Think global, act local: The small‐scale environment mainly influences microbial community development and function in lake sediment

Abstract

The early stages of community development influence longer-term establishment of species, traits, and ultimately ecosystem function. How this process varies with small-and large-scale abiotic and biotic conditions is poorly studied in microbes. Here, we tested how different spatial scales influenced the rate at which taxonomic and functional composition of microbial communities changed over time in lake sediments, and whether these changes occurred synchronously across different environments given the same initial communities. We manipulated the small-scale environment by creating sediments with different terrestrial organic matter (t-OM) quantity and quality, and placing these in two lakes differing in trophic status to vary the large-scale environment. We found that archaeal and bacterial communities, but not fungi, became taxonomically dissimilar over 2 months despite being derived from the same initial leaf material, primarily because of small-scale environmental conditions. Sediment t-OM quantity consistently explained changes in community composition both temporally within mesocosms and spatially between mesocosms in different lakes. Archaea, bacteria, and fungi also varied by up to 10 times in how quickly they changed, providing among the first evidence in the same study system that they respond differently over time to abiotic and biotic conditions. Finally, functional composition was influenced by both small-and large-scale environmental conditions, with genes involved in t-OM decomposition showing some of the largest changes in abundance after 1 yr. Our study highlights that future changes to both sediments and lake waters can modify how sediment microbial communities develop with consequences for important ecosystem functions like carbon cycling.

Organic matter and metal loadings influence the spatial gradient of the benthic bacterial community in a temperate estuary

“…These findings are consistent with observational evidence that the abundance rather than presence of bacterial taxa is limited by resource availability in sediments (Louca et al 2018;Orland et al 2019). Our study, therefore, supports the necessity to sample multiple sites and consider sediments differently from the water column when bacterial processes are upscaled to entire estuary basins (Orland et al 2020).…”

“…Neither bottom water temperature or dissolved NO x concentrations showed significant correlations with the sediment microbiomes, suggesting that bacterial groups are more tightly controlled by local sediment abiotic and biotic parameters rather than large fluctuations in the overlying bottom water. The disconnect between the bottom water and the sediment has important ramifications, because it has been suggested that dynamic water column changes, including nutrient bursts, may have little effect on the compositional dynamics of sediment microbes (Orland et al 2020). These findings suggest that rather than an indication of current state, perhaps our data give some indication of trajectory or temporal stability.…”

Microbial community composition, and not pH, influences lake sediment function

“…Lake sediments are a useful system for studying relationships between microbial community composition and ecosystem function because sediment microbial communities mediate carbon diagenesis and fate and are an important component in carbon cycling (Fitch et al, 2018; Jones & Simon, 1981; Orland et al, 2020; Schwarz et al, 2008). Additionally, differences in the composition of sediment microbial communities have been linked to variation in rates of carbon biogeochemistry (rates of CO 2 and CH 4 production) across the landscape (Bertolet et al, 2019; Matheus Carnevali et al, 2018; Weise et al, 2016).…”

“…pH is widely recognized as an important environmental determinant of sediment microbial community composition (Orland et al, 2020; Tripathi et al, 2018; Xiong et al, 2012), especially of the composition and activity of the methanogen community. Lake sediment methanogen communities are consistently differentiated by pH (Bertolet et al, 2019; Phelps & Zeikus, 1984; Wen et al, 2017).…”

Macrophyte meadows mediate the response of the sediment microbial community to ultraviolet radiation

“…Within the aquatic microbial community organisms tightly linked to the sediment of waterbodies, or the sediment microbial community, are of special interest (Orland et al, 2020). This is a complex assemblage occupying different layers of sediment with distinct physical and chemical conditions (Spring et al, 2000).…”