Time series sampling of aquatic ecosystems is a powerful approach to detecting and perceiving ecosystem change, and the drivers contributing to that change. The concept of the "Invisible Present" states that some changes cannot be observed without extended and sufficiently dense sampling. Microbial communities are sensitive response variables and therefore sentinels of change. Freshwater and marine microbial time series are being used to unravel microbial community dynamics and understand the implications of change with respect to community function. They can also be used to infer terrestrial contributions to aquatic communities, including contaminant organisms delivered in storm water inputs. Attendees will leave the session able to explain why time series are important for understanding microbial ecology and evolution, and what we can (and can't) learn from them. They will also be able to identify major roadblocks preventing advances on this topic, along with proposed near-term next steps.
Lead Organizer: Katherine Mcmahon, University of Wisconsin-Madison (trina.mcmahon@wisc.edu)
Co-organizers:
Ryan Newton, University of Wisconsin Milwaukee (newtonr@uwm.edu)
Presentations
09:00 AM
Bacterial ecology and evolution converge on seasonal and decadal scales (8397)
Primary Presenter: Robin Rohwer, The University of Texas at Austin (robin.rohwer@gmail.com)
Ecology and evolution are distinct theories, but both processes unfold on contemporary time scales in microbiomes. To observe this, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. Using 2,855 representative genomes, we observed recurring annual patterns in species abundance and strain composition for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that strain dynamics similar to both ecological differentiation and competition were common. Overlayed upon seasonal patterns, we observed long-term change in strain composition in one in five species, including gradual changes, step changes, and disturbances followed by resilience. Seven members of the most globally abundant freshwater family, Nanopelagicaceae, experienced abrupt change in an unusually hot and dry year following a species invasion. This shift in strain composition coincided with positive selection of genes involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds are central to freshwater responses to global change. Across all taxa, we observed the same seasonal and decadal dynamics in both interspecific ecological and intraspecific evolutionary processes, with no clear delineation between ecology and evolution. We propose that rather than focusing on feedbacks between separate theories of ecology and evolution, we should adopt a new unified approach that views ecology and evolution as a single continuum.
09:15 AM
THERMAL STRUCTURE OF THE WATER COLUMN CONTROLS FREE-LIVING AND PARTICLE-ASSOCIATED PROKARYOTIC COMMUNITIES IN THE LAURENTIAN GREAT LAKES (8118)
Primary Presenter: Maria Hernandez Limon, University of Chicago (maria_hernandez@alumni.brown.edu)
The range of biogeochemical gradients in the Laurentian Great Lakes, in addition to the Lakes’ rapid warming, make the system a natural laboratory for studying microbial biogeography under climate change. Here we present an eight year timeseries of 16S rRNA sequencing from both free-living and particle-attached prokaryotic communities, collected across the five Great Lakes during episodic spring and summer sampling - totalling over 1600 samples. We find that water strata associated with thermal stratification harbor distinct microbial communities, even in conditions of inverse stratification where the strata differ in temperature by only ~2 degrees. Additionally, water temperature is one of the main drivers of community composition variance between strata. The free-living community is less diverse than the particle-associated community and more sensitive to environmental change. By contrast, individual taxa in the particle associated community have stronger relationships with temperature than those in the free-living size fraction. Overall, the structure of the prokaryotic community, the environmental drivers, and the effect of those drivers differ between size fractions. Together, our results demonstrate the effect of temperature on the community structure of prokaryotes in the Great Lakes and quantify year-to-year variability over 8 years. This baseline understanding is critical for detecting future changes and trends driven by ongoing warming.
09:30 AM
In situ microbial successional dynamics of natural and model freshwater particles (8433)
Primary Presenter: Marian Schmidt, Cornell University (marschmi@cornell.edu)
Anthropogenic disturbances and climate change are increasing the density and modifying the nature of aquatic particles, which serve as important microbial habitats. Here, we conducted a short in situ time-series experiment over 6 days and 13 time points at the Cornell Experimental ponds. We evaluated the impact of increased particulate organic matter on microbial communities by adding model chitin particles to dialysis bag mesocosms in triplicate. We measured both free-living and particle-associated microbial communities through 16S rRNA gene sequencing, performed images analysis for particle aggregation and qPCR for absolute quantification of the 16S rRNA gene in each fraction. While particle richness and eveness did not differ between experimental groups, the evenness of the free-living communities increased with the chitin particle addition. Particle aggregation occurred in both control and experimental mesocosms, with a more prnounced effect in the chitin addition. At peak aggregation, the chitin addition exhibited a simultaneously low evenness in the particle communities. The experimental group was significant and accounted for a greater proportion of variation in the composition of particle communities compared to the free-living communities. Finally, control mesocosms had Cyanobacterial dominated particles composed of filamentous and colonial genera whereas experimental chitin particles had more Bacteroidota and Gammaproteobacterial genera. This experimental approach aids in precise measurement and prediction of microbial community responses to environmental changes using specific particle substrates.
09:45 AM
HIGH-FREQUENCY SAMPLING ACROSS PRECIPITATION EVENTS REVEALS “HIDDEN” DYNAMICS IN MICROBIAL POLLUTANT LOADING TO AN URBAN RIVER (8302)
Primary Presenter: Ryan Newton, University of Wisconsin-Milwaukee (newtonr@uwm.edu)
Many urban rivers have impaired designations and restrictions on recreational uses because of pollutants entering from the surrounding landscape. Precipitation events drive much of this yearly pollutant loading, but discharge regulations are often determined from limited within event sample collection. The Milwaukee River in Milwaukee, WI USA has discharge regulations for water clarity and fecal contamination that are evaluated by total maximum daily load (TMDL) criteria for total suspended solids (TSS) and fecal indicator bacteria (FIB). To better understand the source, timing, and loading of these pollutants, we used high-frequency time-series sampling (2-hour composites) to collect river water for 13 events. During heavy rains, we found that the microbial community could undergo rapid member displacement by rain-driven microbial immigrants. This rapid flux from the landscape included heavy loading of fecal-associated bacteria, but this loading was uncoupled from changes in sediment loading, indicating the pollutants originate from different sources. For regulatory purposes, our results revealed large FIB loading early in precipitation events that far exceeded later event-driven loads. This within-event variability had not been accounted for fully in previous regulatory estimates, which we believe has resulted in TMDL estimates that are >100-fold below current yearly loading conditions. We contend, microbial time-series can reveal the hidden-present for rapidly changing systems as well as serve as indicators of longer-term ecosystem change.
10:00 AM
DEPTH-DEPENDENT DYNAMICS OF PROTIST COMMUNITIES AS AN INTEGRAL PART OF SPRING SUCCESSION IN A FRESHWATER RESERVOIR (7908)
Primary Presenter: Indranil Mukherjee, Biology Centre, Czech Academy of Sciences (indranilmukherjee04@yahoo.com)
Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in deeper strata of temperate lakes. We aimed to address this by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a two-month period covering transition from mixing to stratification, we collected water samples from three depths (0.5, 10 and 30 m) and up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by CARD-FISH. Following the rapid changes in environmental and biotic parameters during spring, microbial communities displayed swift transition from a homogeneous to distinct strata-specific communities. Epilimnion exhibited the prevalence of auto-, mixotrophic protists dominated by cryptophytes and associated with spring algal bloom-specialized bacteria. In contrast, meta- and hypolimnion protist community was dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans and excavates co-occurring with bacteria associated with lake snow. Our high-resolution sampling matching the typical dividing time of microbes along with combined microscopic and molecular approach and inclusion of all the components of microbial food web allowed us to follow depth-specific populations' succession and interactions in a deep lentic ecosystem.
10:15 AM
Ecogenomics of microbes in stratified water columns with a history of mixing disturbance (8383)
Primary Presenter: Katherine Mcmahon, University of Wisconsin-Madison (trina.mcmahon@wisc.edu)
Many freshwater lakes thermally stratify seasonally. Darkly stained bog lakes have especially steep thermal and biogeochemical gradients during the summer, with high oxygen demand driving highly reducing conditions in the hypolimnion. Microbial communities stratify vertically to position themselves at optimal depths based on their lifestyles. This structure can be disrupted by physical water column mixing. Here we describe a dataset spanning 5 years in three humic bog lakes. One is polymictic, one is usually dimictic, and the third is dimictic but was artificially mixed in 2008. Metagenomic sequencing was used to study the community composition and functional potential across the time series. Green sulfur bacteria in the genus Chlorobium were abundant in the two dimitic lakes, but were absent from the polymictic lake. Organisms capable of extracellular electron transfer co-occurred with the Chlorobium, pointing to cryptic cycling of electron carriers in the water. Both the species composition and population-level genetic variation were distinct among the three lakes and thermal layers. These findings shed light on the organisms responsible for biogeochemical cycling in these lakes, which are analogs for boreal lakes with high rates of carbon burial.
SS05 - The Power of Time Series for Unraveling Aquatic Microbial Community Interactions and Functions
Description
Time: 9:00 AM
Date: 3/6/2024
Room: Meeting Room MN