Publications

@article{nokey,

title = {Carbon fixation rates in groundwater similar to those in oligotrophic marine systems},

author = {Will A. Overholt and Susan Trumbore and Xiaomei Xu and Till L. V. Bornemann and Alexander J. Probst and Markus Krüger and Martina Herrmann and Bo Thamdrup and Laura A. Bristow and Martin Taubert and Valérie F. Schwab and Martin Hölzer and Manja Marz and Kirsten Küsel},

doi = {10.1038/s41561-022-00968-5},

year  = {2022},

date = {2022-06-30},

journal = {Nat Geosci},

volume = {15},

pages = {561–567},

abstract = {The terrestrial subsurface contains nearly all of Earth’s freshwater reserves and harbours the majority of our planet’s total prokaryotic biomass. Although genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the photosynthetically derived organic carbon transported from surface environments, direct measurements of carbon fixation in the subsurface are absent. Using an ultra-low level 14C-labelling technique, we estimate in situ carbon fixation rates in a carbonate aquifer. We find these rates are similar to those measured in oligotrophic marine surface waters and up to six-fold greater than those observed in the lower euphotic zone. Our empirical carbon fixation rates agree with nitrification rate data. Metagenomic analyses reveal abundant putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria that may be behind the carbon fixation. On the basis of our determined carbon fixation rates, we conservatively extrapolate global primary production in carbonate groundwaters (10% of global reserves) to be 0.11 Pg carbon per year. These rates fall within the range found for oligotrophic marine surface waters, indicating a substantial contribution of in situ primary production to subsurface ecosystem processes. We further suggest that, just as phototrophs are for marine biogeochemical cycling, such subsurface carbon fixation is potentially foundational to subsurface trophic webs.},

keywords = {groundwater},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers},

author = {Narendrakumar M. Chaudhari and Will A. Overholt and Perla Abigail Figueroa-Gonzalez and Martin Taubert and Till L. V. Bornemann and Alexander J. Probst and Martin Hölzer and Manja Marz and Kirsten Küsel},

doi = {10.1186/s40793-021-00395-w},

year  = {2021},

date = {2021-12-14},

urldate = {2021-12-14},

journal = {Environ Microbiome},

volume = {16},

number = {1},

pages = {24},

abstract = {Background: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.



Results: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).



Conclusion: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.},

keywords = {groundwater, metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{Overholt:20,

title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system},

author = {Will A. Overholt and Martin Hölzer and Patricia Geesink and Celia Diezel and Manja Marz and Kirsten Küsel},

doi = {10.1111/1462-2920.15186},

year  = {2020},

date = {2020-08-05},

urldate = {2020-08-05},

journal = {Environ Microbiol},

volume = {22},

number = {9},

pages = {4000-4013},

publisher = {Wiley},

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.},

keywords = {assembly, DNA / genomics, groundwater, metagenomics, nanopore, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Kallies:19,

title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.},

author = {René Kallies and Martin Hölzer and Rodolfo Brizola Toscan and Ulisses Nunes da Rocha and John Anders and Manja Marz and Antonis Chatzinotas},

doi = {10.3390/v11060484},

year  = {2019},

date = {2019-05-28},

urldate = {2019-01-01},

journal = {Viruses},

volume = {11},

number = {6},

pages = {484},

abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the order were the most abundant group (52.20 to 69.12%) dominated by and . Those, and the high number of unknown viral sequences, substantially expand the known virosphere.},

keywords = {DNA / genomics, groundwater, metagenomics, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Wegner:19,

title = {Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon.},

author = {Carl-Eric Wegner and Michael Gaspar and Patricia Geesink and Martina Herrmann and Manja Marz and Kirsten Küsel},

doi = {10.1128/AEM.02346-18},

year  = {2019},

date = {2019-02-20},

urldate = {2019-01-01},

journal = {Appl Environ Microbiol},

volume = {85},

number = {5},

pages = {e02346-18},

abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbour 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, anammox) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), dependent on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Dominated by few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, 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 dependent on the availability of oxygen and inorganic electron donors like ammonium. 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 hydrochemistry.},

keywords = {bacteria, groundwater, metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{Starke:17,

title = {Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer},

author = {Robert Starke and Martina Müller and Michael Gaspar and Manja Marz and Kirsten Küsel and Kai Uwe Totsche and Martin Bergen and Nico Jehmlich},

doi = {10.1016/j.jprot.2016.11.003},

year  = {2016},

date = {2016-11-10},

urldate = {2016-11-10},

journal = {J Proteomics},

volume = {152},

pages = {153--160},

abstract = {Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3μm glass filters. In total, 3808 protein groups were identified. Interestingly, the two wells (H4/2 and H5/2) differed not only in microbial density but also in the prevalence of different C, N and S cycling pathways. The well H5/2 was dominated by the anaerobic ammonia-oxidizing (anammox) candidate Brocadiales (31%) while other orders such as Burkholderiales (2%) or Nitrospirales (3%) were less abundant. Otherwise, the well H4/2 featured only low biomass and remarkably fewer proteins (391 to 3631 at H5/2). Candidate Brocadiales was affiliated to all major carbon fixation strategies, and to the cycling of N and S implying a major role in biogeochemical processes of groundwater aquifers. The findings of our study support functions which can be linked to the ecosystem services provided by the microbial communities present in aquifers. Subsurface environments especially the groundwater ecosystems represent a large habitat for microbial activity. Microbes are responsible for energy and nutrient cycling and are massively involved in the planet's sustainability. Microbial diversity is tremendous and the central question in current microbial ecology is "Who eats what, where and when?". In this study, we characterize a natural aquifer inhabiting microbial community to obtain evidence for the phylogenetic diversity and the metabolic activity by protein abundance and we highlight important biogeochemical cycling processes. The aquifer was dominated by Candidatus Brocadiales while other phylotypes such as Burkholderiales, Caulobacterales and Nitrospirales were less abundant. The candidate comprised all major carbon fixation strategies, ammonification, anammox and denitrification as well as assimilatory sulfate reduction. Our findings have broad implications for the understanding of microbial activities in this aquifer and consequently specific functions can be linked to the ecosystem services provided by the microbial communities present in aquifers.},

keywords = {bacteria, groundwater, phylogenetics},

pubstate = {published},

tppubtype = {article}

}