Dataset Information

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

ABSTRACT: BACKGROUND:Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology. RESULTS:We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 ? 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. CONCLUSIONS:Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.

SUBMITTER: Reddington K

PROVIDER: S-EPMC7285869 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

Reddington Kate K Eccles David D O'Grady Justin J Drown Devin M DM Hansen Lars Hestbjerg LH Nielsen Tue Kjærgaard TK Ducluzeau Anne-Lise AL Leggett Richard M RM Heavens Darren D Peel Ned N Snutch Terrance P TP Bayega Anthony A Oikonomopoulos Spyridon S Ragoussis Ioannis I Barry Thomas T van der Helm Eric E Jolic Dino D Richardson Hollian H Jansen Hans H Tyson John R JR Jain Miten M Brown Bonnie L BL

GigaScience 20200601 6

<h4>Background</h4>Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be inclu ...[more]

PMID: 32520351

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Project description:BackgroundCoastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling.ResultsTaxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively.ConclusionsOur study demonstrates clear freshwater-saline and sediment-water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems. Video abstract.

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Dataset Information

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

Publications

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

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