Environmental selection shapes the formation of near-surface groundwater microbiomes

Yan, Lijuan; Herrmann, Martina; Kampe, Bernd; Lehmann, Robert; Totsche, Kai Uwe; Küsel, Kirsten

doi:10.1016/j.watres.2019.115341

Cited by 111 publications

(107 citation statements)

References 60 publications

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“…A similar visualization was performed for three other dominant bacterial phyla (Nitrospirota, Actinobacteriota, Proteobacteria) that had previously been shown to be important in the functioning of the groundwater Yan et al , 2019) (Figure S1). There were almost double the number of Nitrospirota associated MAGs (7 vs. 4) recovered with the hybrid approach, and these were amongst the largest of the MAGs recovered.…”

Section: Resultsmentioning

confidence: 86%

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Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Overholt¹,

Hölzer

Geesink³

et al. 2019

Preprint

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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. A ssembly 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

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Section: Resultsmentioning

confidence: 86%

“…The 16S rRNA genes recovered from MAGs were compared using blastn to 97% representative operational taxonomic units (OTUs) from primer pair 341F/785R (Altschul et al , 1990;Yan et al , 2019) . All hits were required to be >98.5 % sequence identity across at least 350 bp.…”

Section: Metagenome Assembly and Binningmentioning

confidence: 99%

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Overholt¹,

Hölzer

Geesink³

et al. 2019

Preprint

Self Cite

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“…In the groundwater of well H41, Gammaproteobacteria are the second most abundant class after Cand. Parcubacteria (Yan et al, 2020). Organisms affiliated with…”

Section: Discussionmentioning

confidence: 99%

Bolstering fitness via opportunistic CO₂fixation: mixotroph dominance in modern groundwater

Taubert

Overholt

Heinze

et al. 2021

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Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity.Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.

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“…They seem to share functional similarity in different environments and to provide a robust microbial ecosystem under environmental uctuation [39,40]. We paid close attention to the core species because they were deemed to re ect the stability of soil communities in wetlands [41]. This result indicates that the methanogenic community has high potential to adjust in response to changes in vegetation type and season.…”

Section: Discussionmentioning

confidence: 99%

Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China

Zhao

Bai

et al. 2020

Preprint

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Background: Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. Result: The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla – Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were closer. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to adaptation to environmental disturbances. Conclusions: This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.

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Environmental selection shapes the formation of near-surface groundwater microbiomes

Cited by 111 publications

References 60 publications

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Bolstering fitness via opportunistic CO₂fixation: mixotroph dominance in modern groundwater

Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China

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Environmental selection shapes the formation of near-surface groundwater microbiomes

Cited by 111 publications

References 60 publications

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Bolstering fitness via opportunistic CO2fixation: mixotroph dominance in modern groundwater

Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China

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Bolstering fitness via opportunistic CO₂fixation: mixotroph dominance in modern groundwater