Floodplain Microbial Communities and Biogeochemical Cycling

Building on the transect approach, a watershed-scale study proposed that meander-bound segments of the floodplain serve as repeatable "scaling motifs" — units whose aggregate microbial capacities can be used to predict biogeochemical function across an entire river corridor (Carnevali et al., 2021). This idea — that complex microbial diversity can be summarized at a tractable landscape scale — has shaped much of the subsequent work in the Gunnison Basin.

Key findings

A central result is that floodplain soils harbor a small but consistent core microbiome amid enormous overall diversity. Across the upper, middle, and lower East River, roughly one-third of reconstructed genomes were found at all three locations, and about 15% of species recurred across two consecutive years. This core was dominated by Betaproteobacteria with capacities for aerobic respiration, carbon monoxide oxidation, and thiosulfate oxidation, suggesting that despite high turnover, certain metabolic functions are reliably present (Carnevali et al., 2021). Importantly, gene and organism abundance did not predict transcription levels — rare microbes and rare genes can drive disproportionately large biogeochemical effects, with nitrification genes (amoCAB, nxrAB) and methanol/formate oxidation genes among the most highly expressed (Carnevali et al., 2021).

More recent depth-resolved sequencing at the Slate River floodplain near Crested Butte has refined the picture of nitrogen and carbon cycling. The dominant ammonia oxidizers are not the textbook ammonia-oxidizing bacteria — none were recovered — but rather Nitrosotalea-like archaea and comammox bacteria of the Palsa-1315 clade, both adapted to low-ammonia (oligotrophic) conditions and equipped to scavenge alternative nitrogen sources such as urea, cyanate, and biuret (Rasmussen et al., 2025). Methane cycling is similarly unconventional: methanogens appear only in deep anoxic sediments, conventional aerobic methanotrophs are absent, and instead the archaeon Candidatus Methanoperedens and uncultured bacterial lineages handle methane oxidation, sometimes reaching extreme local abundance (Rasmussen et al., 2024). Tied to these Methanoperedens archaea, researchers working in comparable wetland sediments discovered "Borgs" — giant linear extrachromosomal DNA elements up to about 1 million base pairs long that carry genes for redox reactions and energy conservation, potentially expanding the metabolic repertoire of their hosts through horizontal gene transfer (Al-Shayeb et al., 2022) (Dance, 2021).

Microbial activity also controls the fate of metals and iron-bearing particles. In contaminated floodplain soils, seasonal redox cycles repeatedly dissolve and reprecipitate iron oxides and sulfides, yet dissolved lead concentrations remain low because lead binds tightly to particulate organic matter that persists across these transitions (Dewey et al., 2021). In anoxic floodplain groundwater, up to 72% of dissolved iron actually travels as mobile colloids — silicon-coated ferrihydrite nanoparticles complexed with organic matter — that survive both oxic and anoxic conditions and can deliver iron, carbon, and nutrients to surface waters (Engel et al., 2023).

Current frontier

Research published since 2020 has shifted from cataloging community composition toward linking microbial function to hydrology in mechanistic, predictive ways. New work integrates depth-resolved metagenomics with measurements of water flow and chemistry to ask how hydrological transitions — snowmelt, drought, beaver-induced flooding — reshape microbial habitats in real time. A multi-year study of vertical exchange between biogeochemically active surface soils and underlying gravel beds showed that flooding events flush anoxic soil porewater downward into the gravel, while snowmelt and drought restore oxic conditions, with direct consequences for downstream water quality (Babey et al., 2024). Complementing this, machine-learning-based groundwater modeling is now being used to quantify how beaver ponds alter vertical fluxes between soil and gravel bed, with vertical-to-lateral flux ratios increasing roughly tenfold during ponded conditions (Wang et al., 2025).

In parallel, manual curation of large extrachromosomal elements and refined MAG recovery are revealing previously hidden players. The continuing discovery of Borgs, oligotrophic comammox bacteria, and uncultured nitrite oxidizers in the Nitrospirales suggests that even well-studied nitrogen and methane cycles are governed by lineages we are only beginning to recognize (Rasmussen et al., 2025) (Rasmussen et al., 2024).

Open questions

Major questions remain about how to translate microbial gene content into ecosystem-scale predictions. We still do not know which rare microbes drive disproportionate fluxes of methane, nitrogen, and trace metals, nor how stable the "core" floodplain microbiome will be as snowmelt timing shifts, beaver populations change, and drought intensifies. The biological role of Borgs and other mobile genetic elements — whether they truly expand host metabolism in situ — is unresolved. Linking colloidal iron transport, redox-driven metal cycling, and microbial activity into integrated models of floodplain water quality is a promising frontier, as is understanding how root-regolith interactions and plant communities couple to the subsurface microbiome. Over the next decade, combining long-term metagenomic monitoring with hydrologic modeling and targeted cultivation of unconventional nitrifiers and methanotrophs will be key to forecasting how Gunnison Basin floodplains respond to a warming, more variable climate.

References

Al-Shayeb, B., et al. (2022). Borgs are giant genetic elements with potential to expand metabolic capacity. Nature. →

Babey, T., et al. (2024). Mountainous floodplain connectivity in response to hydrological transitions. Water Resources Research. →

Carnevali, P. B. M., et al. (2021). Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. Microbiome. →

Dance, A. (2021). Massive DNA "BORG" Structures Perplex Scientists. Nature. →

Dewey, C., et al. (2021). Porewater Lead Concentrations Limited by Particulate Organic Matter Coupled With Ephemeral Iron(III) and Sulfide Phases during Redox Cycles Within Contaminated Floodplain Soils. Environmental Science & Technology. →

Engel, M., et al. (2023). Structure and composition of natural ferrihydrite nano-colloids in anoxic groundwater. Water Research. →

Lavy, A., et al. (2019). Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. Ecology and Evolution. →

Northup, D. E., et al. (2010). Diversity of rock varnish bacterial communities from Black Canyon, New Mexico. Journal of Geophysical Research: Biogeosciences. →

Parchert, K., et al. (2012). Fungal Communities Associated with Rock Varnish in Black Canyon, New Mexico: Casual Inhabitants or Essential Partners? Geomicrobiology Journal. →

Rasmussen, A. N., et al. (2024). Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems. →

Rasmussen, A. N., et al. (2025). Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain. Environmental Microbiology. →

Wang, Y., et al. (2025). Quantifying groundwater response and uncertainty in beaver-influenced mountainous floodplains using machine learning-based model calibration. Water Resources Research. →