Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

Abstract

Small streams and their headwaters are key sources of microbial diversity in fluvial systems and serve as an entry point for bacteria from surrounding environments. Community assembly processes occurring in these streams shape downstream population structure and nutrient cycles. To elucidate the development and stability of microbial communities along the length of a first-through third-order stream, fine-scale temporal and spatial sampling regimes were employed along Mc-Nutt Creek in Athens, GA, USA. 16S rRNA amplicon libraries were constructed from samples collected on a single day from 19 sites spanning the first 16.76 km of the stream. To provide context for this spatial study and evaluate temporal variability, selected sites at the stream's upper, mid, and lower reaches were sampled daily for 5 days preceding and following the spatial study. In a second study, three sites at and near the creek's headwaters were sampled daily for 11 days to understand initial bacterioplankton community assembly. Both studies revealed decreasing alpha and beta diversity with increasing downstream distance. These trends were accompanied by the enrichment of a small fraction of taxa found at low abundance in headwaterproximal sites. Similar sets of taxa consistently increased in relative abundance in downstream samples over time scales ranging from 1 day to 1 year, many of which belong to clades known to be abundant in freshwater environments. These results underpin the importance of headwaters as the site of rapid in-stream selection that results in the reproducible establishment of a highly stable community of freshwater riverine bacteria. IMPORTANCE Headwater streams are critical introduction points of microbial diversity for larger connecting rivers and play key roles in the establishment of taxa that partake in in-stream nutrient cycling. We examined the microbial community composition of a first-through third-order stream using fine-scale temporal and spatial regimes. Our results show that the bacterioplankton community develops rapidly and predictably from the headwater population with increasing total stream length. Along the length of the stream, the microbial community exhibits substantial diversity loss and enriches repeatedly for select taxa across days and years, although the relative abundances of individual taxa vary over time and space. This repeated enrichment of a stable stream community likely contributes to the stability and flexibility of downstream communities.

Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton

“…Bacterioplankton was less diverse than bacterial communities in mature biofilm at downstream sites, reflecting the strong longitudinal reduction in bacterioplankton diversity. A similar negative spatial trend in bacterioplankton diversity, usually with a drop in diversity at 3rd-or 4th-order sites, has been frequently reported (e.g., Nino-Garcia et al, 2016b;Ruiz-González, Niño-García, Berggren, & del Giorgio, 2017b;Teachey et al, 2019) and has usually been interpreted as the loss of soil-derived "tourist" taxa with increasing distance from the source (Niño-García et al, 2016b;…”

“…Water temperature (Hullar et al, 2006;Teachey et al, 2019) and river discharge (Fortunato et al, 2012) are the key environmental of studying bacterioplankton and biofilm communities simultaneously to allow testing of ecological hypotheses about biodiversity patterns in freshwater bacteria.…”

Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

“…Following collection, DNA samples were extracted with the PowerSoil DNA Isolation kit (Qiagen, Hilden, Germany). Wastewater treatment plant (WWTP) influent and effluent were collected by grab sampling, and DNA was extracted using previously described methods (Teachey et al ., 2019). Poultry samples were collected from poultry litter, DNA was extracted and purified using previously described methods (Oladeinde et al ., 2019).…”

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation

“…Previous studies that investigated microbial communities in water mostly used grab samples that provide a snapshot of microbial water quality at the moment of sample collection ( Staley et al, 2013 ; Van Rossum et al, 2015 ; Ghaju Shrestha et al, 2017 ; Hassell et al, 2018 ; Cagle et al, 2019 ; Teachey et al, 2019 ). Here, we used Moore swabs, which act as a filter and capture microorganisms that flow through a stream during the 24 h the swab is deployed.…”