Abstract
BackgroundRiverine 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.ResultsWe 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.ConclusionsDeeper 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.
Highlights
Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments
Because rivers are used extensively for anthropogenic purposes, it is essential to understand how these activities affect the composition of river microbial consortia
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
Summary
River ecosystems are Earth’s biogeochemical powerhouses, and riverine processes largely are driven by the microbial communities that inhabit their water columns and sediments [1]. Groups represented by ≥1% read assignments included Protists of various types (15%: amoebae, flagellates, ciliates), Ascomycota (12%: fungi), Chordata (12%: rodents and insectivores were predominant, followed by amphibians, fishes, and birds), Streptophyta (11%: predominantly castor, Populus, Arabidopsis, grape, followed by wheat, rice, corn, and mosses), Chlorophyta (10%: most Volvox and Chlamydomonas, except for Sydhavnen where the predominant hits were marine prasinophytes), Cnidaria (10%: roughly split between Anthozoa and Hydrozoa, freshwater hydroids), Arthropoda (6%: most hits were insects followed by spiders), Bacillariophyta (5%: diatoms), Apicomplexa (5%: most parasitic), Nematoda (4%: split between free-living nematodes and parasitic filarial roundworms), and Basidiomycota (3%: in decreasing order, mushrooms, yeasts, smuts, and galls) In many cases, these observed taxa were telling of upstream agricultural and urban effects as has been observed in other river metagenomes [7,8,9]. The PCA analysis for families (Fig. 2A and B) grouped samples in a nearly identical fashion as for Subsystem Functions (Fig. 2C), giving support to the contention that microbial function is driving differences among river and waterway metagenomes, not location
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