Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Herrmann, Martina; Wegner, Carl‐Eric; Taubert, Martin; Geesink, Patricia; Lehmann, Katharina; Yan, Lijuan; Lehmann, Robert; Totsche, Kai Uwe; Küsel, Kirsten

doi:10.3389/fmicb.2019.01407

Cited by 181 publications

(152 citation statements)

References 70 publications

(104 reference statements)

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“…Our data suggested that in our fracturedrock ecosystem the alpha diversities of DOM and bacteria were linked. A coupling between the diversities of DOM and bacteria during groundwater recharge could occur as a result of differing processes: (1) combined transport of surface-derived DOM and diverse, allochthonous bacterial communities into the aquifer (Pronk et al, 2006(Pronk et al, , 2009Herrmann et al, 2019).…”

Section: Responses Of the In Situ Biospherementioning

confidence: 99%

Fueling Diversity in the Subsurface: Composition and Age of Dissolved Organic Matter in the Critical Zone

et al. 2019

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Surface ecosystems are rapidly changing on a global scale and it is important to understand how this influences aquifers in the subsurface, as groundwater quality is a major concern for future generations. Dissolved organic matter (DOM) contains molecular and isotopic signals from surface-derived inputs as well as from the biotic and abiotic subsurface environment and is therefore ideal to study the connectivity between both environments. We evaluated a 3-year time series of DOM composition using ultrahigh resolution mass spectrometry and age using 14 C accelerator mass spectrometry along a hillslope well transect in the fractured bedrock of the Hainich Critical Zone Exploratory, Germany. We found a wide range of DOM 14 C depletion, from 14 C = −47.9 to 14 C = −782.4, within different zones of the shallow groundwater. The 14 C content of DOM mirrored the connectivity of the aquifers to the surface. The composition of DOM was highly interrelated with its 14 C age. The proportions of surface-derived DOM components decreased with DOM age, whereas microorganismderived DOM components increased. The intensity of surface-sourced DOM signals differed between the wells and likely reflected the hydrological complexity of fracturedrock environments. During recharge, DOM was more enriched in 14 C, contained more surface-derived molecular components and was more diverse. As a potential response to the varying DOM substrate, bacterial 16S rRNA gene analysis revealed community evolution and increased bacterial diversity during recharge. The influx of diverse, surface-derived DOM potentially fueled evolution within the autochthonous bacterial communities, as in contrast to DOM, the bacterial community did not retreat to the initial diversity and community composition during the recession period. Our results demonstrate on the one hand that combined analyses of the composition and age of groundwater DOM strongly contribute to the understanding of interconnections, community evolution and the functioning of subsurface ecosystems and on the other hand that changes in surface ecosystems have an imprint on subsurface ecosystems.

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Section: Responses Of the In Situ Biospherementioning

confidence: 99%

Fueling Diversity in the Subsurface: Composition and Age of Dissolved Organic Matter in the Critical Zone

et al. 2019

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“…TAG_MAG_00018, from the same phylum (Gracilibacteria class) was in high abundance at TAG (273X) while in low abundance at Rainbow (max 10X; Additional File 4). The predominance of these groups in the Rimicaris holobiont, associated with small genome size for both TAG_MAG_00007 and TAG_MAG_00018 (1,201735 and 841,694 bp, respectively) adds to recent studies showing widespread CPR organisms often in association with abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling [51,52].…”

Section: A Highly Diverse Epibiont Community In Rimicarismentioning

confidence: 62%

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Cambon‐Bonavita

Aubé

Cueff-Gauchard

et al. 2020

Preprint

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BackgroundMutualistic symbioses between invertebrate animals and chemosynthetic bacteria are at the basis of Life in hydrothermal vent ecosystems. The shrimp Rimicaris exoculata, which dominates animal fauna along the Mid Atlantic Ridge, houses in its cephalothorax a complex bacterial community including Campylobacteria, Gamma- Delta- and some recently discovered iron oxyhydroxides-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane and hydrogen as energy sources. Here, we used a DNA extraction procedure adapted to recalcitrant embedded bacteria and generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic community. We aimed reconstructing symbiotic genomes from specimen collected in three geochemically contrasted vent fields, TAG, Rainbow and Snake Pit to unravel the specificity, variability and adaptation of host-microbes associations.ResultsUsing these data we were able to reconstruct 49 high quality metagenome-assembled genomes (MAGs) from TAG and Rainbow vents fields. Most critically, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (ANI < 77% from the closest relative Ghiorsea bivora isolated from TAG and <88% between each other), suggesting potential novel species. Genes for CBB carbon fixation, iron and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and quorum sensing as well as multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts that co-exist in a single shrimp at both basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further insights into the seemingly functional redundancy between those epibionts revealed important differences. ConclusionThese data highlight microniche partitioning in the Rimicaris holobiont and confirm recent works that show functional diversity enables multiple symbiont strains to coexist in animals from hydrothermal vents.

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“…Also of interest was the presence of conserved bacterial species within the order Absconditabacterales, which are classified under the Patescibacteria phylum. Patescibacteria are unusually small bacteria found in groundwater and produce large surface proteins hypothesized to help them attach or associate with other microorganisms that perform nitrogen, sulfur and iron cycling [29]. The presence of these conserved bacteria suggests that the inflow water seeps originate from groundwater.…”

Section: Resultsmentioning

confidence: 99%

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds

Waterworth¹,

Isemonger

Rees³

et al. 2019

Preprint

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13Stromatolites are complex microbial mats that form lithified layers and ancient forms are 14 the oldest evidence of life on earth, dating back over 3.4 billion years. Their emergence 15 aligns with the oxygenation of the Earth's atmosphere and insight into these ancient 16 structures would shed light on the earliest days of Earth. Modern stromatolites are 17 relatively rare but may provide clues about the function and evolution of their ancient 18 counterparts. Previous studies have assessed microbial diversity and overall functional 19 potential but not at a genome-resolved level. In this study, we focus on peritidal 20 stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern 21 South African coastline. We identify functional gene sets in bacterial species conserved 22 across two geographically distinct stromatolite formations and show that these bacteria 23 may promote carbonate precipitation through the reduction of sulfur and nitrogenous 24 compounds and produce calcium ions that are predicted to play an important role in 25 promoting lithified mats. We propose that abundance of extracellular alkaline 26 phosphatases, in combination with the absence of transport regulatory enzymes, may 27 lead to the precipitation of phosphatic deposits within these stromatolites. We conclude 28 that the cumulative effect of several conserved bacterial species drives accretion in 29 these two stromatolite formations. 30 31 3

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Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Cited by 181 publications

References 70 publications

Fueling Diversity in the Subsurface: Composition and Age of Dissolved Organic Matter in the Critical Zone

Fueling Diversity in the Subsurface: Composition and Age of Dissolved Organic Matter in the Critical Zone

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds

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