Polyphosphates (PolyP), i.e. phosphate polymers, are commonly found in pure cultures of various microorganisms. Although they have been the subject of intensive microbiological research in the past, they have never been directly studied in species-rich soil microbial communities. So far, there are only few studies indirectly suggesting that soil microorganisms build up PolyP as a storage for phosphorus (P), and use them when soil P availability decreases. We attempted to provide direct evidence for PolyP presence in soil microorganisms, and test if the PolyP can be detected in the soil microbial biomass P pool applying the standard chloroform-fumigation extraction method. Twelve different soil samples were collected along the gradient of forest recovery after the bark beetle outbreak in the catchments of two adjacent glacier lakes (Plešné and Čertovo, Bohemian forest, Czech Republic). The presence of PolyP in the samples was assessed by staining in a manipulative experiment designed to deplete any PolyP present. Carbon (C), nitrogen (N), and P in the microbial biomass were estimated by the chloroform-fumigation extraction method and soil slurries of fresh samples stained by the Neisser method. The soils were then mixed with sterile sand and supplemented with growth medium without P. The rate of growth of microbial biomass was estimated from oxygen consumption during one week incubation at dark. After one week, the microbial biomass C, N, and the P were estimated again and samples stained. The combination of the incubation experiment and staining proved that the soil microorganisms in the collected samples contained PolyP and that PolyP were used to achieve maximum growth rate under P-limited conditions. The C to N to P ratio increased significantly over one week of incubation reflecting the changing PolyP content. To further confirm that the fumigation extraction method is sensitive to PolyP content, manufactured PolyP was added to all soils at different steps of the fumigation extraction method, and its recovery was estimated. Recovery ranged from 80 to 100%. Abiotic depolymerisation at acidic conditions required for the correct quantification of P-PO 4 using molybdenum-blue method was very likely responsible for half of the recovery, the remaining being enzymatic depolymerisation. We conclude that PolyP are ubiquitous in soils and affect microbial biomass P estimation. The high recovery rate of PolyP around 90% implies that presence of PolyP can cause a significant overestimation of the microbial biomass P when typical correction factor 0.4 is used.
聚磷酸盐(PolyP)，即磷酸盐聚合物，通常存在于各种微生物的纯培养物中。虽然它们在过去一直是微生物学研究的重点，但它们从未在物种丰富的土壤微生物群落中被直接研究过。到目前为止，只有很少的研究间接地表明土壤微生物建立息肉作为磷(P)的储存，并在土壤P有效性降低时利用它们。我们试图提供PolyP在土壤微生物中存在的直接证据，并使用标准的氯仿熏蒸提取方法测试PolyP是否可以在土壤微生物生物量P库中检测到。在邻近的两个冰川湖(Plešné和Čertovo，波西米亚森林，捷克共和国)的集水区，沿树皮甲虫爆发后森林恢复的梯度收集了12种不同的土壤样品。在一个操作实验中，通过染色来评估样品中息肉的存在，该实验旨在消除任何息肉。微生物生物量中的碳(C)、氮(N)和磷(P)通过氯仿熏蒸提取法和Neisser法染色的新鲜样品土壤浆液进行估算。然后将土壤与无菌砂混合，并补充不含磷的生长培养基，通过黑暗培养1周的耗氧量估算微生物生物量的生长速度。一周后，再次测定微生物生物量C、N和P，并对样品进行染色。培养实验和染色相结合，证明了所采集样品中的土壤微生物中含有PolyP，并且在限制p的条件下，PolyP的生长速度最大。C / N / P比值在1周内显著升高，反映出息肉P含量的变化。为了进一步证实熏蒸提取方法对PolyP含量的敏感性，在熏蒸提取方法的不同步骤中，将制备好的PolyP添加到所有土壤中，并估计其回收率。回收率从80%到100%不等。在酸性条件下，使用钼蓝法正确定量p - po4所需的非生物解聚很可能占回收率的一半，其余的是酶解聚合。我们认为，水螅体在土壤中普遍存在，并影响微生物生物量磷的估算。PolyP的高回收率约为90%，这意味着当使用典型的校正因子0.4时，PolyP的存在会导致微生物生物量P的显著高估。
{"title":"On the presence and detectability of polyphosphates in soil microbial biomass","authors":"Petr Čapek, Adéla Tupá","doi":"10.3897/aca.6.e108187","DOIUrl":"https://doi.org/10.3897/aca.6.e108187","url":null,"abstract":"Polyphosphates (PolyP), i.e. phosphate polymers, are commonly found in pure cultures of various microorganisms. Although they have been the subject of intensive microbiological research in the past, they have never been directly studied in species-rich soil microbial communities. So far, there are only few studies indirectly suggesting that soil microorganisms build up PolyP as a storage for phosphorus (P), and use them when soil P availability decreases. We attempted to provide direct evidence for PolyP presence in soil microorganisms, and test if the PolyP can be detected in the soil microbial biomass P pool applying the standard chloroform-fumigation extraction method. Twelve different soil samples were collected along the gradient of forest recovery after the bark beetle outbreak in the catchments of two adjacent glacier lakes (Plešné and Čertovo, Bohemian forest, Czech Republic). The presence of PolyP in the samples was assessed by staining in a manipulative experiment designed to deplete any PolyP present. Carbon (C), nitrogen (N), and P in the microbial biomass were estimated by the chloroform-fumigation extraction method and soil slurries of fresh samples stained by the Neisser method. The soils were then mixed with sterile sand and supplemented with growth medium without P. The rate of growth of microbial biomass was estimated from oxygen consumption during one week incubation at dark. After one week, the microbial biomass C, N, and the P were estimated again and samples stained. The combination of the incubation experiment and staining proved that the soil microorganisms in the collected samples contained PolyP and that PolyP were used to achieve maximum growth rate under P-limited conditions. The C to N to P ratio increased significantly over one week of incubation reflecting the changing PolyP content. To further confirm that the fumigation extraction method is sensitive to PolyP content, manufactured PolyP was added to all soils at different steps of the fumigation extraction method, and its recovery was estimated. Recovery ranged from 80 to 100%. Abiotic depolymerisation at acidic conditions required for the correct quantification of P-PO 4 using molybdenum-blue method was very likely responsible for half of the recovery, the remaining being enzymatic depolymerisation. We conclude that PolyP are ubiquitous in soils and affect microbial biomass P estimation. The high recovery rate of PolyP around 90% implies that presence of PolyP can cause a significant overestimation of the microbial biomass P when typical correction factor 0.4 is used.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135992642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S Ruff, Pauline Humez, Isabella Hrabe de Angelis, Muhe Diao, Michael Nightingale, Sara Cho, Liam Connors, Olukayode Kuloyo, Alan Seltzer, Samuel Bowman, Scott Wankel, Cynthia McClain, Bernhard Mayer, Marc Strous
Around 50% of humankind relies on groundwater as a source of drinking water. We investigated the age, geochemistry, and microbiology of 138 groundwater samples from 87 monitoring wells (<250 m depth) located in 14 aquifers in Canada (Fig. 1). Geochemistry and microbiology showed consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contained on average more cells than younger groundwaters, challenging current estimates of subsurface cell abundances. We observed substantial concentrations of dissolved oxygen in older groundwaters that could support aerobic lifestyles in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicated that “dark oxygen” was produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth Ruff et al. 2023). Title, Abstract, and Figure 1 are reproduced from (Ruff et al. 2023) without adaptations, according to the terms of http://creativecommons.org/licenses/by/4.0/.
大约50%的人类依赖地下水作为饮用水的来源。我们研究了来自加拿大14个含水层87口监测井(深度250 m)的138个地下水样本的年龄、地球化学和微生物学(图1)。地球化学和微生物学显示出一致的趋势，表明不同的微生物群落进行了大规模的好氧和厌氧氢、甲烷、氮和硫循环。较老的地下水，特别是在富有机碳地层的含水层中，平均比较年轻的地下水含有更多的细胞，这对目前对地下细胞丰度的估计提出了挑战。我们在古老的地下水中观察到大量的溶解氧，这些溶解氧可以在前所未有的规模上支持地下生态系统中的有氧生活方式。宏基因组学、氧同位素分析和混合模型表明，“暗氧”是通过微生物突变在原位产生的。我们表明，古代地下水维持了生产性群落，并强调了地球现在和过去地下生态系统中被忽视的氧气来源(Ruff等人，2023)。根据http://creativecommons.org/licenses/by/4.0/的条款，标题、摘要和图1摘自(Ruff et al. 2023)，未经改编。
{"title":"Hydrogen and Dark Oxygen drive Microbial Productivity in diverse Groundwater Ecosystems","authors":"S Ruff, Pauline Humez, Isabella Hrabe de Angelis, Muhe Diao, Michael Nightingale, Sara Cho, Liam Connors, Olukayode Kuloyo, Alan Seltzer, Samuel Bowman, Scott Wankel, Cynthia McClain, Bernhard Mayer, Marc Strous","doi":"10.3897/aca.6.e108163","DOIUrl":"https://doi.org/10.3897/aca.6.e108163","url":null,"abstract":"Around 50% of humankind relies on groundwater as a source of drinking water. We investigated the age, geochemistry, and microbiology of 138 groundwater samples from 87 monitoring wells (&lt;250 m depth) located in 14 aquifers in Canada (Fig. 1). Geochemistry and microbiology showed consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contained on average more cells than younger groundwaters, challenging current estimates of subsurface cell abundances. We observed substantial concentrations of dissolved oxygen in older groundwaters that could support aerobic lifestyles in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicated that “dark oxygen” was produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth Ruff et al. 2023). Title, Abstract, and Figure 1 are reproduced from (Ruff et al. 2023) without adaptations, according to the terms of http://creativecommons.org/licenses/by/4.0/.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135993498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ivan Strakhov, Zach DiLoreto, Jassim Al-Khayat, Maria Dittrich
Deep insight into the low-temperature mineralization mechanism of dolomite in sediments has remained elusive. This issue is popularly termed “The Dolomite Problem” due to its multifactorial nature. Dolomite has been observed to mineralize in the exopolymeric substances produced by microbial mat communities (Bontognali et al. 2013), where productivity is high. One working hypothesis suggests that degrading organic matter in hypersaline environments releases the necessary component ions, increasing saturation with respect to dolomite (DiLoreto et al. 2019, Dupraz et al. 2009, Petrash et al. 2017). Other models suggest a dissolution-reprecipitation reaction of calcite to dolomite (Rivers 2023). High-resolution micro-spectroscopy techniques (such as transmission electron microscopy, TEM; and scanning transmission X-ray microscopy, STXM) can be used to determine chemical changes in crystals nucleating in a matrix, however to date very little studies have focused on observing dolomite mineralization at the nano-scale. The present study investigates microbial mats collected from hypersaline salt flats in the Persian gulf at micro- to nano-meter scales using high-spatial and -energy resolution TEM (Thermo Scientific Talos 200X at the Canadian Centre for Electron Microscopy) and STXM (PolLux Beamline at the Swiss Light Source at Paul Scherrer Institut), specifically to see changes in carbonate mineralization due to interactions with organic matter. C, Ca and O elemental maps of carbonate crystals were obtained with EDXS (energy-dispersive X-ray spectroscopy) in TEM. These crystals were also indexed by SAED (selected area electron diffraction in TEM). Fine spectral signatures (near-edge X-ray absorption fine structures, or NEXAFS) at the C K-edge (280-290 eV) and Ca L 2,3 -edge (344-356 eV) in STXM were used to determine the chemical identity of carbonate minerals and surrounding organic matter of the microbial mats. The results of the study show that dolomite nucleates in close association with the organic matter of the mats, where degradation is highest (defined in our adjacent study as the increase in C:N ratio). In TEM, polycrystalline dolomite is seen mineralizing in the matrix of the microbial mat organic material (Fig. 1). In STXM, the identity of the carbonate mineral changes from calcite on the outside to dolomite on the inside of the microbial mat particle (Fig. 2). In addition, our microsensor observations of elevated H 2 S concentrations, surface oxygenation from oxygenic phototrophy, high reduction potential, high organic carbon, high Mg:Ca ratio and high organic matter degradation (by C:N ratio) in each of the studied microbial mats confirms that the ideal dolomite mineralization conditions according to models of the dolomite problem are present in each case.
{"title":"Organomineralization of dolomite in hypersaline microbial mats from Qatar sabkhas visualized by TEM &amp; STXM","authors":"Ivan Strakhov, Zach DiLoreto, Jassim Al-Khayat, Maria Dittrich","doi":"10.3897/aca.6.e108262","DOIUrl":"https://doi.org/10.3897/aca.6.e108262","url":null,"abstract":"Deep insight into the low-temperature mineralization mechanism of dolomite in sediments has remained elusive. This issue is popularly termed “The Dolomite Problem” due to its multifactorial nature. Dolomite has been observed to mineralize in the exopolymeric substances produced by microbial mat communities (Bontognali et al. 2013), where productivity is high. One working hypothesis suggests that degrading organic matter in hypersaline environments releases the necessary component ions, increasing saturation with respect to dolomite (DiLoreto et al. 2019, Dupraz et al. 2009, Petrash et al. 2017). Other models suggest a dissolution-reprecipitation reaction of calcite to dolomite (Rivers 2023). High-resolution micro-spectroscopy techniques (such as transmission electron microscopy, TEM; and scanning transmission X-ray microscopy, STXM) can be used to determine chemical changes in crystals nucleating in a matrix, however to date very little studies have focused on observing dolomite mineralization at the nano-scale. The present study investigates microbial mats collected from hypersaline salt flats in the Persian gulf at micro- to nano-meter scales using high-spatial and -energy resolution TEM (Thermo Scientific Talos 200X at the Canadian Centre for Electron Microscopy) and STXM (PolLux Beamline at the Swiss Light Source at Paul Scherrer Institut), specifically to see changes in carbonate mineralization due to interactions with organic matter. C, Ca and O elemental maps of carbonate crystals were obtained with EDXS (energy-dispersive X-ray spectroscopy) in TEM. These crystals were also indexed by SAED (selected area electron diffraction in TEM). Fine spectral signatures (near-edge X-ray absorption fine structures, or NEXAFS) at the C K-edge (280-290 eV) and Ca L 2,3 -edge (344-356 eV) in STXM were used to determine the chemical identity of carbonate minerals and surrounding organic matter of the microbial mats. The results of the study show that dolomite nucleates in close association with the organic matter of the mats, where degradation is highest (defined in our adjacent study as the increase in C:N ratio). In TEM, polycrystalline dolomite is seen mineralizing in the matrix of the microbial mat organic material (Fig. 1). In STXM, the identity of the carbonate mineral changes from calcite on the outside to dolomite on the inside of the microbial mat particle (Fig. 2). In addition, our microsensor observations of elevated H 2 S concentrations, surface oxygenation from oxygenic phototrophy, high reduction potential, high organic carbon, high Mg:Ca ratio and high organic matter degradation (by C:N ratio) in each of the studied microbial mats confirms that the ideal dolomite mineralization conditions according to models of the dolomite problem are present in each case.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"172 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135993545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microorganisms have the capability to produce antimicrobial compounds through secondary metabolism, which are not essential within their natural environments, but have been found to have many effects on the ecosystem. Antimicrobial production genes have been identified in a wide range of microorganisms; however, research into natural ecosystems has historically been limited to continental soil environments. Antimicrobial production research has been limited in the deep continental subsurface and marine environments, especially deeply buried marine sediments. We analyzed 466 high-quality metagenome assembled genomes (MAGs) collected from continental and marine subsurface environments through the Deep Carbon Observatory’s Census of Deep Life. A total of 383 MAGs contained biosynthetic gene clusters, namely Type I and Type III polyketide synthase genes, non-ribosomal peptide synthetase genes, and other unspecified ribosomally synthesized and post-translationally modified peptide products. All of these genes were found across continental mines, subglacial lakes, hotsprings, and serpentinizing environments. These environments have previously not been investigated via metagenomics for antimicrobial gene diversity, which may be produced for competition or communication purposes. All other biosynthetic genes identified in this study were less than 50% similar to reference biosynthesis genes indicating the novelty of secondary metabolism in subsurface microorganisms. The majority of predicted antimicrobial products were found to be produced exergonically, which could indicate microbial populations use energy-conserving mechanisms to produce compounds that could offer a competitive advantage.
{"title":"Global distribution and diversity of antimicrobial genes across subsurface bacterial and archaeal metagenome assembled genomes","authors":"Brandi Kiel Reese, Megan Mullis, Jason Selwyn","doi":"10.3897/aca.6.e108167","DOIUrl":"https://doi.org/10.3897/aca.6.e108167","url":null,"abstract":"Microorganisms have the capability to produce antimicrobial compounds through secondary metabolism, which are not essential within their natural environments, but have been found to have many effects on the ecosystem. Antimicrobial production genes have been identified in a wide range of microorganisms; however, research into natural ecosystems has historically been limited to continental soil environments. Antimicrobial production research has been limited in the deep continental subsurface and marine environments, especially deeply buried marine sediments. We analyzed 466 high-quality metagenome assembled genomes (MAGs) collected from continental and marine subsurface environments through the Deep Carbon Observatory’s Census of Deep Life. A total of 383 MAGs contained biosynthetic gene clusters, namely Type I and Type III polyketide synthase genes, non-ribosomal peptide synthetase genes, and other unspecified ribosomally synthesized and post-translationally modified peptide products. All of these genes were found across continental mines, subglacial lakes, hotsprings, and serpentinizing environments. These environments have previously not been investigated via metagenomics for antimicrobial gene diversity, which may be produced for competition or communication purposes. All other biosynthetic genes identified in this study were less than 50% similar to reference biosynthesis genes indicating the novelty of secondary metabolism in subsurface microorganisms. The majority of predicted antimicrobial products were found to be produced exergonically, which could indicate microbial populations use energy-conserving mechanisms to produce compounds that could offer a competitive advantage.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135993636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jerzy Weber, Peter Leinweber, Yakov Kuzyakov, Edyta Hewelke, Magdalena Frąc, Michael Hayes, Vaclovas Boguzas, Andy Gregory, Lilla Mielnik, Urszula Norton, Maria Jerzykiewicz, Magdalena Debicka, Elżbieta Jamroz, Irmina Ćwieląg-Piasecka, Andrzej Kocowicz
SOMPACS is a project recommended by EJP SOIL for funding under the 1st External Call "Towards Healthy, Resilient and Sustainable Agricultural Soils". The goal of this project is to assess management practices that enrich organic matter pools that are resilient to rapid microbial decomposition. The project started in 2022 as a consortium of 12 research institutions from Poland, Germany, Ireland, Lithuania, UK, Italy and USA for a period of three years. Soil and vegetation samples from eight long-term experiments that differ in soil management practices (i.e., conventional vs. no-tillage; mineral vs. organic fertilization; with and without catch crop; and arable land vs. undisturbed grassland) are investigated. Study sites include: 22- and 54-year long experiments in Lithuania; 26-year long experiment in Italy; 30- and 40-year long experiments in Ireland; 30- and 46- and 100-year long experiments in Poland; and 178-year long Broadbalk experiment in Great Britain. Additional experimentation includes assessing the impact of root growth promoting amendments (commercially available humic substances, biochar and biogas digestate) on stable organic matter pools. In parallel with soil sampling, plant productivity are measured in all field experiments. This investigation is couples fields studies with small-scale experimental plots and laboratory incubations under controlled conditions. In addition to assessing basic soil properties, the following state-of-the-art analyses are conducted: SOM composition and stability by Py-GC-MS; fractionation of aggregate size classes and C pools of increasing physicochemical protection; isotopic analysis of δ13C and δ15N performed on different SOM pools; microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism); enzymatic activity; soil water retention and soil water repellency; mineral composition of clay fraction; (8) soil structure stability. SOM composition and stability by Py-GC-MS; fractionation of aggregate size classes and C pools of increasing physicochemical protection; isotopic analysis of δ13C and δ15N performed on different SOM pools; microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism); enzymatic activity; soil water retention and soil water repellency; mineral composition of clay fraction; (8) soil structure stability. The most resistant SOM pool (humin) are isolated by different methods (isolation vs. extraction) and examined for chemical composition and structure, using spectrometric and spectroscopic techniques (mass spectrometry, NMR, FTIR, EPR
{"title":"Soil management effects on soil organic matter properties and carbon sequestration (SOMPACS)","authors":"Jerzy Weber, Peter Leinweber, Yakov Kuzyakov, Edyta Hewelke, Magdalena Frąc, Michael Hayes, Vaclovas Boguzas, Andy Gregory, Lilla Mielnik, Urszula Norton, Maria Jerzykiewicz, Magdalena Debicka, Elżbieta Jamroz, Irmina Ćwieląg-Piasecka, Andrzej Kocowicz","doi":"10.3897/aca.6.e108213","DOIUrl":"https://doi.org/10.3897/aca.6.e108213","url":null,"abstract":"SOMPACS is a project recommended by EJP SOIL for funding under the 1st External Call \"Towards Healthy, Resilient and Sustainable Agricultural Soils\". The goal of this project is to assess management practices that enrich organic matter pools that are resilient to rapid microbial decomposition. The project started in 2022 as a consortium of 12 research institutions from Poland, Germany, Ireland, Lithuania, UK, Italy and USA for a period of three years.\u0000 Soil and vegetation samples from eight long-term experiments that differ in soil management practices (i.e., conventional vs. no-tillage; mineral vs. organic fertilization; with and without catch crop; and arable land vs. undisturbed grassland) are investigated. Study sites include: 22- and 54-year long experiments in Lithuania; 26-year long experiment in Italy; 30- and 40-year long experiments in Ireland; 30- and 46- and 100-year long experiments in Poland; and 178-year long Broadbalk experiment in Great Britain. Additional experimentation includes assessing the impact of root growth promoting amendments (commercially available humic substances, biochar and biogas digestate) on stable organic matter pools. In parallel with soil sampling, plant productivity are measured in all field experiments. This investigation is couples fields studies with small-scale experimental plots and laboratory incubations under controlled conditions. In addition to assessing basic soil properties, the following state-of-the-art analyses are conducted:\u0000 \u0000 \u0000 \u0000 SOM composition and stability by Py-GC-MS;\u0000 \u0000 \u0000 fractionation of aggregate size classes and C pools of increasing physicochemical protection;\u0000 \u0000 \u0000 isotopic analysis of δ13C and δ15N performed on different SOM pools;\u0000 \u0000 \u0000 microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism);\u0000 \u0000 \u0000 enzymatic activity;\u0000 \u0000 \u0000 soil water retention and soil water repellency;\u0000 \u0000 \u0000 mineral composition of clay fraction; (8) soil structure stability.\u0000 \u0000 \u0000 \u0000 SOM composition and stability by Py-GC-MS;\u0000 fractionation of aggregate size classes and C pools of increasing physicochemical protection;\u0000 isotopic analysis of δ13C and δ15N performed on different SOM pools;\u0000 microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism);\u0000 enzymatic activity;\u0000 soil water retention and soil water repellency;\u0000 mineral composition of clay fraction; (8) soil structure stability.\u0000 The most resistant SOM pool (humin) are isolated by different methods (isolation vs. extraction) and examined for chemical composition and structure, using spectrometric and spectroscopic techniques (mass spectrometry, NMR, FTIR, EPR","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135995959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guaymas Basin, located in the Gulf of California, Mexico, is a young marginal ocean basin with high sedimentation rates of >1 mm/year, active seafloor spreading, and steep geothermal gradients in its sediment. It hosts a unique microbial subseafloor biosphere as these conditions lead to thermal cracking of sedimentary organic matter and the production of bioavailable organic carbon compounds and hydrocarbons already at shallow depths. The abundance and diversity of potential microbial substrates raise the question of which substrates are being used for catabolic and anabolic microbial metabolism. We thus analyzed the microbial uptake of hydrocarbons and inorganic nitrogen using nanoscale secondary ion mass spectrometry (NanoSIMS) analysis after incubation with stable-isotope labeled substrates. Incubations were carried out with samples from two International Ocean Discovery Program (IODP) Exp. 385 drill sites. Site U1545 is characterized by undisturbed sedimentary strata and a temperature gradient of 225°C/km, whereas Site U1546 has experienced a sill intrusion at greater depth, below the cored interval. The intrusion led to temporary heating of the sediment, but a temperature gradient of 221°C/km indicates thermal equilibration with the surrounding sediment since sill emplacement. Incubations were carried out with 13 C-benzene + 2 H-hexadecane + 15 NH 4 Cl or 13 C-methane + 15 NH 4 Cl at in-situ temperature (4-62°C) and pressure (25 MPa) for 42 days. Additionally, sulfate reduction rates (SRR) were measured by incubating the samples with four aliphatic hydrocarbons + four aromatic hydrocarbons or methane and radioisotope-labeled 35 SO 4 2- for 10 days, also at in-situ temperature and pressure. The NanoSIMS analyses reveal that a few samples showed detectable microbial assimilation of hydrocarbons. Nitrogen was significantly assimilated in some samples incubated with methane. The assimilation mostly occurred in samples from near the seafloor (2 and 44 meter below seafloor (mbsf)). Our results indicate that anaerobic microorganisms in Guaymas Basin take up measurable amounts of hydrocarbons and inorganic nitrogen even in the relatively short incubation time of 42 days. The results of the SRR measurements indicate that a mixture of hydrocarbons and methane increases the SRR in samples from near the seafloor (2 mbsf) and around the sulfate-methane transition zone (44 and 55 mbsf) but not in samples from greater depths. Our results show that anaerobic microorganisms in Guaymas Basin can use hydrocarbons for anabolic and catabolic metabolism in this extreme environment. Given the high abundance of various carbon compounds, nitrogen appears to be a limiting factor for cellular growth.
{"title":"Anabolic and Catabolic Microbial Activity in Hydrocarbon-rich Sediments of Guaymas Basin","authors":"Toshiki Nagakura, Yuki Morono, Motoo Ito, Jens Kallmeyer","doi":"10.3897/aca.6.e108382","DOIUrl":"https://doi.org/10.3897/aca.6.e108382","url":null,"abstract":"Guaymas Basin, located in the Gulf of California, Mexico, is a young marginal ocean basin with high sedimentation rates of &gt;1 mm/year, active seafloor spreading, and steep geothermal gradients in its sediment. It hosts a unique microbial subseafloor biosphere as these conditions lead to thermal cracking of sedimentary organic matter and the production of bioavailable organic carbon compounds and hydrocarbons already at shallow depths. The abundance and diversity of potential microbial substrates raise the question of which substrates are being used for catabolic and anabolic microbial metabolism. We thus analyzed the microbial uptake of hydrocarbons and inorganic nitrogen using nanoscale secondary ion mass spectrometry (NanoSIMS) analysis after incubation with stable-isotope labeled substrates. Incubations were carried out with samples from two International Ocean Discovery Program (IODP) Exp. 385 drill sites. Site U1545 is characterized by undisturbed sedimentary strata and a temperature gradient of 225°C/km, whereas Site U1546 has experienced a sill intrusion at greater depth, below the cored interval. The intrusion led to temporary heating of the sediment, but a temperature gradient of 221°C/km indicates thermal equilibration with the surrounding sediment since sill emplacement. Incubations were carried out with 13 C-benzene + 2 H-hexadecane + 15 NH 4 Cl or 13 C-methane + 15 NH 4 Cl at in-situ temperature (4-62°C) and pressure (25 MPa) for 42 days. Additionally, sulfate reduction rates (SRR) were measured by incubating the samples with four aliphatic hydrocarbons + four aromatic hydrocarbons or methane and radioisotope-labeled 35 SO 4 2- for 10 days, also at in-situ temperature and pressure. The NanoSIMS analyses reveal that a few samples showed detectable microbial assimilation of hydrocarbons. Nitrogen was significantly assimilated in some samples incubated with methane. The assimilation mostly occurred in samples from near the seafloor (2 and 44 meter below seafloor (mbsf)). Our results indicate that anaerobic microorganisms in Guaymas Basin take up measurable amounts of hydrocarbons and inorganic nitrogen even in the relatively short incubation time of 42 days. The results of the SRR measurements indicate that a mixture of hydrocarbons and methane increases the SRR in samples from near the seafloor (2 mbsf) and around the sulfate-methane transition zone (44 and 55 mbsf) but not in samples from greater depths. Our results show that anaerobic microorganisms in Guaymas Basin can use hydrocarbons for anabolic and catabolic metabolism in this extreme environment. Given the high abundance of various carbon compounds, nitrogen appears to be a limiting factor for cellular growth.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136032660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annette Engel, Mireille Steck, Audrey Paterson, Amir Van Gieson, Megan Porter, Rebecca Chong
Roots are common features in basaltic lava tube caves on the island of Hawai‘i. For the past 50 years, new species of cave-adapted invertebrates, including cixiid planthoppers, crickets, thread-legged bugs, and spiders, have been discovered from root patches in lava tubes on different volcanoes and across variable climatic conditions. Assessing vegetation on the surface above lava tube passages, as well as genetic characterization of roots from within lava tubes, suggest that most roots belong to the native pioneer tree, ‘ōhi‘a lehua ( Metrosideros polymorpha ). Planthoppers are the primary consumers of sap at the base of the subsurface food web. However, root physicochemistry and rhizobiome microbial diversity and functional potential have received little attention. This study focuses on characterizing the ‘ōhi‘a rhizobiome, accessed from free-hanging roots inside lava tubes. Using these results, we can begin to evaluate the development and evolution of plant-microbe-invertebrate relationships. We explored lava tubes formed in flows of differing elevations and ages, from about 140 to 3000 years old, on Mauna Loa, Kīlauea, and Hualālai volcanoes on Hawai‘i Island. Invertebrate diversity was evaluated from root galleries and non-root galleries, in situ fluid physicochemistry was measured, and root and bare rock fluids (e.g., water, sap) were collected to determine major ion concentrations, as well as non-purgeable organic carbon (NPOC) and total nitrogen (TN) content. To verify root identity, DNA was extracted, and three sets of primers were used. After screening for only Metrosideros spp., the V4 region of the 16S rRNA gene was sequenced and taxonomy was assigned. Root fluids were viscous and ranged in color from clear to yellow to reddish orange. Root fluids had 2X to 10X higher major ion concentrations compared to rock water. The average root NPOC and TN concentrations were 192 mg/L and 5.2 mg/L, respectively, compared to rock water that had concentrations of 6.8 mg/L and 1.8 mg/L, respectively. Fluids from almost 300 root samples had pH values that ranged from 2.2 to 5.6 (average pH 4.63) and were lower than rock water (average pH 6.39). Root fluid pH was comparable to soil pH from montane wet forests dominated by ‘ōhi‘a (Selmants et al. 2016), which can grow in infertile soil with pH values as low as 3.6. On Hawai‘i, rain water pH averages 5.2 at sea level and systematically decreases with elevation to pH 4.3 at 2500 m (Miller and Yoshinaga 2012), but root fluid pH did not correlate with elevation, temperature, relative humidity, inorganic and organic constituents, or age of flow. Root fluid acidity is likely due to concentrated organic compounds, sourced as root exudates, and this habitat is acidic for the associated invertebrates. From 62 root samples, over 66% were identified to the genus Metrosideros . A few other identifications of roots from lava tube systems where there had been extensive clear-cutting and ranching included monkey pod
根是夏威夷岛上玄武岩熔岩管洞的共同特征。在过去的50年里，在不同的火山和不同的气候条件下，在熔岩管的根部斑块中发现了新的洞穴适应无脊椎动物物种，包括水栖飞虱、蟋蟀、丝腿虫和蜘蛛。评估熔岩管通道上方表面的植被，以及熔岩管内根系的遗传特征，表明大多数根系属于本地先锋树' ōhi ' a lehua (Metrosideros polymorpha)。飞虱是地下食物网底部汁液的主要消费者。然而，对根系物理化学和根瘤菌群微生物多样性和功能潜力的研究却很少受到重视。本研究的重点是表征“ōhi”根瘤菌群，从熔岩管内自由悬挂的根中获取。利用这些结果，我们可以开始评估植物-微生物-无脊椎动物关系的发展和进化。我们探索了在夏威夷岛的莫纳罗亚火山、kk lauea火山和Hualālai火山上形成的不同海拔和年龄的熔岩管，从大约140年到3000年不等。从根廊和非根廊评估无脊椎动物多样性，测量原位流体物理化学，收集根和裸岩流体(如水、树液)以确定主要离子浓度，以及不可净化有机碳(NPOC)和总氮(TN)含量。为了验证根的身份，提取DNA，使用三组引物。筛选到单株Metrosideros spp.后，对其16S rRNA基因V4区进行测序并进行分类。根液是粘稠的，颜色从透明到黄色到红橙色不等。根液的主要离子浓度比岩石水高2至10倍。与岩石水的平均NPOC和TN浓度分别为6.8 mg/L和1.8 mg/L相比，其根平均NPOC和TN浓度分别为192 mg/L和5.2 mg/L。来自近300个根系样本的液体的pH值在2.2到5.6之间(平均pH值4.63)，低于岩水(平均pH值6.39)。根液pH值与以' ōhi ' a (Selmants et al. 2016)为主的山地湿润森林的土壤pH值相当，该森林可以在pH值低至3.6的贫瘠土壤中生长。在夏威夷，雨水的pH值在海平面上平均为5.2，在海拔2500米处随海拔高度系统地降低至pH值4.3 (Miller and Yoshinaga 2012)，但根液pH值与海拔、温度、相对湿度、无机和有机成分或水流年龄无关。根液的酸性可能是由于根分泌物中浓缩的有机化合物，而这个栖息地对相关的无脊椎动物来说是酸性的。从62份根样中鉴定出66%以上的根属属。在大量砍伐和放牧的熔岩管系统中，还发现了一些其他的树根，包括猴荚树、椰子树、榕树和丝栎。16S rRNA基因序列调查显示，根菌群落以burkholderaceae、Acetobacteraceae、Sphingomonadaceae、acidobacteraceae、Gemmataceae、Xanthobacteraceae和Chitinophagaceae等少数类群为主。然而，大多数的reads不能归类到一个特定的属，这表明根瘤菌群具有新的多样性。湿润气候的多样性更高。根群落不同于先前在“ōhi”中描述的花朵和叶子(Junker and Keller 2015)以及熔岩管岩石表面(Hathaway et al. 2014)，其中微生物群被特别假定能够异养、甲烷化、重氮化和硝化。尽管大多数分类群可能是需氧异养生物，但对根瘤菌群代谢的推断较少。在burkholderaceae中，与Paraburkholderia属相关的序列相对丰度较高，其中包括已知的植物共生体，以及来自Acetobacteraceae的嗜酸属Acidocella和Acidisoma，这些序列主要来自最古老的熔岩流洞穴中，这些洞穴也具有最低的根pH值。这些细菌群很可能能够降解渗出物，并为无脊椎动物提供营养基质，而这些营养基质不是单独由根液(即韧皮部)提供的。由于“ōhi”a的生物化学细节一直缺失，表征熔岩管中的根瘤菌群将有助于更好地了解植物-微生物-无脊椎动物的潜在相互作用以及随着时间的推移的生态和进化关系。
{"title":"Rhizobiome of ‘Ōhi‘a Lehua (Metrosideros polymorpha) Offers Insight into Plant-Microbe-Invertebrate Interactions in the Subsurface","authors":"Annette Engel, Mireille Steck, Audrey Paterson, Amir Van Gieson, Megan Porter, Rebecca Chong","doi":"10.3897/aca.6.e108263","DOIUrl":"https://doi.org/10.3897/aca.6.e108263","url":null,"abstract":"Roots are common features in basaltic lava tube caves on the island of Hawai‘i. For the past 50 years, new species of cave-adapted invertebrates, including cixiid planthoppers, crickets, thread-legged bugs, and spiders, have been discovered from root patches in lava tubes on different volcanoes and across variable climatic conditions. Assessing vegetation on the surface above lava tube passages, as well as genetic characterization of roots from within lava tubes, suggest that most roots belong to the native pioneer tree, ‘ōhi‘a lehua ( Metrosideros polymorpha ). Planthoppers are the primary consumers of sap at the base of the subsurface food web. However, root physicochemistry and rhizobiome microbial diversity and functional potential have received little attention. This study focuses on characterizing the ‘ōhi‘a rhizobiome, accessed from free-hanging roots inside lava tubes. Using these results, we can begin to evaluate the development and evolution of plant-microbe-invertebrate relationships. We explored lava tubes formed in flows of differing elevations and ages, from about 140 to 3000 years old, on Mauna Loa, Kīlauea, and Hualālai volcanoes on Hawai‘i Island. Invertebrate diversity was evaluated from root galleries and non-root galleries, in situ fluid physicochemistry was measured, and root and bare rock fluids (e.g., water, sap) were collected to determine major ion concentrations, as well as non-purgeable organic carbon (NPOC) and total nitrogen (TN) content. To verify root identity, DNA was extracted, and three sets of primers were used. After screening for only Metrosideros spp., the V4 region of the 16S rRNA gene was sequenced and taxonomy was assigned. Root fluids were viscous and ranged in color from clear to yellow to reddish orange. Root fluids had 2X to 10X higher major ion concentrations compared to rock water. The average root NPOC and TN concentrations were 192 mg/L and 5.2 mg/L, respectively, compared to rock water that had concentrations of 6.8 mg/L and 1.8 mg/L, respectively. Fluids from almost 300 root samples had pH values that ranged from 2.2 to 5.6 (average pH 4.63) and were lower than rock water (average pH 6.39). Root fluid pH was comparable to soil pH from montane wet forests dominated by ‘ōhi‘a (Selmants et al. 2016), which can grow in infertile soil with pH values as low as 3.6. On Hawai‘i, rain water pH averages 5.2 at sea level and systematically decreases with elevation to pH 4.3 at 2500 m (Miller and Yoshinaga 2012), but root fluid pH did not correlate with elevation, temperature, relative humidity, inorganic and organic constituents, or age of flow. Root fluid acidity is likely due to concentrated organic compounds, sourced as root exudates, and this habitat is acidic for the associated invertebrates. From 62 root samples, over 66% were identified to the genus Metrosideros . A few other identifications of roots from lava tube systems where there had been extensive clear-cutting and ranching included monkey pod ","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136033412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Over the course of this century, it will be important to identify cost effective/low maintenance solutions for treating contaminants in receiving watersheds. Adopting these strategies will involve a better understanding of what defines a “natural” environment compared to these contaminated sites. Traditional geochemical testing and standard microbial community analyses (e.g., DNA profiling) or using isolates can be limited with respect to their ability to infer real-time, active processes of bacterial communities. In recent years the application of genomics to identify the microbial microbiome in anthropogenic stressed conditions has advanced considerably. In many cases, the activity of microorganisms will directly impact the chemical conditions in both surface and subsurface water column and contaminated sediment environments controlling the fate of nutrients and contaminants alike. Questions arise such as: What are the baselines or reference systems that can be used? What indices can be used to study the long-term and short-term controls on the mobility, cycling, and bioavailability of toxic metals and organic contaminants? What are the baselines or reference systems that can be used? What indices can be used to study the long-term and short-term controls on the mobility, cycling, and bioavailability of toxic metals and organic contaminants? In many cases the balance of chemical oxidizing and reducing components in water will control the development of chemical and nutrient gradients observed in either natural and/or applied systems (e.g., constructed wetlands or bioreactors). In these cases, biogeochemical systems will determine the direction and onset of specific metabolic pathways as defined by their favorable thermodynamic outcome, an issue for most bioremediators (i.e., microorganisms). Also, the degree of chemical alteration (toxicity or degradation products) can be directly linked to the proportion of their biological activity. In this presentation, contrasting case studies highlighting natural (baseline) and anthropogenically impacted landscapes will be discussed. The focus will be on identifying and linking physicochemical processes to microbial community function using emerging omics for geochemical applications and ascertaining novel contaminant bioindicators.
{"title":"Improving our Understanding of Environmental Stress Impacts and Responses of the Microbiome","authors":"Christopher Weisener","doi":"10.3897/aca.6.e108809","DOIUrl":"https://doi.org/10.3897/aca.6.e108809","url":null,"abstract":"Over the course of this century, it will be important to identify cost effective/low maintenance solutions for treating contaminants in receiving watersheds. Adopting these strategies will involve a better understanding of what defines a “natural” environment compared to these contaminated sites. Traditional geochemical testing and standard microbial community analyses (e.g., DNA profiling) or using isolates can be limited with respect to their ability to infer real-time, active processes of bacterial communities. In recent years the application of genomics to identify the microbial microbiome in anthropogenic stressed conditions has advanced considerably. In many cases, the activity of microorganisms will directly impact the chemical conditions in both surface and subsurface water column and contaminated sediment environments controlling the fate of nutrients and contaminants alike. Questions arise such as: What are the baselines or reference systems that can be used? What indices can be used to study the long-term and short-term controls on the mobility, cycling, and bioavailability of toxic metals and organic contaminants? What are the baselines or reference systems that can be used? What indices can be used to study the long-term and short-term controls on the mobility, cycling, and bioavailability of toxic metals and organic contaminants? In many cases the balance of chemical oxidizing and reducing components in water will control the development of chemical and nutrient gradients observed in either natural and/or applied systems (e.g., constructed wetlands or bioreactors). In these cases, biogeochemical systems will determine the direction and onset of specific metabolic pathways as defined by their favorable thermodynamic outcome, an issue for most bioremediators (i.e., microorganisms). Also, the degree of chemical alteration (toxicity or degradation products) can be directly linked to the proportion of their biological activity. In this presentation, contrasting case studies highlighting natural (baseline) and anthropogenically impacted landscapes will be discussed. The focus will be on identifying and linking physicochemical processes to microbial community function using emerging omics for geochemical applications and ascertaining novel contaminant bioindicators.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136032536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emma Bell, Karin Holmfeldt, Jarone Pinhassi, Anders Andersson
Bacteria and archaea are key drivers of all major element cycles. Viruses that infect bacteria and archaea also play a fundamental role by altering the metabolic state of their host during infection and causing cell death. The CRISPR-Cas system is one of many strategies employed by bacteria and archaea to defend against viral infection. Invading viral DNA is incorporated into a CRISPR array as a short sequence (spacer) that is then recognised during the next viral encounter providing an adaptive immunity. The temporal dynamics of this system in the environment, however, is not well constrained. Using a meta-omic dataset spanning several years of sampling, we leveraged the CRISPR-Cas system to explore microbe-virus interactions in the Baltic Sea. Our goal was to understand how quickly microbes in the environment adapt to virus predation, and conversely how quickly viruses adapt to the microbial defence mechanism by developing mutations in the spacer-targeted region. To explore these interactions, we first generated a database consisting of thousands of complete and high-quality viral genomes recovered from viromes collected from the Baltic Sea. CRISPR arrays were then identified in microbial metagenome assembled genomes (MAGs), metagenomic contigs, and unassembled metagenomic reads from corresponding sampling time points. Virus-host dynamics were uncovered by matching quality-filtered spacers from CRISPR arrays to the viral database. The results show that spacer turnover over time can be captured in temporal meta-omic datasets. In the Baltic Sea, this has implications for the termination of microbial blooms, biogeochemical cycling, and resource turnover.
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The deep, dark fracture zones of the continental crust host a fascinating interplay between water, rocks, and microbes, resulting in the production and consumption of gases, including methane, volatile organic compounds (VOCs), and hydrogen. Various geological factors influence the formation and release of these crustal gases, including the local rock type with its concentration of radioactive elements and carbon, temperature, and the connectivity and dynamics of fracture systems with each other and to the surface. To understand the formation, accumulation, and release of crustal gases, methodologies of hydrogeochemistry, biogeochemistry, and isotope geochemistry can be employed. Sample collection from drill holes and mines, coupled with on-line monitoring of gas flux rate and composition, provides important data. Furthermore, the integration of molecular biological methods enhances our understanding of the water-rock-microbe interactions that shape the deep subsurface gas realm. Crustal gases have crucial implications for life in extreme environments, including those outside of our planet Earth, but potentially also pose significant challenges to drilling, mining, and their environmental impact. Moreover, crustal gases hold relevance for the energy sector, contributing to both the long-term safety of geological disposal of nuclear waste, carbon footprint of geothermal wells, and the exploration of hydrogen as a sustainable energy resource.
{"title":"What the Flux? – Water-Rock-Microbe Interactions and Crustal Gases in the Deep Subsurface","authors":"Riikka Kietäväinen","doi":"10.3897/aca.6.e108428","DOIUrl":"https://doi.org/10.3897/aca.6.e108428","url":null,"abstract":"The deep, dark fracture zones of the continental crust host a fascinating interplay between water, rocks, and microbes, resulting in the production and consumption of gases, including methane, volatile organic compounds (VOCs), and hydrogen. Various geological factors influence the formation and release of these crustal gases, including the local rock type with its concentration of radioactive elements and carbon, temperature, and the connectivity and dynamics of fracture systems with each other and to the surface. To understand the formation, accumulation, and release of crustal gases, methodologies of hydrogeochemistry, biogeochemistry, and isotope geochemistry can be employed. Sample collection from drill holes and mines, coupled with on-line monitoring of gas flux rate and composition, provides important data. Furthermore, the integration of molecular biological methods enhances our understanding of the water-rock-microbe interactions that shape the deep subsurface gas realm. Crustal gases have crucial implications for life in extreme environments, including those outside of our planet Earth, but potentially also pose significant challenges to drilling, mining, and their environmental impact. Moreover, crustal gases hold relevance for the energy sector, contributing to both the long-term safety of geological disposal of nuclear waste, carbon footprint of geothermal wells, and the exploration of hydrogen as a sustainable energy resource.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"73 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136033432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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