Groundwater bacterial communities evolve over time in response to recharge

Yan, Lijuan; Hermans, Syrie M.; Totsche, Kai Uwe; Lehmann, Robert; Herrmann, Martina; Küsel, Kirsten

doi:10.1016/j.watres.2021.117290

Cited by 45 publications

(46 citation statements)

References 55 publications

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“…Patescibacteria taxa (Fig. 2 ) were less pronounced than those observed in other bacteria in groundwater of the Hainich CZE [ 37 , 45 ], and despite their streamlined genomes, we could highlight certain environmental preferences of the Cand . Patescibacteria.…”

Section: Discussionmentioning

confidence: 83%

“…To have an idea about the temporal co-occurrence patterns of other groundwater microbes with Patescibacteria, we additionally utilized time-series data based on 16S rRNA gene amplicon sequencing from the same groundwater transect from three wells (H41, H43 and H52) measured over more than six years [ 45 ]. We observed that Patescibacteria co-occurred mostly with members of phyla Proteobacteria (mostly order Burkholderiales) and Nitrospirota (order Thermodesulfovibrionia), in the well H41; Verrucomicrobiota, in the well H43 and Planctomycetota (mostly genus Brocadia ) in the well H52.…”

Section: Resultsmentioning

confidence: 99%

“…The permanently high O 2 concentration in well H32 (2.23 ± 0.56 mg/L) and especially in well H41 (4.83 ± 1.7 mg/L) [ 45 , 48 ], did not lead to enrichment of groundwater Patescibacteria MAGs with genetic traits of energy harvesting mechanisms through aerobic respiration. Exposure to oxygen is not exceptional for Cand.…”

Section: Discussionmentioning

confidence: 99%

“…As some Nitrospirota MAGs (n = 51) were enriched exclusively in oxic wells, their preference might have determined the distribution pattern of putative CPR episymbionts. Nitrospirota species were also found to be consistently co-occurring with Patescibacteria in some of the studied wells based on OTU abundances from 16S rRNA gene amplicon sequencing data collected over 6.5 years [ 45 ] as well as MAG abundances from this study across the groundwater transect. At the minimum, these observations suggest common niche preferences between some members of these two phyla.…”

Section: Discussionmentioning

confidence: 99%

“…To elucidate other possible associations of Patescibacteria with other prokaryotes, we utilized above mentioned time-series data that revealed consistent co-occurrence of Patescibacteria OTUs with OTUs from Proteobacteria, Verrucomicrobiota, and Planctomycetota in addition to OTUs from Nitrospirota [ 45 ]. There are in silico predictions of acquisition of few unique genes by human-associated CPR bacteria (Saccharibacteria) during mammalian host adaptation [ 53 ].…”

Section: Discussionmentioning

confidence: 99%

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

Chaudhari

Overholt

Figueroa-Gonzalez

et al. 2021

Environmental Microbiome

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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.

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Section: Discussionmentioning

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 3 more Smart Citations

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

Chaudhari

Overholt

Figueroa-Gonzalez

et al. 2021

Environmental Microbiome

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View full text Add to dashboard Cite

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Rapid detection of subterranean fauna from passive sampling of groundwater eDNA

van der Heyde,

Alexander,

Nevill

et al. 2023

Environmental DNA

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Groundwater is an essential source of freshwater that supports surface ecosystems as well as organisms adapted to living underground. The impacts of anthropogenic climate change, extraction, and pollution pose major threats to groundwater ecosystem health, prompting a need for efficient and reliable means to detect and monitor subterranean faunal communities. Conventional survey of subterranean fauna relies on the collection of organisms for morphological identification, which can be biased, labor intensive, and often indeterminate at lower taxonomic levels. Environmental DNA (eDNA)‐based methods can dramatically improve on stygofaunal surveys, but currently rely on time consuming active water filtration that limits the number of samples that can be processed. Passive eDNA sampling, which involves submersion of absorbent material (e.g. filter membrane, sponge etc.) into the sampled environment for a fixed period, has shown promise as a viable alternative to active filtration in aquatic ecosystems and may be applicable to groundwater systems. Here, we compared groundwater eDNA collected from active pump filtered water samples, membranes submerged in water for 10 min and 24 h, and haul‐net samples morphologically identified from bores at two geographically distinct locations in Western Australia. Our results show that while the relative abundance of eDNA in groundwater (measured through qPCR) is 100–800 times lower in passive samples, the species richness detected is comparable between passive and active eDNA collection. Additionally, standard metabarcoding assays (18S and COI) of passive eDNA samples detected most subterranean orders identified morphologically (12/17), and this proportion may be improved with increased sampling and application of DNA extraction methods that increase DNA yield. Our findings demonstrate that passive eDNA sample collection is a non‐invasive survey method with the potential to improve the efficiency and replication level of stygofaunal surveys but will benefit from further development.

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Evaluating a robust and easy-to-use biological-activity-based method to assess the presence of potentially adverse bacteria at two riverbank filtration sites along the Danube river: A case study

Oudega,

Leifels,

Steinbacher

et al. 2023

Österr Wasser- und Abfallw

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The Laboratory Biological Activity Reaction Test (LAB-BART) is an easy-to-use assay that utilizes metabolic capabilities to process an array of substrates to semi-quantitatively assess the presence of potentially adverse bacteria in a groundwater sample. Here, we evaluated LAB-BART for the assessment of groundwater samples obtained under real-life conditions from two riverbank filtration (RBF) sites in Austria. Samples were taken monthly for an overall experimental period of six months and analyzed following the manufacturer’s recommendations for measuring iron-related, sulfate-reducing, slime-forming and denitrifying bacteria. Additional measurements were done for analyzing chemical water composition, as well as bacterial community structure to evaluate the suitability of LAB-BART by identifying relevant bacteria. Results imply that while LAB-BART could not give detailed information on bacterial concentrations, it might be able to indicate hydrologically induced changes in biogeochemical processes in a subsurface system, thus allowing operators to determine an adequate response to a potential influx of undesired bacteria. Despite its limitations, LAB-BART might therefore be a valuable tool for monitoring purposes due to its ease of use, but more research is necessary to determine its accuracy in measuring bacterial activity.

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Groundwater bacterial communities evolve over time in response to recharge

Cited by 45 publications

References 55 publications

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

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

Rapid detection of subterranean fauna from passive sampling of groundwater eDNA

Evaluating a robust and easy-to-use biological-activity-based method to assess the presence of potentially adverse bacteria at two riverbank filtration sites along the Danube river: A case study

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