Microbial metabolisms drive many important biogeochemical processes in all aquatic ecosystems. In turn, microbial activity depends on the availability of nutrients like carbon, nitrogen, or phosphorus, which can also profoundly affect microbial community assembly. Recent technological advances in microbial and biogeochemical techniques have provided novel insights into the coupling between microbial activity and geochemistry, but it remains challenging to predict the effects of present and future environmental changes. Sequencing approaches such as metagenomics have opened the “black box” of environmental microbiology, using the presence of key genes to predict the metabolism of novel microbes. However, a disconnect still exists between connecting in situ geochemical measurements, such as nutrient cycling rates and fluxes, with the genetic potential of resident microbial communities.

This session highlights advances in linking aquatic geochemistry and microbiology. Any work related to microbial processes and biogeochemistry is welcome; methods from both fields need not be included in each presentation, as long as data has relevance to both microbes and biogeochemistry. For instance, studies of biogeochemical rate measurements or models are welcome, provided they are focused on microbially-driven processes, and as are studies solely on microbial ecology but focused on microbes with biogeochemical relevance. Studies may include field sampling, method development, computational analysis, and/or modeling. Biogeochemical focus may include any cycles and processes, including “traditional” cycles as well as other aquatic contaminants such as antimicrobial resistance genes, pharmaceuticals, PFAS, and others. We welcome submissions studying any aquatic ecosystem, whether freshwater, brackish, or marine, and including benthic and/or water column data. Studies including microbial data may use broad community-level data or targeted experiments with specific populations or species. We take a broad definition of “microbe” and welcome studies of archaea, bacteria, eukaryotic microbes, and viruses. In individual presentations or in the session as a whole, we strive to bring together interdisciplinary work using a variety of approaches to explore the intersection of aquatic microbial ecology and biogeochemistry and integrate knowledge from disparate fields and a wide range of ecosystems.

Lead Organizer: Julian Damashek, Hamilton College (jdamashe@hamilton.edu)

Co-organizers:

Benjamin Kramer, University of Minnesota Duluth (bjkramer@umn.edu)

Cody Sheik, University of Minnesota Duluth (cssheik@d.umn.edu)

Annika Mosier, University of Colorado Denver (annika.mosier@ucdenver.edu)

Presentations

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04:00 PM

Drops to data: Harnessing the power of community science to decode aquatic microbiomes (8297)

Tutorial/Invited: Invited, Tutorial

Primary Presenter: Mikayla Borton, Colorado State University (mborton@colostate.edu)

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. To address the fundamental question of how microbial community composition and metabolic function varies across river basins, we employed a community science effort reliant on collaborations with over 150 scientists to facilitate the sampling of >500 surface water samples across the globe. Microbiomes from all sites were characterized using genome resolved metagenomics, offering an unprecedented sampling of the microbial strains and their functional contributions to river biogeochemistry. To openly share this content, we created the Genome Resolved Open Watershed database (GROWdb), which contains the identity and distribution of thousands of unique microbial genomes across rivers. This spatial sampling scheme coupled to a breadth of ecological dimensions (e.g. stream order, chemistry, land use) enabled us to systematically identify the most cosmopolitan microbiome members within the Proteobacteria, Actinobacteria, and Bacteroidetes, while also revealing local drivers of strain specific endemism. Approximately a third of the samples have paired metatranscriptomes and metabolomes, highlighting members of the Methylopumilus, Polynucleobacter, and Planktophila as highly active community members. Notably, we provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices.

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04:30 PM

EXPLORING ONTOGENETIC CHANGES IN THE GUT MICROBIOMES OF TWO COMMON FISH & THEIR CONNECTIONS TO NUTRIENT EXCRETION (8243)

Primary Presenter: Carrie Ann Sharitt, Miami University (OH) (sharitca@miamioh.edu)

Fish make significant contributions to the cycling of nutrients within aquatic ecosystems, and traits such as  body size, phylogeny, and trophic level impact the quality and quantity of excretion from consumers. Previous studies have shown environmental and organismal traits impact the gut microbiomes of consumers. However, few studies have examined ontogenetic trends in fish gut microbiomes and how gut microbiomes influence nutrient cycling. Understanding the relationship between gut microbiome and developmental stage may be important for understanding nutrient cycling by fish.   We conducted an exploratory study on the gut microbiomes of two fish species common in the Midwest USA, gizzard shad (Dorosoma cepedianum) and bluegill (Lepomis macrochirus), throughout their development. Both species undergo diet shifts with age. We collected 8 fish per age class (larvae, 1-year old, and 2+ year old) of each species every month from May-September in Acton Lake (Ohio). Gut microbial communities were studied via amplicon sequencing of the 16s rRNA. Additional 16S rRNA libraries were collected from lake water and sediment.   Our project explores the community composition of the microbiome through fish development, with an emphasis on dietary transitions, as well as how the environmental microbial communities and geochemistry influence the gut microbiome. We aim to also relate microbial community composition to the excretion rates of nitrogen (N) and phosphorus (P) in each age class. This builds a foundation for future work that links the role of microbiomes to ecosystem processes.

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04:45 PM

IDENTIFYING THE ACTIVE MICROBIAL COMMUNITY IN YELLOWSTONE RIVER WATER AMENDED WITH METHYLATED SUBSTRATES (8213)

Primary Presenter: William Christian, Montana State University (wcchrist@mtu.edu)

Rivers connect ecosystems and play a key role in nutrient cycling. Despite their importance, most microbiology research done on rivers has failed to account for microbial activity, instead focusing solely on marker gene or metagenomic surveys. Metagenomic studies are useful for profiling microbial communities and defining their metabolic potential, but they fail to provide information about the activity of the extant microbes or determine under which conditions that metabolic potential is realized. This results in a systemic disconnect between our understanding of the diversity of microbial communities and their biogeochemical functions. To bridge this gap, our work introduces the use of BioOrthogonal Non-Canonical Amino acid Tagging coupled to Fluorescence Activated Cell Sorting (BONCAT-FACS) to examine Yellowstone River samples. BONCAT-FACS depends on the incorporation of an amino acid analog into the proteins of translationally active cells. This amino acid analog can then be tagged with a fluorescent dye. Using a cell sorter, the fluorescently labeled cells can be separated, allowing for the identification of the anabolically active community. In this work, BONCAT-FACS was preceded by incubating Yellowstone River water with methylated substrates (methylamine, glycine betaine) implicated in aerobic methane production, under light and dark conditions. We demonstrate that BONCAT-FACS is a powerful tool to determine the members of the riverine microbial community actively involved in carbon cycling and, in this instance, potentially involved in methane production.

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05:00 PM

Driving the adaptation of microbial communities of the thawing permafrost: Mobile genetic elements at play (8170)

Primary Presenter: Valentine Cyriaque, Institut National de la Recherche Scientifique (valentine.cyriaque@inrs.ca)

Climate change is driving significant transformations in northern ecosystems, impacting the structure and functioning of these environments. Permafrost thaw results in the expansion of thermokarst ponds and lakes, which are known to contribute to greenhouse gas (GHG) emissions. Despite the recognition of a high microbial biodiversity in these environments, little is known about the adaptation mechanisms of these microbial communities. Mobile genetic elements like plasmids, could inflect their eco-evolutionary path, contributing to the adaptation of microbes transitioning from terrestrial to aquatic habitats.  This study investigates the role of plasmids in the evolutionary trajectory of these microbial communities using metagenomics. Samples were collected along soil-water continua (active layer, sediments and water) from thermokarst ponds in sporadic (Québec, Canada) and continuous (Nunavut, Canada) permafrost regions.  Among metagenomes collected in sporadic permafrost, preliminary analyses identified 524 contigs out of 253,146 (>1000 bp) as belonging to plasmids. They were particularly abundant in the bottom of the water ponds and in the interstitial water of the active layer. Plasmid beta-diversity was found to be distinct from taxonomic beta-diversity, indicating a unique ecological role. Current efforts are focused on identifying key functions encoded by these plasmids, including genes involved in nutrient cycles and GHG emissions. Preliminary findings suggest that plasmids contribute to the eco-evolutionary dynamics of microbial communities in the thawing permafrost.

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05:15 PM

Symbiotic relationships couple nitrogen and carbon cycles for the production of greenhouse gases in thermokarst ponds (8179)

Primary Presenter: Martial Leroy, Institut national de la recherche scientifique (martial.leroy@inrs.ca)

With the rapid warming of the Arctic, permafrost-affected landscapes are undergoing transitions, including the formation of thermokarst ponds. However, the mechanisms driving greenhouse gases (GHG) cycles in these systems remain relatively unexplored. Previous research showed that thermokarst microbial communities are strongly shaped by nitrogen species and by the quality of dissolved organic matter (DOM). Here, we hypothesized that potential symbiotic or consortium relationships influence GHG production by coupling carbon (C) and nitrogen (N) cycles. As these associations can be influenced by the state of permafrost degradation, we investigated the key functions and pathways of N and GHGs cycles in two permafrost degradation state, a sporadic subarctic permafrost (Whapmagoostui-Kuujjuarapik, Québec) and a continuous Arctic permafrost site showing early signs of degradation (Bylot Island, Nunavut). We used hybrid next-generation sequencing combining short-read paired-end Illumina and long-read Oxford Nanopore for pathways and metagenome-assembled genomes (MAGs) reconstruction. First results revealed various pathways potentially fueling methanogenesis in subarctic thermokarst ponds, notably the involvement of symbiotic relationships between acetate producers and archaeal methanogens, and their link to the quality of the DOM. Ongoing metagenomic analyses of the continuous permafrost site will elucidate whether similar patterns are in place. This research sheds light on the complex interplay between microbial communities, GHG dynamics, C and N cycles in thermokarsts ponds.

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