The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

Affiliation
German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
Chaudhari, Narendrakumar M.;
GND
1278286837
ORCID
0000-0002-2897-6991
Affiliation
Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
Overholt, Will A.;
Affiliation
Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
Figueroa-Gonzalez, Perla Abigail;
GND
1026380642
ORCID
0000-0002-9498-0841
Affiliation
Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
Taubert, Martin;
Affiliation
Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
Bornemann, Till L. V.;
Affiliation
Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
Probst, Alexander J.;
Affiliation
Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
Hölzer, Martin;
Affiliation
FLI Leibniz Institute for Age Research, Jena, Germany
Marz, Manja;
ORCID
0000-0002-5396-0975
Affiliation
German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
Küsel, Kirsten

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.

Cite

Citation style:
Could not load citation form.

Rights

License Holder: © The Author(s) 2021

Use and reproduction: