Clemens Karwautz, Alice Retter, Johannes Haas, Steffen Birk, Christian Griebler
Rivers extend into the underlying groundwater which represents the unseen freshwater majority. Understanding microbial community composition and dynamics of shallow groundwater and lotic ecosystems is thus crucial, due to their potential impact on ecosystem processes and functioning. A 300 km section of the Mur river valley, from 2000 m.a.s.l. in the Austrian alps to the flats (200 m.a.s.l.) at the Slovenian border, was followed, analyzing river water from 14 stations and groundwater from 45 wells in early summer and late autumn. The active (RNA derived) and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
{"title":"From the Mountain to the Valley - Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor","authors":"Clemens Karwautz, Alice Retter, Johannes Haas, Steffen Birk, Christian Griebler","doi":"10.3897/aca.6.e108227","DOIUrl":"https://doi.org/10.3897/aca.6.e108227","url":null,"abstract":"Rivers extend into the underlying groundwater which represents the unseen freshwater majority. Understanding microbial community composition and dynamics of shallow groundwater and lotic ecosystems is thus crucial, due to their potential impact on ecosystem processes and functioning. A 300 km section of the Mur river valley, from 2000 m.a.s.l. in the Austrian alps to the flats (200 m.a.s.l.) at the Slovenian border, was followed, analyzing river water from 14 stations and groundwater from 45 wells in early summer and late autumn. The active (RNA derived) and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"26 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":"135993625","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 Emil Ruff, Isabella Hrabe de Angelis, Megan Mullis, Jerome Payet, Brandi Kiel Reese, Karen Lloyd, Andrew Steen, Hilary Morrison, Mitchell Sogin, Joshua Ladau, Frederick Colwell
Marine and terrestrial subsurface sediments, rocks, and water may represent the largest habitat for microbial life on Earth. Despite the global importance of subsurface ecosystems for biogeochemical cycling and microbial diversity, essential questions remain unanswered. These concern the abundance of novel microbial clades in the subsurface, the difference between marine and terrestrial microbiomes, as well as between subsurface and surface microbiomes, and the adaptation of specific clades to environmental conditions of the subsurface. Here, we analyzed 523 archaeal and 1,211 bacterial 16S rRNA gene amplicon sequence datasets and 146 shotgun metagenomes from surface, interface, and subsurface ecosystems worldwide, including lakes, saltmarshes, hot springs, caves, mines, methane seeps, hydrothermal vents, and seafloor sediments. We found that archaeal and bacterial alpha diversity (per sample richness and evenness) and beta diversity (community differentiation) varied continuously between surface and subsurface biomes, but differed abruptly between marine and terrestrial subsurface ecosystems. Bacterial alpha diversity tended to be lower in subsurface than surface ecosystems. However, subsurface archaeal alpha diversity often exceeded that of surface ecosystems suggesting that the subsurface holds a considerable and largely underestimated fraction of Earth’s archaeal diversity. Overall, microbial communities of marine subsurface ecosystems exhibited greater alpha diversity, while gamma diversity (total richness and evenness) was higher in the terrestrial subsurface, potentially due to greater habitat diversity. We identify diagnostic clades, especially for the archaea, that are widespread in marine (e.g., Lokiarchaeia, Bathyarchaeia) and terrestrial (e.g., Hadarchaeia, Methanococci) subsurface ecosystems. The substantial community overlap along depth transects and between surface, interface and subsurface realms suggests a global gradient between the surface and subsurface rather than a discrete and defined subsurface biosphere. Finally, none of the included subsurface ecosystems seem to be exhaustively sampled, leaving much biodiversity and metabolic capability yet to be discovered.
{"title":"A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide","authors":"S Emil Ruff, Isabella Hrabe de Angelis, Megan Mullis, Jerome Payet, Brandi Kiel Reese, Karen Lloyd, Andrew Steen, Hilary Morrison, Mitchell Sogin, Joshua Ladau, Frederick Colwell","doi":"10.3897/aca.6.e108531","DOIUrl":"https://doi.org/10.3897/aca.6.e108531","url":null,"abstract":"Marine and terrestrial subsurface sediments, rocks, and water may represent the largest habitat for microbial life on Earth. Despite the global importance of subsurface ecosystems for biogeochemical cycling and microbial diversity, essential questions remain unanswered. These concern the abundance of novel microbial clades in the subsurface, the difference between marine and terrestrial microbiomes, as well as between subsurface and surface microbiomes, and the adaptation of specific clades to environmental conditions of the subsurface. Here, we analyzed 523 archaeal and 1,211 bacterial 16S rRNA gene amplicon sequence datasets and 146 shotgun metagenomes from surface, interface, and subsurface ecosystems worldwide, including lakes, saltmarshes, hot springs, caves, mines, methane seeps, hydrothermal vents, and seafloor sediments. We found that archaeal and bacterial alpha diversity (per sample richness and evenness) and beta diversity (community differentiation) varied continuously between surface and subsurface biomes, but differed abruptly between marine and terrestrial subsurface ecosystems. Bacterial alpha diversity tended to be lower in subsurface than surface ecosystems. However, subsurface archaeal alpha diversity often exceeded that of surface ecosystems suggesting that the subsurface holds a considerable and largely underestimated fraction of Earth’s archaeal diversity. Overall, microbial communities of marine subsurface ecosystems exhibited greater alpha diversity, while gamma diversity (total richness and evenness) was higher in the terrestrial subsurface, potentially due to greater habitat diversity. We identify diagnostic clades, especially for the archaea, that are widespread in marine (e.g., Lokiarchaeia, Bathyarchaeia) and terrestrial (e.g., Hadarchaeia, Methanococci) subsurface ecosystems. The substantial community overlap along depth transects and between surface, interface and subsurface realms suggests a global gradient between the surface and subsurface rather than a discrete and defined subsurface biosphere. Finally, none of the included subsurface ecosystems seem to be exhaustively sampled, leaving much biodiversity and metabolic capability yet to be discovered.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"38 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":"135994284","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}
Hydrothermal vents provide windows into the rocky subseafloor on Earth and serve as terrestrial analog sites for extraterrestrial environments. By studying patterns of community assembly in hydrothermal vents and using geochemical models, we can better understand how the deep-sea biosphere contributes to local and global biogeochemical cycling and gather valuable information about how similar communities may arise on Earth and beyond Earth. One prevailing thought is that vent microbial community assembly is driven by deterministic factors such as the thermodynamic favorability of redox reactions. We hypothesized that subsurface microbial communities may also be significantly influenced by other factors, such as differential cell yields, varying optimal growth temperatures, and stochasticity. At Axial Seamount in the Pacific Ocean, H 2 -consuming methanogens of the genera Methanocaldococcus (T opt 82°C) and Methanothermococcus (T opt 65°C) and H 2 -consuming sulfur reducers of the genus Desulfurobacterium (T opt 72°C) are the most abundant autotrophs that grow optimally at or above 65°C (Fortunato et al. 2017). At one low-temperature hydrothermal vent site, Marker 113, methanogens are the predominant thermophilic autotrophs while at another site, Marker 33, thermophilic autotrophic sulfur reducers predominate. There is no apparent geochemical or thermodynamic explanation for the differences in community composition. In this study, we performed a series of co-culture competition experiments using Methanocaldococcus jannaschii , Methanothermococcus thermolithotrophicus , and Desulfurobacterium thermolithotrophum HR11 as representative methanogens and sulfur reducers common to hydrothermal vents to explain the variations in community composition between thermophilic autotrophs. M. jannaschii increases its cell yield (cells produced per mole of CH 4 produced) when grown on very low H 2 concentrations as part of a growth rate-growth yield tradeoff (Topçuoğlu et al. 2019). This increase in cell yield could provide methanogens with a competitive growth advantage over H 2 -consuming sulfur reducers, who otherwise catalyze a more thermodynamically favorable growth reaction. Competition co-culture experiments were conducted between M. jannaschii and D. thermolithotrophum at 72°C and between M. thermolithotrophicus and D. thermolithotrophum at 65°C, both at 1:1 ratios and initial aqueous H 2 concentrations of 1.2 mM (high H 2 ) and 85 μM (low H 2 ) to determine the effects of temperature and H 2 availability on autotroph competition. For both methanogens, the growth rate, maximum cell concentration, and total CH 4 produced decreased when they were grown in co-culture, at low H 2 , or both relative to monocultures grown with high H 2 . The methanogen cell yields generally increased in co-culture and at low H 2 . At both experimental temperatures, the growth rate of D. thermolithotrophum remained unchanged in co-culture and at low H 2 relative to monocultures
{"title":"Non-Deterministic Factors Affect Competition Between Thermophilic Autotrophs from Deep-Sea Hydrothermal Vents","authors":"Briana Kubik, James Holden","doi":"10.3897/aca.6.e108248","DOIUrl":"https://doi.org/10.3897/aca.6.e108248","url":null,"abstract":"Hydrothermal vents provide windows into the rocky subseafloor on Earth and serve as terrestrial analog sites for extraterrestrial environments. By studying patterns of community assembly in hydrothermal vents and using geochemical models, we can better understand how the deep-sea biosphere contributes to local and global biogeochemical cycling and gather valuable information about how similar communities may arise on Earth and beyond Earth. One prevailing thought is that vent microbial community assembly is driven by deterministic factors such as the thermodynamic favorability of redox reactions. We hypothesized that subsurface microbial communities may also be significantly influenced by other factors, such as differential cell yields, varying optimal growth temperatures, and stochasticity. At Axial Seamount in the Pacific Ocean, H 2 -consuming methanogens of the genera Methanocaldococcus (T opt 82°C) and Methanothermococcus (T opt 65°C) and H 2 -consuming sulfur reducers of the genus Desulfurobacterium (T opt 72°C) are the most abundant autotrophs that grow optimally at or above 65°C (Fortunato et al. 2017). At one low-temperature hydrothermal vent site, Marker 113, methanogens are the predominant thermophilic autotrophs while at another site, Marker 33, thermophilic autotrophic sulfur reducers predominate. There is no apparent geochemical or thermodynamic explanation for the differences in community composition. In this study, we performed a series of co-culture competition experiments using Methanocaldococcus jannaschii , Methanothermococcus thermolithotrophicus , and Desulfurobacterium thermolithotrophum HR11 as representative methanogens and sulfur reducers common to hydrothermal vents to explain the variations in community composition between thermophilic autotrophs. M. jannaschii increases its cell yield (cells produced per mole of CH 4 produced) when grown on very low H 2 concentrations as part of a growth rate-growth yield tradeoff (Topçuoğlu et al. 2019). This increase in cell yield could provide methanogens with a competitive growth advantage over H 2 -consuming sulfur reducers, who otherwise catalyze a more thermodynamically favorable growth reaction. Competition co-culture experiments were conducted between M. jannaschii and D. thermolithotrophum at 72°C and between M. thermolithotrophicus and D. thermolithotrophum at 65°C, both at 1:1 ratios and initial aqueous H 2 concentrations of 1.2 mM (high H 2 ) and 85 μM (low H 2 ) to determine the effects of temperature and H 2 availability on autotroph competition. For both methanogens, the growth rate, maximum cell concentration, and total CH 4 produced decreased when they were grown in co-culture, at low H 2 , or both relative to monocultures grown with high H 2 . The methanogen cell yields generally increased in co-culture and at low H 2 . At both experimental temperatures, the growth rate of D. thermolithotrophum remained unchanged in co-culture and at low H 2 relative to monocultures ","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"1 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":"135994288","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}
Nitrate-dependent iron oxidation (NDFO) is a novel mechanism for microbial bioremediation of metal and metalloid contaminants. During NDFO, microbes catalyze a redox reaction wherein nitrate is reduced to nitrite and nitrogen gas while Fe(II) is oxidized to solid Fe(III) hydroxide minerals. Metalloid contaminants such as selenium and arsenic have a propensity for adsorption to iron minerals produced during NDFO; some contaminants may also be concurrently bioreduced. A number of bacterial isolates have been shown to be capable of NDFO (e.g., Kappler et al. (2005), Kiskira et al. (2017)), but little work has been done to date characterizing mixed microbial communities performing NDFO. Some autotrophic communities have been characterized, with high relative abundances for strains of Gallionellaceae in both a freshwater sediment enrichment culture and an activated sludge culture (Blöthe and Roden 2009, Tian et al. 2020). In mixotrophic activated sludge cultures, the concentration of Fe(II) amendment was found to significantly impact microbial community composition; these cultures were fed with methanol in addition to Fe(II), and the dominant community members were Methyloversatilis and other methylotrophic strains (Liu et al. 2018). The work presented here examines microbial communities performing NDFO in the context of remediation, and in particular how differences between NDFO and heterotrophic communities may influence remediation effectiveness. This research characterizes and compares microbial communities performing NDFO versus heterotrophic denitrification during removal of selenium and nickel from mining wastewater. Sediment and influent water from a subsurface bioreactor treating mining wastewater were used to construct batch bioreactors, which were amended with selenium and nickel as well as either Fe(II) or methanol to investigate contaminant removal and microbial community composition in NDFO versus heterotrophic microbial communities. Both Fe(II) and methanol reactors removed total aqueous selenium to below the quantification limit, but Fe(II) reactors removed it more rapidly, likely due to adsorption of selenite. For nickel, removal to below the detection limit was achieved with methanol amendment, while Fe(II) amendment resulted in 42-95% removal. This was likely due to precipitation of nickel sulfide during sulfate reduction in methanol-amended reactors. DNA from the batch bioreactors will be sequenced and the results analyzed for differences among communities. Permutational multivariate analysis of variance and non-metric multidimensional scaling will be used to determine significant correlations of community composition with experimental variables, selenium and nickel removal, and NDFO (Roberts 2023, Kruskal 1964). Indicator species analyses (De Cáceres et al. 2010) will be applied to identify taxa found significantly more often (i.e., at a higher relative abundance) in one group of microbial communities than in any other group. The
硝酸盐依赖铁氧化(NDFO)是微生物修复金属和类金属污染物的一种新机制。在NDFO过程中，微生物催化氧化还原反应，其中硝酸盐被还原为亚硝酸盐和氮气，而铁(II)被氧化成固体铁(III)氢氧化物矿物。类金属污染物，如硒和砷，有吸附倾向的铁矿物产生的NDFO;一些污染物也可以同时被生物还原。许多细菌分离株已被证明能够进行NDFO(例如，Kappler等人(2005)，Kiskira等人(2017))，但迄今为止，对执行NDFO的混合微生物群落进行表征的工作很少。一些自养群落的特征是，在淡水沉积物富集培养和活性污泥培养中，Gallionellaceae菌株的相对丰度都很高(Blöthe and Roden 2009, Tian et al. 2020)。在混合营养活性污泥培养中，发现铁(II)修正浓度显著影响微生物群落组成;在这些培养物中添加甲醇和Fe(II)，优势群落成员是methylomultilis和其他甲基营养菌株(Liu et al. 2018)。本文介绍的工作考察了在修复背景下执行NDFO的微生物群落，特别是NDFO和异养群落之间的差异如何影响修复效果。本研究表征并比较了在去除采矿废水中的硒和镍过程中进行NDFO和异养反硝化的微生物群落。利用处理采矿废水的地下生物反应器的沉积物和进水构建间歇式生物反应器，并对其进行硒和镍以及铁(II)或甲醇的改性，以研究NDFO与异养微生物群落的污染物去除和微生物群落组成。Fe(II)反应器和甲醇反应器对水中总硒的去除率均低于定量限制，但Fe(II)反应器的去除率更快，可能是由于亚硒酸盐的吸附。甲醇对镍的去除率低于检出限，而Fe(II)的去除率为42-95%。这可能是由于在甲醇改性反应器中硫酸盐还原过程中硫化镍的沉淀。将对间歇式生物反应器的DNA进行测序，并对结果进行分析，以确定不同群落之间的差异。将使用置换多元方差分析和非度量多维尺度来确定群落组成与实验变量、硒和镍去除以及NDFO之间的显著相关性(Roberts 2023, Kruskal 1964)。指示物种分析(De Cáceres et al. 2010)将用于识别在一组微生物群落中比在任何其他组中更频繁(即相对丰度更高)发现的分类群。指示种分析可以揭示在NDFO条件下占优势的反硝化菌群与在异养反硝化过程中占优势的反硝化菌群之间是否存在差异。这些微生物群落分析的结果，结合地球化学分析，将提高我们对在修复环境中执行NDFO的微生物群落的理解。
{"title":"Differences Between Heterotrophic and Nitrate-dependent Iron-oxidizing Microbial Communities in Bioreactor Sediment Treating Mine Wastewater","authors":"Hannah Koepnick, Brent Peyton, Ellen Lauchnor","doi":"10.3897/aca.6.e108177","DOIUrl":"https://doi.org/10.3897/aca.6.e108177","url":null,"abstract":"Nitrate-dependent iron oxidation (NDFO) is a novel mechanism for microbial bioremediation of metal and metalloid contaminants. During NDFO, microbes catalyze a redox reaction wherein nitrate is reduced to nitrite and nitrogen gas while Fe(II) is oxidized to solid Fe(III) hydroxide minerals. Metalloid contaminants such as selenium and arsenic have a propensity for adsorption to iron minerals produced during NDFO; some contaminants may also be concurrently bioreduced. A number of bacterial isolates have been shown to be capable of NDFO (e.g., Kappler et al. (2005), Kiskira et al. (2017)), but little work has been done to date characterizing mixed microbial communities performing NDFO. Some autotrophic communities have been characterized, with high relative abundances for strains of Gallionellaceae in both a freshwater sediment enrichment culture and an activated sludge culture (Blöthe and Roden 2009, Tian et al. 2020). In mixotrophic activated sludge cultures, the concentration of Fe(II) amendment was found to significantly impact microbial community composition; these cultures were fed with methanol in addition to Fe(II), and the dominant community members were Methyloversatilis and other methylotrophic strains (Liu et al. 2018). The work presented here examines microbial communities performing NDFO in the context of remediation, and in particular how differences between NDFO and heterotrophic communities may influence remediation effectiveness. This research characterizes and compares microbial communities performing NDFO versus heterotrophic denitrification during removal of selenium and nickel from mining wastewater. Sediment and influent water from a subsurface bioreactor treating mining wastewater were used to construct batch bioreactors, which were amended with selenium and nickel as well as either Fe(II) or methanol to investigate contaminant removal and microbial community composition in NDFO versus heterotrophic microbial communities. Both Fe(II) and methanol reactors removed total aqueous selenium to below the quantification limit, but Fe(II) reactors removed it more rapidly, likely due to adsorption of selenite. For nickel, removal to below the detection limit was achieved with methanol amendment, while Fe(II) amendment resulted in 42-95% removal. This was likely due to precipitation of nickel sulfide during sulfate reduction in methanol-amended reactors. DNA from the batch bioreactors will be sequenced and the results analyzed for differences among communities. Permutational multivariate analysis of variance and non-metric multidimensional scaling will be used to determine significant correlations of community composition with experimental variables, selenium and nickel removal, and NDFO (Roberts 2023, Kruskal 1964). Indicator species analyses (De Cáceres et al. 2010) will be applied to identify taxa found significantly more often (i.e., at a higher relative abundance) in one group of microbial communities than in any other group. The","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"1 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":"135992637","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}
Chantel C. Furgason, Angela Smirnova, Joel Dacks, Peter Dunfield
Alberta oilsands mining and extraction have produced over 1 trillion litres of tailings wastewater (AER 2021) containing several compounds of concern (Cossey et al. 2021). End-pit lakes are a low-cost, long-term proposed strategy of tailings reclamation that sequester tailings in a mined-out pit under a freshwater cap. Through dilution and biogeochemical processes, the water cap should over time develop into a functional ecosystem integrable with the local watershed (Cossey et al. 2021, Saborimanesh 2021). Established in 2012, Base Mine Lake is currently the only full-scale pilot end pit lake developed by the Alberta oilsands industry and requires further investigation to validate end pit lakes as a tailings reclamation technology (Cossey et al. 2021). The first stage of reclamation requires the development of a phytoplankton community, which serves as the base of the aquatic food web (CEMA 2012). The primary objective of this study was to characterize the phytoplanktxon community over time in BML from 2016 to 2021 to determine how community composition and abundances shift over seasons and years. Characterization used Illumina gene sequencing targeting 16S rRNA, 18S rRNA, and 23S rRNA gene amplicons, giving relative abundance data over time for phytoplankton. Cell count data was used to verify gene sequencing results. The phytoplankton community composition and diversity in Base Mine Lake was compared to those of a freshwater reservoir and a tailings pond. Analysis of gene sequencing data revealed that major genera of phytoplankton included Cryptomonas ( Cryptophyceae ), Choricystis ( Trebouxiophyceae ), Euglena ( Euglenales ), and Synechococcus ( Synechococcales ), all of which appear to exhibit seasonal blooms during 2016-2021 (Fig. 1). Sequencing analysis also indicated that Base Mine Lake and its freshwater input source Beaver Creek Reservoir shared many of the same genera but different strains/species of those genera. This suggested that the distinct conditions in each aquatic site may have selected for distinct strains. Diversity analyses of gene sequencing data revealed that phytoplankton diversity in Base Mine Lake was intermediate between that of its freshwater input reservoir and a tailings pond. There currently exists no low-cost, large-scale treatment method that fully reclaims tailings water (Cossey et al. 2021, Saborimanesh 2021). End-pit lakes retain tailings until recalcitrant compounds are degraded to near-environmental levels (Saborimanesh 2021, CEMA 2012), but further research is required before end-pit lakes can be approved as a viable reclamation technology (Cossey et al. 2021). Although research is available now on native microbial communities in tailings waters, knowledge on their contributions to an aquatic microbial food web is limited (Saborimanesh 2021). This proposed research is the first of its kind to examine the contribution of phytoplankton to end pit lake food web ecology. This will advance knowledge of end-pit l
艾伯塔省油砂开采和提取产生了超过1万亿升的尾矿废水(AER 2021)，其中含有几种令人担忧的化合物(Cossey et al. 2021)。尾坑湖是一种低成本、长期的尾矿回收策略，它将尾矿隔离在淡水帽下的采出坑中。通过稀释和生物地球化学过程，随着时间的推移，水帽将发展成为与当地流域可整合的功能性生态系统(Cossey et al. 2021, Saborimanesh 2021)。Base Mine Lake成立于2012年，是目前阿尔伯塔省油砂行业开发的唯一一个全面的试验性尾坑湖，需要进一步调查以验证尾坑湖作为尾矿回收技术的有效性(Cossey et al. 2021)。复垦的第一阶段需要发展浮游植物群落，这是水生食物网的基础(CEMA 2012)。本研究的主要目的是表征2016年至2021年BML浮游植物群落随时间的变化，以确定群落组成和丰度如何随季节和年份变化。利用Illumina基因测序对16S rRNA、18S rRNA和23S rRNA基因扩增子进行鉴定，获得浮游植物随时间变化的相对丰度数据。细胞计数数据用于验证基因测序结果。将基地矿湖的浮游植物群落组成和多样性与淡水水库和尾矿库进行了比较。基因测序数据分析显示，浮游植物的主要属包括隐单胞菌(Cryptophyceae)、毛囊藻(Trebouxiophyceae)、藻芽藻(Euglenales)和聚球菌(Synechococcales)，它们在2016-2021年期间都出现了季节性华(图1)。测序分析还表明，Base Mine Lake及其淡水输入源Beaver Creek Reservoir具有许多相同的属，但这些属的菌株/种不同。这表明，每个水生地点的不同条件可能选择了不同的菌株。基因测序数据的多样性分析表明，基矿湖浮游植物多样性介于其淡水输入库和尾矿库之间。目前还没有低成本、大规模的完全回收尾矿水的处理方法(Cossey et al. 2021, Saborimanesh 2021)。尾坑湖保留尾矿，直到顽固性化合物降解到接近环境的水平(Saborimanesh 2021, CEMA 2012)，但在尾坑湖被批准为可行的回收技术之前，还需要进一步的研究(Cossey et al. 2021)。虽然目前对尾矿水中的原生微生物群落进行了研究，但对它们对水生微生物食物网的贡献的了解有限(Saborimanesh 2021)。本研究首次探讨了浮游植物对尾坑湖食物网生态的贡献。这将促进对尾坑湖的认识，将其作为一种复垦战略，努力减少尾矿水的环境足迹。
{"title":"Phytoplankton Ecology in an Oilsands End Pit Lake","authors":"Chantel C. Furgason, Angela Smirnova, Joel Dacks, Peter Dunfield","doi":"10.3897/aca.6.e108385","DOIUrl":"https://doi.org/10.3897/aca.6.e108385","url":null,"abstract":"Alberta oilsands mining and extraction have produced over 1 trillion litres of tailings wastewater (AER 2021) containing several compounds of concern (Cossey et al. 2021). End-pit lakes are a low-cost, long-term proposed strategy of tailings reclamation that sequester tailings in a mined-out pit under a freshwater cap. Through dilution and biogeochemical processes, the water cap should over time develop into a functional ecosystem integrable with the local watershed (Cossey et al. 2021, Saborimanesh 2021). Established in 2012, Base Mine Lake is currently the only full-scale pilot end pit lake developed by the Alberta oilsands industry and requires further investigation to validate end pit lakes as a tailings reclamation technology (Cossey et al. 2021). The first stage of reclamation requires the development of a phytoplankton community, which serves as the base of the aquatic food web (CEMA 2012). The primary objective of this study was to characterize the phytoplanktxon community over time in BML from 2016 to 2021 to determine how community composition and abundances shift over seasons and years. Characterization used Illumina gene sequencing targeting 16S rRNA, 18S rRNA, and 23S rRNA gene amplicons, giving relative abundance data over time for phytoplankton. Cell count data was used to verify gene sequencing results. The phytoplankton community composition and diversity in Base Mine Lake was compared to those of a freshwater reservoir and a tailings pond. Analysis of gene sequencing data revealed that major genera of phytoplankton included Cryptomonas ( Cryptophyceae ), Choricystis ( Trebouxiophyceae ), Euglena ( Euglenales ), and Synechococcus ( Synechococcales ), all of which appear to exhibit seasonal blooms during 2016-2021 (Fig. 1). Sequencing analysis also indicated that Base Mine Lake and its freshwater input source Beaver Creek Reservoir shared many of the same genera but different strains/species of those genera. This suggested that the distinct conditions in each aquatic site may have selected for distinct strains. Diversity analyses of gene sequencing data revealed that phytoplankton diversity in Base Mine Lake was intermediate between that of its freshwater input reservoir and a tailings pond. There currently exists no low-cost, large-scale treatment method that fully reclaims tailings water (Cossey et al. 2021, Saborimanesh 2021). End-pit lakes retain tailings until recalcitrant compounds are degraded to near-environmental levels (Saborimanesh 2021, CEMA 2012), but further research is required before end-pit lakes can be approved as a viable reclamation technology (Cossey et al. 2021). Although research is available now on native microbial communities in tailings waters, knowledge on their contributions to an aquatic microbial food web is limited (Saborimanesh 2021). This proposed research is the first of its kind to examine the contribution of phytoplankton to end pit lake food web ecology. This will advance knowledge of end-pit l","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"1 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":"135993430","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}
Metallurgical coal mining generates significant amounts of waste rock, which can release nitrate and selenate upon atmospheric exposure, with resulting changes in surface water and ground water quality. Microorganisms residing on waste rock in the local subsurface have the metabolic potential to denitrifyand reduce selenium to treat mine-affected waters and stabilize waste rock. To support these processes, waste rock facilities have been designed to inject nutrients (e.g., methanol and phosphoric acid) in semi-passive water treatment of mine-impacted waters. Microbial community data regularly collected fromsubsurface semi-passive reactors throughout the startup and operations phases showed that native heterotrophic denitrifying bacteria and selenium reducing bacteria were enriched as a result of nutrient amendment. The microbial community was stable while the source water and geochemical parameters remained unchanged; however, a significant shift in the microbial community coincided with changes in the source of water treated. Metagenomic sequencing of microbial communities within the active treatment zone revealed multiple biochemical pathways of nitrate reduction. Geochemical and water quality data indicate near complete selenate reduction, yet a low abundance of in known selenate reduction genes were recovered. This may suggest that biologically mediated selenium reduction may be more widespread, both functionally and taxonomically. Further research into these pathways and mechanisms for nitrate and selenium reduction will help to strengthen our understanding of selenium reduction mechanisms and their application in mine water waste management.
{"title":"Microbiological Treatment of Nitrate and Selenate from Coal Mine-Affected Water in a Subsurface,Semi-Passive, and in situ Water Treatment Facility","authors":"Rachel Spietz, Lisa Kirk","doi":"10.3897/aca.6.e108259","DOIUrl":"https://doi.org/10.3897/aca.6.e108259","url":null,"abstract":"Metallurgical coal mining generates significant amounts of waste rock, which can release nitrate and selenate upon atmospheric exposure, with resulting changes in surface water and ground water quality. Microorganisms residing on waste rock in the local subsurface have the metabolic potential to denitrifyand reduce selenium to treat mine-affected waters and stabilize waste rock. To support these processes, waste rock facilities have been designed to inject nutrients (e.g., methanol and phosphoric acid) in semi-passive water treatment of mine-impacted waters. Microbial community data regularly collected fromsubsurface semi-passive reactors throughout the startup and operations phases showed that native heterotrophic denitrifying bacteria and selenium reducing bacteria were enriched as a result of nutrient amendment. The microbial community was stable while the source water and geochemical parameters remained unchanged; however, a significant shift in the microbial community coincided with changes in the source of water treated. Metagenomic sequencing of microbial communities within the active treatment zone revealed multiple biochemical pathways of nitrate reduction. Geochemical and water quality data indicate near complete selenate reduction, yet a low abundance of in known selenate reduction genes were recovered. This may suggest that biologically mediated selenium reduction may be more widespread, both functionally and taxonomically. Further research into these pathways and mechanisms for nitrate and selenium reduction will help to strengthen our understanding of selenium reduction mechanisms and their application in mine water waste management.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"26 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":"135994843","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}
Sabina Pang, Triet Tran, Robert Bowers, Tanja Woyke, Peter Dunfield
Historically, discovery and subsequent characterization of microbial species relied on pure cultures. Some challenges associated with creating pure cultures have been overcome with advances in culture independent and DNA-based molecular methods such as single-cell genomics, metagenomics, or large scale amplicon sequencing. With these advances, the rate of discovery of new species from genomic data has quickly outpaced the number of organisms with cultured representatives. As description and characterization still rely on cultures, our understanding of yet uncultured species is greatly lacking. Major lineages in the bacterial domain equivalent to phyla that lack any cultured representatives are termed “candidate phyla.” Candidate phyla are found across the bacterial tree of life, and many uncultured organisms are found to be dominant in understudied environments. Extreme environments such as thermal springs are an example of understudied environments, making them excellent environments for studying novel microbial lineages. The objective of this research is to characterize uncultured bacterial lineages from Dewar Creek hot spring in Western Canada, with a focus on DNA and protein metabolizing bacteria. Based on previous genomic data from organisms in this hot spring, we hypothesize that the candidate phylum S2R-29, with extremely low GC content, metabolizes extracellular DNA or protein Dewar Creek is a thermal spring located in the Purcell Wilderness Conservancy in British Colombia, Western Canada. It is one of Canada’s hottest springs, reaching temperatures of up to 83˚C. Samples of DNA extracted from the Dewar Creek hot spring were PCR-amplified with primers for the v3v4 region of the 16S rRNA gene to detect S2R-29, and then sequenced on an Illumina Miseq. S2R-29 was found in samples ranging in temperature from 60˚C to 77 ˚C. In addition to samples from Dewar Creek, samples from other thermal springs in Canada, as well as samples from springs in New Zealand are also being sequenced with the same primers to determine the prevalence of this candidate phylum in other similar environments. This will give a better idea of the growth conditions and range of this organism. Previously, S2R-29 single amplified genomes (SAGs) were generated from Dewar Creek samples. Analysis of these SAGs suggests that S2R-29 has the potential to use peptides and DNA as carbon sources (Fig. 1). To test the potential to metabolize DNA and protein, enrichments of samples with 13C labelled dNTPs or 13C labelled protein have been started. These enrichments will be used for stable isotope probing (SIP) to determine if any organisms in Dewar Creek are metabolizing dNTPs or protein. In addition to SIP, primers specific for S2R-29 for quantitative PCR (qPCR) have been designed and will be run on the enrichments to determine if there are any changes in the abundance of S2R-29 over time in these enrichments, further testing the metabolic potential of these organisms. Finally, probe
{"title":"Characterization of DNA Degrading Microorganisms from Dewar Creek Hot Springs in Western Canada","authors":"Sabina Pang, Triet Tran, Robert Bowers, Tanja Woyke, Peter Dunfield","doi":"10.3897/aca.6.e108170","DOIUrl":"https://doi.org/10.3897/aca.6.e108170","url":null,"abstract":"Historically, discovery and subsequent characterization of microbial species relied on pure cultures. Some challenges associated with creating pure cultures have been overcome with advances in culture independent and DNA-based molecular methods such as single-cell genomics, metagenomics, or large scale amplicon sequencing. With these advances, the rate of discovery of new species from genomic data has quickly outpaced the number of organisms with cultured representatives. As description and characterization still rely on cultures, our understanding of yet uncultured species is greatly lacking. Major lineages in the bacterial domain equivalent to phyla that lack any cultured representatives are termed “candidate phyla.” Candidate phyla are found across the bacterial tree of life, and many uncultured organisms are found to be dominant in understudied environments. Extreme environments such as thermal springs are an example of understudied environments, making them excellent environments for studying novel microbial lineages. The objective of this research is to characterize uncultured bacterial lineages from Dewar Creek hot spring in Western Canada, with a focus on DNA and protein metabolizing bacteria. Based on previous genomic data from organisms in this hot spring, we hypothesize that the candidate phylum S2R-29, with extremely low GC content, metabolizes extracellular DNA or protein Dewar Creek is a thermal spring located in the Purcell Wilderness Conservancy in British Colombia, Western Canada. It is one of Canada’s hottest springs, reaching temperatures of up to 83˚C. Samples of DNA extracted from the Dewar Creek hot spring were PCR-amplified with primers for the v3v4 region of the 16S rRNA gene to detect S2R-29, and then sequenced on an Illumina Miseq. S2R-29 was found in samples ranging in temperature from 60˚C to 77 ˚C. In addition to samples from Dewar Creek, samples from other thermal springs in Canada, as well as samples from springs in New Zealand are also being sequenced with the same primers to determine the prevalence of this candidate phylum in other similar environments. This will give a better idea of the growth conditions and range of this organism. Previously, S2R-29 single amplified genomes (SAGs) were generated from Dewar Creek samples. Analysis of these SAGs suggests that S2R-29 has the potential to use peptides and DNA as carbon sources (Fig. 1). To test the potential to metabolize DNA and protein, enrichments of samples with 13C labelled dNTPs or 13C labelled protein have been started. These enrichments will be used for stable isotope probing (SIP) to determine if any organisms in Dewar Creek are metabolizing dNTPs or protein. In addition to SIP, primers specific for S2R-29 for quantitative PCR (qPCR) have been designed and will be run on the enrichments to determine if there are any changes in the abundance of S2R-29 over time in these enrichments, further testing the metabolic potential of these organisms. Finally, probe","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"12 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":"135993499","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}
Tillmann Lueders, Christopher Mechela, Felix Beulig, Martin Obst
Providing evidence for presumed chemolithoautotrophic manganese oxidation remains a major and challenging objective in subsurface microbiology. Here, we report on the dissection of blackish, leathery microbial biofilms discovered in the “Goldene Falk”, a historic copper mine in Northern Bavaria, with mine shafts originating back to the 15 th centrury. Biogeochemical analysis of the biofilm indicated a notable enrichment of manganese oxides (MnOX), with Mn making up for more than 10% (dry weight) of the deposits. STXM analysis suggested a clear biogenic origin of MnOX in situ . Characteristic nodules of MnOX with microbial cells attached were also found in aerobic Mn-oxidizing enrichment cultures set up in minimal media in the lab. The biofilms obtained from the mine were also subjected to amplicon and metagenomic sequencing,revealing a vast diversity of presumably chemolithoautotrophic and heterotrophic microbial lineages, including members of the Pyrinomonadaceae , Rhizobiales , Methylomirabilaceae and also lineages within the Nitrospiraceae previously reported to be associated with lithotrophic Mn oxidation. We reconstructed >100 high-quality bacterial genomes (MAGs), many of them carrying genomic signatures of biogenic Mn oxidation (albeit non-lithotrophic). We continue to investigate the biofilms, our enrichment cultures and the metagenomic data obtained from the mine for further evidence of possible autotrophic manganese oxidation, the macroscopic leathery biofilm representing a likely habitat for these still enigmatic microbes. Indications for nitrogen and sulfur cycling also ongoing in the biofilms will also be discussed. This research contributes to a better understanding of the yet-enigmatic capacities of the microbiota in man-made subsurface environments.
{"title":"Investigating Manganese-oxidizing microbial Biofilms in a historic Copper Mine of Upper Frankonia","authors":"Tillmann Lueders, Christopher Mechela, Felix Beulig, Martin Obst","doi":"10.3897/aca.6.e108107","DOIUrl":"https://doi.org/10.3897/aca.6.e108107","url":null,"abstract":"Providing evidence for presumed chemolithoautotrophic manganese oxidation remains a major and challenging objective in subsurface microbiology. Here, we report on the dissection of blackish, leathery microbial biofilms discovered in the “Goldene Falk”, a historic copper mine in Northern Bavaria, with mine shafts originating back to the 15 th centrury. Biogeochemical analysis of the biofilm indicated a notable enrichment of manganese oxides (MnOX), with Mn making up for more than 10% (dry weight) of the deposits. STXM analysis suggested a clear biogenic origin of MnOX in situ . Characteristic nodules of MnOX with microbial cells attached were also found in aerobic Mn-oxidizing enrichment cultures set up in minimal media in the lab. The biofilms obtained from the mine were also subjected to amplicon and metagenomic sequencing,revealing a vast diversity of presumably chemolithoautotrophic and heterotrophic microbial lineages, including members of the Pyrinomonadaceae , Rhizobiales , Methylomirabilaceae and also lineages within the Nitrospiraceae previously reported to be associated with lithotrophic Mn oxidation. We reconstructed >100 high-quality bacterial genomes (MAGs), many of them carrying genomic signatures of biogenic Mn oxidation (albeit non-lithotrophic). We continue to investigate the biofilms, our enrichment cultures and the metagenomic data obtained from the mine for further evidence of possible autotrophic manganese oxidation, the macroscopic leathery biofilm representing a likely habitat for these still enigmatic microbes. Indications for nitrogen and sulfur cycling also ongoing in the biofilms will also be discussed. This research contributes to a better understanding of the yet-enigmatic capacities of the microbiota in man-made subsurface environments.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"44 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":"135993631","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}
Groundwater is an essential part of everyday life, serving as agricultural irrigation, supporting numerous industrial processes, and providing drinking water for many. It is also home to a diverse range of unexplored microbial communities. This is especially true in Alberta, Canada, due to the rich geological history of the region and the close proximity of aquifer locations to areas ranging from oil sand-rich to agricultural to populous cities. Through collaborations with the Environment and Protected Areas division of the Alberta government we have access to more than 250 wells throughout the province, 25 of which were selected for metagenomics analysis. More than 750 metagenome-assembled genomes were recovered and coupled with historic geochemical, isotopic, and dissolved gas data, allowing us to interpret the lifestyles of microbial communities inhabiting Alberta groundwater. Results show a strong presence of organisms involved in C1-cycling, indicative of a productive subsurface environment, as well as members belonging to the Candidate Phyla Radiation (CPR). We explore likely roles of CPR, including their potential for ecological interactions via secondary metabolites. This research shows that Alberta groundwater is home to diverse, productive microbial communities that have the capacity to further our knowledge in microbial ecology.
{"title":"Prominence of Candidate Phyla Radiation (CPR) in Alberta Groundwater","authors":"Damon Mosier","doi":"10.3897/aca.6.e110344","DOIUrl":"https://doi.org/10.3897/aca.6.e110344","url":null,"abstract":"Groundwater is an essential part of everyday life, serving as agricultural irrigation, supporting numerous industrial processes, and providing drinking water for many. It is also home to a diverse range of unexplored microbial communities. This is especially true in Alberta, Canada, due to the rich geological history of the region and the close proximity of aquifer locations to areas ranging from oil sand-rich to agricultural to populous cities. Through collaborations with the Environment and Protected Areas division of the Alberta government we have access to more than 250 wells throughout the province, 25 of which were selected for metagenomics analysis. More than 750 metagenome-assembled genomes were recovered and coupled with historic geochemical, isotopic, and dissolved gas data, allowing us to interpret the lifestyles of microbial communities inhabiting Alberta groundwater. Results show a strong presence of organisms involved in C1-cycling, indicative of a productive subsurface environment, as well as members belonging to the Candidate Phyla Radiation (CPR). We explore likely roles of CPR, including their potential for ecological interactions via secondary metabolites. This research shows that Alberta groundwater is home to diverse, productive microbial communities that have the capacity to further our knowledge in microbial ecology.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"32 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":"135994414","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}
Karst systems represent an important carbon and freshwater reservoirs. Although karst systems have been studied for many years, a new paradigm has emerged that suggests some of them could be formed by ghost-rock processes (Dubois et al. 2014 ) . Contrarily to the classical total karstification, ghost-rock karstification leaves in place a weathered rock, called the ghost-rock, that can constitute a microbial habitat (Spilde et al. 2005). The first results of a geomicrobiological study of the Sterkfontein’s cave system in South Africa show that these ghost-rocks are mainly composed of iron and manganese oxides mixed with organic matter of putative microbial origin (Pisapia et al. in prep). To further understand the microbial community inhabiting these ghost-rocks, its specificity compared to groundwater, and its functional impact on the karst system of Sterkfontein, a metagenomic analysis from both ghost-rocks and groundwater samples was performed. It was completed by laser microdissection of the microorganisms attached to the mineral particles, followed by whole-genome amplification and transmission electron microscopy to analyze both the nature of the mineral particles and the microorganisms associated with them. The results highlight the differences in community between these two environments (with higher abundance of Actinobacteriota and Acidobacteriota in ghost-rock samples compared to ground water in particular), and suggest a high importance of microbe-minerals interactions in the ghost rocks, through metallophores production and extracellular electron transfer processes between bacteria and metallic ions.
喀斯特系统是重要的碳和淡水储集层。尽管对喀斯特系统的研究已经进行了多年，但一种新的范式已经出现，认为其中一些喀斯特系统可能是由鬼岩过程形成的(Dubois et al. 2014)。与经典的全岩溶作用相反，鬼岩岩溶作用留下了风化的岩石，称为鬼岩，可以构成微生物栖息地(Spilde et al. 2005)。对南非Sterkfontein洞穴系统进行的地球微生物学研究的初步结果表明，这些鬼岩主要由铁和锰的氧化物组成，并混合了假定的微生物来源的有机物(Pisapia等人)。为了进一步了解这些鬼岩中的微生物群落、其与地下水的特异性及其对Sterkfontein岩溶系统的功能影响，对鬼岩和地下水样品进行了宏基因组分析。通过激光显微解剖附着在矿物颗粒上的微生物，然后进行全基因组扩增和透射电子显微镜来分析矿物颗粒及其相关微生物的性质。结果突出了这两种环境之间的群落差异(特别是与地下水相比，鬼岩样品中放线菌群和酸杆菌群的丰度更高)，并表明鬼岩中微生物-矿物相互作用的高度重要性，通过金属基团的产生和细菌与金属离子之间的细胞外电子转移过程。
{"title":"The impact of subsurface life on ghost-rock karstification processes and cave formation","authors":"Guillaume Peugnet, Céline Pisapia, Laurent Bruxelles, Cédric Champollion, Philippe Vernant, Léna Lecourt, Bénédicte Ménèz, Emmanuelle Gérard","doi":"10.3897/aca.6.e108695","DOIUrl":"https://doi.org/10.3897/aca.6.e108695","url":null,"abstract":"Karst systems represent an important carbon and freshwater reservoirs. Although karst systems have been studied for many years, a new paradigm has emerged that suggests some of them could be formed by ghost-rock processes (Dubois et al. 2014 ) . Contrarily to the classical total karstification, ghost-rock karstification leaves in place a weathered rock, called the ghost-rock, that can constitute a microbial habitat (Spilde et al. 2005). The first results of a geomicrobiological study of the Sterkfontein’s cave system in South Africa show that these ghost-rocks are mainly composed of iron and manganese oxides mixed with organic matter of putative microbial origin (Pisapia et al. in prep). To further understand the microbial community inhabiting these ghost-rocks, its specificity compared to groundwater, and its functional impact on the karst system of Sterkfontein, a metagenomic analysis from both ghost-rocks and groundwater samples was performed. It was completed by laser microdissection of the microorganisms attached to the mineral particles, followed by whole-genome amplification and transmission electron microscopy to analyze both the nature of the mineral particles and the microorganisms associated with them. The results highlight the differences in community between these two environments (with higher abundance of Actinobacteriota and Acidobacteriota in ghost-rock samples compared to ground water in particular), and suggest a high importance of microbe-minerals interactions in the ghost rocks, through metallophores production and extracellular electron transfer processes between bacteria and metallic ions.","PeriodicalId":101714,"journal":{"name":"ARPHA Conference Abstracts","volume":"90 1 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":"136033566","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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