17 results on '"Patricia Geesink"'
Search Results
2. Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome
- Author
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Patricia Geesink, Martin Taubert, Nico Jehmlich, Martin von Bergen, and Kirsten Küsel
- Subjects
groundwater ,necromass ,surface input ,stable isotope probing ,metaproteomics ,subsurface ,Microbiology ,QR1-502 - Abstract
ABSTRACT Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation. IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.
- Published
- 2022
- Full Text
- View/download PDF
3. Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions
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Martina Herrmann, Carl-Eric Wegner, Martin Taubert, Patricia Geesink, Katharina Lehmann, Lijuan Yan, Robert Lehmann, Kai Uwe Totsche, and Kirsten Küsel
- Subjects
shallow subsurface ,ultra-small bacteria ,oligotrophy ,community assembly ,co-occurrence ,Cand. Patescibacteria ,Microbiology ,QR1-502 - Abstract
Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.
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- 2019
- Full Text
- View/download PDF
4. Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes
- Author
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Swatantar Kumar, Martina Herrmann, Bo Thamdrup, Valérie F. Schwab, Patricia Geesink, Susan E. Trumbore, Kai-Uwe Totsche, and Kirsten Küsel
- Subjects
anammox ,chemolithoautotrophy ,denitrification ,groundwater ,ladderane lipids ,subsurface ,Microbiology ,QR1-502 - Abstract
Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L−1 d−1, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L−1 oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.
- Published
- 2017
- Full Text
- View/download PDF
5. Expanding Archaeal Diversity and Phylogeny : Past, Present, and Future
- Author
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Thijs J. G. Ettema, Patricia Geesink, and Guillaume Tahon
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archaea ,media_common.quotation_subject ,Microbial diversity ,Ecology (disciplines) ,phylogeny ,Microbiology ,03 medical and health sciences ,taxonomy ,Phylogenetics ,Microbiologie ,RNA, Ribosomal, 16S ,universal primers ,14. Life underwater ,030304 developmental biology ,media_common ,0303 health sciences ,Ecology ,biology ,030306 microbiology ,Genomics ,respiratory system ,biology.organism_classification ,Evolutionary biology ,microbial diversity ,Microbial Evolution ,Taxonomy (biology) ,16S rRNA gene ,Microbiële Evolutie ,human activities ,Diversity (politics) ,Archaea - Abstract
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA gene amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community.
- Published
- 2021
6. Innovations to culturing the uncultured microbial majority
- Author
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Diana Z. Sousa, Guillaume Tahon, Thijs J. G. Ettema, William H Lewis, and Patricia Geesink
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2. Zero hunger ,0303 health sciences ,General Immunology and Microbiology ,biology ,030306 microbiology ,business.industry ,Microorganism ,MicPhys ,15. Life on land ,Isolation (microbiology) ,biology.organism_classification ,Microbiology ,Biotechnology ,03 medical and health sciences ,Infectious Diseases ,Experimental testing ,Microbiologie ,Microbial Evolution ,Life Science ,Microbial genome ,Microbiële Evolutie ,business ,Archaea - Abstract
Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
- Published
- 2020
7. Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest
- Author
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Kirsten Küsel, Ronny Richter, Patricia Geesink, and Martina Herrmann
- Subjects
Canopy ,Floodplain ,Tilia cordata ,Soil Science ,Acer ,Forests ,Trees ,Quercus robur ,Quercus ,Germany ,RNA, Ribosomal, 16S ,Temperate climate ,Tilia ,Ecology, Evolution, Behavior and Systematics ,geography ,geography.geographical_feature_category ,Ecology ,biology ,Microbiota ,High-Throughput Nucleotide Sequencing ,Biodiversity ,Acer pseudoplatanus ,biology.organism_classification ,Actinobacteria ,Plant Leaves ,Habitat ,Canopy crane ,Species richness ,Phyllosphere ,Plant Microbe Interactions - Abstract
The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position—top, mid, and bottom at a height between 31 and 20 m—and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species—maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)—at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55–57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and—in contrast to other temperate or tropical forests—a strong predominance of Actinobacteria. Electronic supplementary material The online version of this article (10.1007/s00248-020-01565-y) contains supplementary material, which is available to authorized users.
- Published
- 2020
8. Genome‐inferred spatio‐temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater
- Author
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Hang T. Dam, Alexander J. Probst, Anne-Kristin Kaster, Carl-Eric Wegner, Kirsten Küsel, Patricia Geesink, and Martina Herrmann
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Microorganism ,Chemie ,Bacterial Physiological Phenomena ,Microbiology ,Genome ,Nitrospirae ,03 medical and health sciences ,Spatio-Temporal Analysis ,Abundance (ecology) ,RNA, Ribosomal, 16S ,Ecosystem ,Lactic Acid ,Symbiosis ,Groundwater ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Bacteria ,biology ,030306 microbiology ,Phylum ,Ecology ,Microbiota ,Amplicon ,biology.organism_classification ,Carbon ,Microbial population biology ,Microbial Interactions ,Metagenomics - Abstract
Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.
- Published
- 2019
9. It takes a village - overcoming gender-biased mentorship in academia
- Author
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Rocio Deanna, Ivan Baxter, Kwok Pan Chun, Bethann Garramon Merkle, Rui Zuo, Luisa Maria Diele-Viegas, Patricia Geesink, Valeria Aschero, Deborah Navarro-Rosenblatt, Alejandro Bortolus, Pamela A. Ribone, Elina Welchen, Maria Jose de Leone, Sonia Oliferuk, Nora H. Oleas, Mariana Grossi, Andrea Cosacov, Sandra Knapp, Alicia López-Mendez, and Gabriela Auge
- Abstract
Effective mentoring implies a two-way relationship in which mentees obtain benefits from the knowledge and training provided by mentors, and mentors gain the possibility of contemplating and learning new perspectives, of self-evaluating their roles and, in consequence, growing as professionals. Mentorship relationships cannot be separated from cultural and societal backgrounds. Thus, they often reflect systemic biases requiring active effort to counteract institutional inequities. Such efforts, particularly when formalized as programs, expand training opportunities for both mentors and mentees. Mentorship networks, in which multiple mentor-mentee relationships are involved, therefore increase collective performance by magnifying resources. Importantly, mentorship exceeds the relationships of students and their direct supervisors (often reflected in co-authorship in publications), and in fact, mentors are often purposely picked outside the direct publication network. A recent large data analysis by AlShebli et al. (2020) showed results of presumed “mentor-protege” relationships after mining millions of coauthor pairs in publications over time, suggesting gender-insensitive changes in institutional mentorship policies based on value-skewed academic success. Because mentorship engages a broader sense of community in academia, mentorship outcomes cannot be quantified solely by the impact of publications.
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- 2020
10. Innovations to culturing the uncultured microbial majority
- Author
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William H, Lewis, Guillaume, Tahon, Patricia, Geesink, Diana Z, Sousa, and Thijs J G, Ettema
- Subjects
Bacteriological Techniques ,Bacteria ,Archaea ,Culture Media - Abstract
Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
- Published
- 2020
11. Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system
- Author
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Martin Hölzer, Patricia Geesink, Manja Marz, Will A. Overholt, Kirsten Küsel, and Celia Diezel
- Subjects
Whole genome sequencing ,0303 health sciences ,Whole Genome Sequencing ,030306 microbiology ,High-Throughput Nucleotide Sequencing ,Shotgun ,Computational biology ,Ribosomal RNA ,Biology ,Microbiology ,Genome ,03 medical and health sciences ,Genome, Microbial ,Nanopore Sequencing ,nervous system ,Metagenomics ,Microbial genetics ,Metagenome ,Nanopore sequencing ,Water Microbiology ,Groundwater ,Ecology, Evolution, Behavior and Systematics ,Illumina dye sequencing ,030304 developmental biology - Abstract
Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing platform. Assembly and metagenome-assembled genome (MAG) metrics for both microbes and viruses were determined from an Illumina-only assembly, ONT-only assembly, and a hybrid assembly approach. The hybrid approach recovered 2× more mid to high-quality MAGs compared to the Illumina-only approach and 4× more than the ONT-only approach. A similar number of viral genomes were reconstructed using the hybrid and ONT methods, and both recovered nearly fourfold more viral genomes than the Illumina-only approach. While yielding fewer MAGs, the ONT-only approach generated MAGs with a high probability of containing rRNA genes, 3× higher than either of the other methods. Of the shared MAGs recovered from each method, the ONT-only approach generated the longest and least fragmented MAGs, while the hybrid approach yielded the most complete. This work provides quantitative data to inform a cost-benefit analysis of the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.
- Published
- 2019
12. Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system
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Patricia Geesink, Manja Marz, Martin Hölzer, Kirsten Küsel, Will A. Overholt, and Celia Diezel
- Subjects
Metagenomics ,Shotgun ,Nanopore sequencing ,Computational biology ,Biology ,Hybrid approach ,Genome ,Illumina dye sequencing - Abstract
Assembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments. In order to compare the recovery of genomes from microorganisms and their phages from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. Assembly and metagenome-assembled genome (MAG) metrics for both microbes and viruses were determined from Illumina-only assemblies and a hybrid assembly approach. Strikingly, the hybrid approach more than doubled the number of mid to high-quality MAGs (> 50% completion, < 10% redundancy), generated nearly four-fold more phage genomes, and improved all associated genome metrics relative to the Illumina only method. The hybrid assemblies yielded MAGs that were on average 7.8% more complete, with 133 fewer contigs and a 14 kbp greater N50. Furthermore, the longer contigs from the hybrid approach generated microbial MAGs that had a higher proportion of rRNA genes. We demonstrate this usefulness by linking microbial MAGs containing 16S rRNA genes with extensive amplicon dataset. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.
- Published
- 2019
13. Tracking active groundwater microbes with D 2 O labelling to understand their ecosystem function
- Author
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Petra Rösch, Nico Jehmlich, Patricia Geesink, Kirsten Küsel, Martin Taubert, Sophie Girnus, Stephan Stöckel, Martin von Bergen, and Jürgen Popp
- Subjects
0301 basic medicine ,biology ,Microorganism ,Heterotroph ,Microbial metabolism ,biology.organism_classification ,Microbiology ,Sphingomonadaceae ,03 medical and health sciences ,Metabolic pathway ,030104 developmental biology ,Environmental chemistry ,Labelling ,Metaproteomics ,Microcosm ,Ecology, Evolution, Behavior and Systematics - Abstract
Microbial activity is key in understanding the contribution of microbial communities to ecosystem functions. Metabolic labelling with heavy water (D2 O) leads to the formation of carbon-deuterium bonds in active microorganisms. We illustrated how D2 O labelling allows monitoring of metabolic activity combined with a functional characterization of active populations in complex microbial communities. First, we demonstrated by single cell Raman microspectroscopy that all measured bacterial cells from groundwater isolates growing in complex medium with D2 O were labelled. Next, we conducted a labelling approach with the total groundwater microbiome in D2 O amended microcosms. Deuterium was incorporated in most measured cells, indicating metabolic activity in the oligotrophic groundwater. Moreover, we spiked the groundwater microbiome with organic model compounds. We discovered that heterotrophs assimilating veratric acid, a lignin derivative, showed higher labelling than heterotrophs assimilating methylamine, a degradation product of biomass. This difference can be explained by dilution of the deuterium through hydrogen from the organic compounds. Metaproteomics identified Sphingomonadaceae and Microbacteriaceae as key players in veratric acid degradation, and the metabolic pathways employed. Methylamine, in contrast, stimulated various proteobacterial genera. We propose this combined approach of Raman microspectroscopy and metaproteomics for elucidating the complex metabolic response of microbial populations to different stimuli.
- Published
- 2017
14. Erratum for Wegner et al., 'Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon'
- Author
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Carl-Eric Wegner, Patricia Geesink, Manja Marz, Michael Gaspar, Martina Herrmann, and Kirsten Küsel
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Physics ,0303 health sciences ,Biogeochemical cycle ,Ecology ,030306 microbiology ,Thermodynamics ,chemistry.chemical_element ,Applied Microbiology and Biotechnology ,Sulfur ,Nitrogen ,Data availability ,03 medical and health sciences ,chemistry ,Environmental Microbiology ,Carbon ,Food Science ,Biotechnology - Abstract
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium. IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.
- Published
- 2019
15. Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater
- Author
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Kirsten Küsel, Lijuan Yan, Kai Uwe Totsche, Patricia Geesink, Robert Lehmann, and Martina Herrmann
- Subjects
Chemoautotrophic Growth ,Food Chain ,Environmental Engineering ,0208 environmental biotechnology ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,Animals ,Ecosystem ,Groundwater ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Apex predator ,Trophic level ,Biomass (ecology) ,Ecology ,Ecological Modeling ,Biota ,Groundwater recharge ,Pollution ,Food web ,020801 environmental engineering ,Environmental science - Abstract
Groundwater ecosystems face the challenge of energy limitation due to the absence of light-driven primary production. Lack of space and low oxygen availability might further contribute to generally assumed low food web complexity. Chemolithoautotrophy provides additional input of carbon within the subsurface, however, we still do not understand how abundances of chemolithoautotrophs, differences in surface carbon input, and oxygen availability control subsurface food web complexity. Using a molecular approach, we aimed to disentangle the different levels of potential trophic interactions in oligotrophic groundwater along a hillslope setting of alternating mixed carbonate-/siliciclastic bedrock with contrasting hydrochemical conditions and hotspots of chemolithoautotrophy. Across all sites, groundwater harbored diverse protist communities including Ciliophora, Cercozoa, Centroheliozoa, and Amoebozoa but correlations with hydrochemical parameters were less pronounced for eukaryotes compared to bacteria. Ciliophora-affiliated reads dominated the eukaryotic data sets across all sites. DNA-based evidence for the presence of metazoan top predators such as Cyclopoida (Arthropoda) and Stenostomidae (Platyhelminthes) was only found at wells where abundances of functional genes associated with chemolithoautotrophy were 10–100 times higher compared to wells without indications of these top predators. At wells closer to recharge areas with presumably increased inputs of soil-derived substances and biota, fungi accounted for up to 85% of the metazoan-curated eukaryotic sequence data, together with a low potential for chemolithoautotrophy. Although we did not directly observe higher organisms, our results point to the existence of complex food webs with several trophic levels in oligotrophic groundwater. Chemolithoautotrophy appears to provide strong support to more complex trophic interactions, feeding in additional biomass produced by light-independent CO2-fixation.
- Published
- 2020
16. Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon
- Author
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Martina Herrmann, Patricia Geesink, Kirsten Küsel, Manja Marz, Carl-Eric Wegner, and Michael Gaspar
- Subjects
Biogeochemical cycle ,Denitrification ,Groundwater flow ,Nitrogen ,Aquifer ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,Ammonium Compounds ,Proteobacteria ,Organic matter ,Ecosystem ,Groundwater ,Phylogeny ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,geography ,geography.geographical_feature_category ,Ecology ,Bacteria ,030306 microbiology ,Bacteroidetes ,Microbiota ,Groundwater recharge ,Archaea ,Nitrification ,Carbon ,chemistry ,Environmental chemistry ,Environmental science ,Metagenomics ,Erratum ,Water Microbiology ,Sulfur ,Food Science ,Biotechnology - Abstract
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.
- Published
- 2018
17. Growth Promotion and Inhibition Induced by Interactions of Groundwater Bacteria
- Author
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Charlotte van de Velde, Olaf Tyc, Patricia Geesink, Kirsten Küsel, Martin Taubert, Swatantar Kumar, Paolina Garbeva, and Microbial Ecology (ME)
- Subjects
0301 basic medicine ,Staphylococcus aureus ,Firmicutes ,Microorganism ,030106 microbiology ,Microbial metabolism ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Proteobacteria ,medicine ,Escherichia coli ,Groundwater ,Ecology ,biology ,Bacteria ,Bacteroidetes ,Antimicrobial ,biology.organism_classification ,Anti-Bacterial Agents ,030104 developmental biology ,chemistry ,international ,Microbial Interactions ,Growth inhibition - Abstract
Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth-inhibiting and -promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (Staphylococcus aureus 533R4 and Escherichia coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth-promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both growth-inhibiting and -promoting effects, this method will enable further studies to elaborate and better understand complex inter-specific interactions and networks in aquatic communities as well as in other environments.
- Published
- 2018
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