Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff

Abstract

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances ( p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira , and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher ( p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii , two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.

Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment

“…Freshwater ecosystems are altered by both natural and anthropogenic pulse disturbances that alter community composition and functioning for varying periods of time. Previously, our laboratory found that long-term press disturbance from manure fertilization runoff resulted in sediment microbial communities that reached a new steady state within 5 months post-disturbance (Beattie et al, 2020). However, we were not able to capture the full dynamics of manure F I G U R E 2 Relative abundance of amplicon sequence variants (ASVs) mapped to 'highly abundant' genera, or those with a relative abundance of at least 0.25% across all samples post-experimental setup.…”

“…Two mesocosm replicates from each treatment on Days 1, 3, 7, 14 and 28 were also sequenced. Sequencing parameters and quality control have been described fully elsewhere (Beattie et al, 2020). Briefly, samples were sequenced using the Illumina MiSeq Platform at the University of Wisconsin Biotechnology Center (Madison, Wisconsin, USA) using 16S rRNA primers for the V3‐V4 hypervariable region.…”

“…Previously, we found that long‐term, press disturbance of manure fertilization runoff in a natural system alters sediment microbiomes beyond the point of recovery, resulting in a new steady state (Beattie et al, 2020). However, we were unable to tease apart the impact of the manure microbial community versus the impact of the nutrients within manure as the primary driver of these lasting microbiome changes.…”

Probiotics beyond the farm: Benefits, costs, and considerations of using antibiotic alternatives in livestock

“…Aquatic ecosystems support a wide variety of habitats that may be altered by anthropogenic contamination contributing to the decline of water quality worldwide. Water quality is a significant concern, especially in areas of intensive livestock farming (Burkholder et al, 2007;Li et al, 2015;Jacobs et al, 2019;Beattie et al, 2020). Runoff from agricultural fields has been shown to contain elevated levels of livestock contaminants including ammonia, nitrogen, and ARB (Sobsey et al, 2006;Beattie et al, 2018;Le et al, 2018;Tang et al, 2020).…”

Deciphering Historical Water-Quality Changes Recorded in Sediments Using eDNA

“…Our results showed that after decades of biogeochemical cycles, the concentrations of TOC, Br and Cl turned out to be main factors affecting the microbial communities in sediments from the degraded stage (Figure 2). Another possible reason for the "records" might be the weak resilience of microbial communities under anthropogenic disturbance (Beattie et al, 2020). Chen et al reported geological evidence for the fragility of Hongfeng Reservoir and another karst reservoir that can hardly recover from pollution even after a long period (Chen et al, 2020).…”