Research Article: Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers

Date Published: March 28, 2017

Publisher: Public Library of Science

Author(s): Jason T. Payne, Justin J. Millar, Colin R. Jackson, Clifford A. Ochs, John J. Kelly.


We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct sub-basins, river cities, and extended stretches without major inputs to the Mississippi. The composition and proportional abundance of dominant bacterial phyla was distinct for free-living and particle-associated cells, and constant along the entire reach, except for a substantial but transient disturbance near the city of Memphis, Tennessee. At a finer scale of taxonomic resolution (operational taxonomic units, OTUs), however, there were notable patterns in downriver variation in bacterial community alpha diversity (richness within a site) and beta diversity (variation in composition among sites). There was a strong and steady increase downriver in alpha diversity of OTUs on suspended particles, suggesting an increase in particle niche heterogeneity, and/or particle colonization. Relatively large shifts in beta diversity of free-living and particle-associated communities occurred following major tributary confluences and transiently at Memphis, while in long stretches between these points diversity typically varied more gradually. We conclude that the Mississippi River possesses a bacterioplankton microbiome distinct in diversity from other large river microbiomes in the Mississippi River Basin, that at major river confluences or urban point sources its OTU diversity may shift abruptly and substantially, presumably by immigration of distinct external microbiomes, but that where environmental conditions are more stable along the downriver gradient, microbiome diversity tends to vary gradually, presumably by a process of successional change in community composition.

Partial Text

All ecosystems have a microbial community, or microbiome, from the tissues and organs of individual animal and plant hosts [1, 2], to aquatic or terrestrial environments [3]. The microbiome is involved with essential ecosystem processes whether it is contributing to host metabolism [4–6] or biogeochemical cycling of nutrients at regional or global spatial scales [7]. Hence, variation in microbiome composition may have implications for the functional attributes, services, or adaptability of the ecosystem [8].

From examining the bacterioplankton microbiome along a 1,300 rkm downriver transect of the Mississippi River, and concurrently at the mouths of five tributaries to the Mississippi, we can reach several important conclusions about the biogeography of the microbiome(s) of this large river system, and perhaps large rivers in general.

Influenced by its major tributary inputs, the Illinois, Missouri, and Ohio Rivers, the three sections of the Mississippi River (the Upper Mississippi, Middle Mississippi, and Lower Mississippi River) are distinguishable from each other in physical and chemical properties. After one day of flow below confluences with these major tributaries there were usually major shifts in diversity of the Mississippi River microbiome compared to pre-tributary diversity. This is in contrast with stretches of the river more distant in distance and time from major confluences, where changes between adjacent sites in diversity tended to be more gradual. We conclude that while flowing downriver, diversity of the Mississippi River microbiome is modified by point source inputs of external microbiomes from major tributaries draining distinct sub-watersheds, complemented by a gradual process of community succession along intervening stretches of more stable environmental conditions.




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