides Difficile

DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane.

scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

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 Lipidomics Provides New Insight into Pathogenesis and Therapeutic Targets of the Ischemia—Reperfusion Injury

2021 ◽  
Vol 22 (6) ◽  
pp. 2798
Author(s):  
Zoran Todorović ◽  
Siniša Đurašević ◽  
Maja Stojković ◽  
Ilijana Grigorov ◽  
Slađan Pavlović ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Time Course ◽  
Membrane Lipids ◽  
Lipid Analysis ◽  
Cell Damage ◽  
Ischemia Reperfusion ◽  
Enzyme Inactivation ◽  
Critical Event ◽  
Tissue Ischemia ◽  
Insight Into

Lipids play an essential role in both tissue protection and damage. Tissue ischemia creates anaerobic conditions in which enzyme inactivation occurs, and reperfusion can initiate oxidative stress that leads to harmful changes in membrane lipids, the formation of aldehydes, and chain damage until cell death. The critical event in such a series of harmful events in the cell is the unwanted accumulation of fatty acids that leads to lipotoxicity. Lipid analysis provides additional insight into the pathogenesis of ischemia/reperfusion (I/R) disorders and reveals new targets for drug action. The profile of changes in the composition of fatty acids in the cell, as well as the time course of these changes, indicate both the mechanism of damage and new therapeutic possibilities. A therapeutic approach to reperfusion lipotoxicity involves attenuation of fatty acids overload, i.e., their transport to adipose tissue and/or inhibition of the adverse effects of fatty acids on cell damage and death. The latter option involves using PPAR agonists and drugs that modulate the transport of fatty acids via carnitine into the interior of the mitochondria or the redirection of long-chain fatty acids to peroxisomes.

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