Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

Abstract

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered.Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

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

“…Temporal variability of freshwater bacterial communities has been much less studied than its spatial counterpart although temporal patterns in community composition can be even stronger than those occurring through space (Portillo et al, 2012 ; Veach et al, 2016 ). Some evidence, mainly from lentic environments, suggests that temporal patterns in bacterial communities may be relatively predictable (Shade et al, 2013 ; Veach et al, 2016 ), with annually recurring seasonal variability in community composition (Crump and Hobbie, 2005 ; David et al, 2021 ; Staley et al, 2015 ). Water temperature (Hullar et al, 2006 ; Teachey et al, 2019 ) and river discharge (Fortunato et al, 2012 ) are the key environmental factors reported to underlie seasonal variability in bacterial communities.…”

Metagenome-derived virus-microbe ratios across ecosystems

“…By contrast, in the case of freshwater Etang des Vallées (EdV) samples, mVMR values were at least 3-4 times higher than fVMRs. This difference seems to suggest that, in addition to VPs, intracellular lytic viruses and proviruses were highly prevalent in the freshwater plankton of this highly diverse shallow lake 33 . The ratio of putative proviruses versus cells was indeed of ~3-7 for EdV samples (depending on the annotation strategy) but very low (<0.3) for marine samples, which seems consistent with the prevalent genome streamlining of marine prokaryotes 34 .…”

“…Actinobacteria and Acidobacteria were dominant in soils. Some actinobacterial taxa were also abundant in the freshwater system 33 . Microbial eukaryotes consistently occurred in most ecosystems, albeit in minor proportions.…”

Variability of the structure of winter microbial communities in Chelyabinsk lakes

“…Moreover, microorganisms have a high response rate to changes in environmental conditions, which gives them value as indicators of water quality and ecosystem condition (Ji et al, 2019;Sagova-Mareckova et al, 2021). Therefore, taxonomic and functional changes in microbial communities in lake water can lead to disturbances in ecosystem processes (David et al, 2021;Xie et al, 2021).…”

“…The abundance of microorganisms can be determined by natural environmental and climatic factors such as (1) temperature, (2) the degree of photosynthetically active radiation penetration, (3) water salinity, (4) the level of dissolved oxygen, (5) the amount of organic and nutrient substances, etc. (Butler et al, 2019;Yue et al, 2020;David et al, 2021). Therefore, the question of which human activities affect the overall structure and diversity of the microbial community in freshwater lakes remains mostly unknown (Cavaco et al, 2019;Nnadozie & Odume, 2019;Yang et al, 2020).…”