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1. Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

   https://doi.org/10.1186/s40168-024-01831-y  

   Krinos, Arianna I.; Bowers, Robert M.; Rohwer, Robin R.; McMahon, Katherine D.; Woyke, Tanja; Schulz, Frederik (July 2024, Microbiome)

   Abstract BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. ResultsBased on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. ConclusionsWe demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction. 

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2. Decoupled trophic responses to long‐term recovery from acidification and associated browning in lakes

   https://doi.org/10.1111/gcb.14580  

   Leach, Taylor H.; Winslow, Luke A.; Hayes, Nicole M.; Rose, Kevin C. (February 2019, Global Change Biology)

   Abstract Increases in the concentration of dissolved organic matter (DOM) have been documented in many inland waters in recent decades, a process known as “browning”. Previous studies have often used space‐for‐time substitution to examine the direct consequences of increased DOM on lake ecosystems. However, browning often occurs concomitant with other ecologically important water chemistry changes that may interact with or overwhelm any potential ecological response to browning itself. Here we examine a long‐term (~20 year) dataset of 28 lakes in the Adirondack Park, New York, USA, that have undergone strong browning in response to recovery from acidification. With these data, we explored how primary producer and zooplankton consumer populations changed during this time and what physical and chemical changes best predicted these long‐term ecosystem changes. Our results indicate that changes in primary producers are likely driven by reduced water clarity due to browning, independent of changes in nutrients, counter to previously hypothesized primary producer response to browning. In contrast, declines in calcium concomitant with browning play an important role in driving long‐term declines in zooplankton biomass. Our results indicate that responses to browning at different trophic levels are decoupled from one another. Concomitant chemical changes have important implications for our understanding of the response of aquatic ecosystems to browning. 

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3. The role of long-term power-law memory in controlling large-scale dynamical networks

   https://doi.org/10.1038/s41598-023-46349-9  

   Reed, Emily_A; Ramos, Guilherme; Bogdan, Paul; Pequito, Sérgio (November 2023, Scientific Reports)

   Abstract Controlling large-scale dynamical networks is crucial to understand and, ultimately, craft the evolution of complex behavior. While broadly speaking we understand how to control Markov dynamical networks, where the current state is only a function of its previous state, we lack a general understanding of how to control dynamical networks whose current state depends on states in the distant past (i.e. long-term memory). Therefore, we require a different way to analyze and control the more prevalent long-term memory dynamical networks. Herein, we propose a new approach to control dynamical networks exhibiting long-term power-law memory dependencies. Our newly proposed method enables us to find the minimum number of driven nodes (i.e. the state vertices in the network that are connected to one and only one input) and their placement to control a long-term power-law memory dynamical network given a specific time-horizon, which we define as the ‘time-to-control’. Remarkably, we provide evidence that long-term power-law memory dynamical networks require considerably fewer driven nodes to steer the network’s state to a desired goal for any given time-to-control as compared with Markov dynamical networks. Finally, our method can be used as a tool to determine the existence of long-term memory dynamics in networks. 

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4. Aggression Results in the Phosphorylation of ERK1/2 in the Nucleus Accumbens and the Dephosphorylation of mTOR in the Medial Prefrontal Cortex in Female Syrian Hamsters

   https://doi.org/10.3390/ijms24021379  

   Borland, Johnathan M.; Dempsey, Desarae A.; Peyla, Anna C.; Hall, Megan A.; Kohut-Jackson, Abigail L.; Mermelstein, Paul G.; Meisel, Robert L. (January 2023, International Journal of Molecular Sciences)

   Like many social behaviors, aggression can be rewarding, leading to behavioral plasticity. One outcome of reward-induced aggression is the long-term increase in the speed in which future aggression-based encounters is initiated. This form of aggression impacts dendritic structure and excitatory synaptic neurotransmission in the nucleus accumbens, a brain region well known to regulate motivated behaviors. Yet, little is known about the intracellular signaling mechanisms that drive these structural/functional changes and long-term changes in aggressive behavior. This study set out to further elucidate the intracellular signaling mechanisms regulating the plasticity in neurophysiology and behavior that underlie the rewarding consequences of aggressive interactions. Female Syrian hamsters experienced zero, two or five aggressive interactions and the phosphorylation of proteins in reward-associated regions was analyzed. We report that aggressive interactions result in a transient increase in the phosphorylation of extracellular-signal related kinase 1/2 (ERK1/2) in the nucleus accumbens. We also report that aggressive interactions result in a transient decrease in the phosphorylation of mammalian target of rapamycin (mTOR) in the medial prefrontal cortex, a major input structure to the nucleus accumbens. Thus, this study identifies ERK1/2 and mTOR as potential signaling pathways for regulating the long-term rewarding consequences of aggressive interactions. Furthermore, the recruitment profile of the ERK1/2 and the mTOR pathways are distinct in different brain regions. 

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5. Ground-truthing daily and lunar patterns of coral reef fish call rates on a US Virgin Island reef

   https://doi.org/10.3354/ab00755  

   Ferguson, SR; Jensen, FH; Hyer, MD; Noble, A; Apprill, A; Mooney, TA (July 2022, Aquatic Biology)

   Coral reefs comprise some of the most biodiverse habitats on the planet. These ecosystems face a range of stressors, making quantifying community assemblages and potential changes vital to effective management. To understand short- and long-term changes in biodiversity and detect early warning signals of decline, new methods for quantifying biodiversity at scale are necessary. Acoustic monitoring techniques have proven useful in observing species activities and biodiversity on coral reefs through aggregate approaches (i.e. energy as a proxy). However, few studies have ground-truthed these acoustic analyses with human-based observations. In this study, we sought to expand these passive acoustic methods by investigating biological sounds and fish call rates on a healthy reef, providing a unique set of human-confirmed, labeled acoustic observations. We analyzed acoustic data from Tektite Reef, St. John, US Virgin Islands, over a 2 mo period. A subset of acoustic files was manually inspected to identify recurring biotic sounds and quantify reef activity throughout the day. We found a high variety of acoustic signals in this soundscape. General patterns of call rates across time conformed to expectations, with dusk and dawn showing important and significantly elevated peaks in soniferous fish activity. The data reflected high variability in call rates across days and lunar phases. Call rates did not correspond to sound pressure levels, suggesting that certain call types may drive crepuscular trends in sound levels while lower-level critical calls, likely key for estimating biodiversity and behavior, may be missed by gross sound level analyses. 

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