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Two decades of bacterial ecology and evolution in a freshwater lake
Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. Further, these genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.
Intelligent Electrochemical Sensors for Precise Identification of Volatile Organic Compounds Enabled by Neural Network Analysis
The volatile organic compounds (VOCs) in a wide spectrum of categories were identified as biomarkers in aquatic environments, playing an important role in marine and freshwater ecology and global atmospheric chemistry. VOCs released from biofuel have also attracted increasing attention. Although the importance has been recognized, the portable detection and analysis methods of VOC in aquatic systems have not yet been well developed and understood. Here, in this work, we innovatively proposed an intelligent electrochemical sensing approach to classify and quantify VOCs in solution. Utilizing the cyclic voltammetry (CV) method with an ionic liquid (IL)-based electrolyte, we analyzed 50 μL samples of various VOC analytes, including acetic acid (AC), acetone, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethanol, formaldehyde, formic acid, methanol, methyl formate (MF), toluene, and a formaldehyde-methanol mixture, along with deionized water (DI water). The generated voltammograms were subsequently analyzed using our uniquely designed and optimized 1-D convolutional neural network (1D-CNN). This deep-learning algorithm achieved a 99.09% accuracy in VOC classification validated through fivefold cross-validation and demonstrated an impressive 94.4% test accuracy for methanol detection within a 10 μL error range. For quantification, the system accurately categorized methanol volumes ranging from 0 to 50 μL in 10 μL increments, achieving a 98.18% accuracy. A notable linear correlation (R2 = 95.56%) was found between max current density at the oxidation peak and methanol volume, with the limit of detection (LOD) at 9.3 μL. Such a sensing method exhibits potential for portability, high accuracy, and generalization in the classification and quantification, ultimately reshaping the realm of VOC analysis in solution.
Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie
Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.
Integrating the Social, Hydrological and Ecological Dimensions of Freshwater Health: The Freshwater Health Index
Degradation of freshwater ecosystems and the services they provide is a primary cause of increasing water insecurity, raising the need for integrated solutions to freshwater management. While methods for characterizing the multi-faceted challenges of managing freshwater ecosystems abound, they tend to emphasize either social or ecological dimensions and fall short of being truly integrative. This paper suggests that management for sustainability of freshwater systems needs to consider the linkages between human water uses, freshwater ecosystems and governance. We present a conceptualization of freshwater resources as part of an integrated social-ecological system and propose a set of corresponding indicators to monitor freshwater ecosystem health and to highlight priorities for management. We demonstrate an application of this new framework -the Freshwater Health Index (FHI) - in the Dongjiang River Basin in southern China, where stakeholders are addressing multiple and conflicting freshwater demands. By combining empirical and modeled datasets with surveys to gauge stakeholders' preferences and elicit expert information about governance mechanisms, the FHI helps stakeholders understand the status of freshwater ecosystems in their basin, how ecosystems are being manipulated to enhance or decrease water-related services, and how well the existing water re-source management regime is equipped to govern these dynamics over time. This framework helps to operationalize a truly integrated approach to water resource management by recognizing the interplay between governance, stakeholders, freshwater ecosystems and the services they provide
Experimental evidence for recovery of mercury-contaminated fish populations
Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions in fish MeHg concentrations following reductions in Hg additions to a boreal lake and its watershed. During the seven-year addition phase, we applied enriched Hg isotopes to increase local Hg wet deposition rates fivefold. The Hg isotopes became increasingly incorporated into the food web as MeHg, predominantly from additions to the lake because most of those in the watershed remained there. Thereafter, isotopic additions were stopped, resulting in an approximately 100% reduction in Hg loading to the lake. The concentration of labelled MeHg quickly decreased by up to 91% in lower trophic level organisms, initiating rapid decreases of 38–76% of MeHg concentration in large-bodied fish populations in eight years. Although Hg loading from watersheds may not decline in step with lowering deposition rates, this experiment clearly demonstrates that any reduction in Hg loadings to lakes, whether from direct deposition or runoff, will have immediate benefits to fish consumers.
Challenges of open data in aquatic sciences: issues faced by data users and data providers
Free use and redistribution of data (i.e., Open Data) increases the reproducibility, transparency, and pace of aquatic sciences research. However, barriers to both data users and data providers may limit the adoption of Open Data practices. Here, we describe common Open Data challenges faced by data users and data providers within the aquatic sciences community (i.e., oceanography, limnology, hydrology, and others). These challenges were synthesized from literature, authors’ experiences, and a broad survey of 174 data users and data providers across academia, government agencies, industry, and other sectors. Through this work, we identified seven main challenges: 1) metadata shortcomings, 2) variable data quality and reusability, 3) open data inaccessibility, 4) lack of standardization, 5) authorship and acknowledgement issues 6) lack of funding, and 7) unequal barriers around the globe. Our key recommendation is to improve resources to advance Open Data practices. This includes dedicated funds for capacity building, hiring and maintaining of skilled personnel, and robust digital infrastructures for preparation, storage, and long-term maintenance of Open Data. Further, to incentivize data sharing we reinforce the need for standardized best practices to handle data acknowledgement and citations for both data users and data providers. We also highlight and discuss regional disparities in resources and research practices within a global perspective.
Diel variation in CO 2 flux is substantial in many lakes
Lakes play a significant role in the global carbon cycle, acting as sources and sinks of carbon dioxide (CO 2 ). In situ measurements of CO 2 flux (FCO 2 ) from lakes have generally been collected during daylight, despite indications of significant diel variability. This introduces bias when scaling up to whole-lake annual aquatic carbon budgets. We conducted an international sampling program to ascertain the extent of diel variation in FCO 2 across lakes. We sampled 21 lakes over 41 campaigns and measured FCO 2 at 4-h intervals over a full diel cycle. Rates of FCO 2 ranged from −3.16 to 4.39 mmol m −2 h −1 . Integrated over a day, FCO 2 ranged from −381.68 to 878.49 mg C m −2 d −1 (mean = 76.54) across campaigns. We identified three characteristic diel patterns in FCO 2 related to trophic status and show that for half of the campaigns, daily flux estimates were biased by > 50% if based on a single (daytime) measurement.
A meta-evaluation of the quality of reporting and execution in ecological meta-analyses
Quantitatively summarizing results from a collection of primary studies with meta-analysis can help answer ecological questions and identify knowledge gaps. The accuracy of the answers depends on the quality of the meta-analysis. We reviewed the literature assessing the quality of ecological meta-analyses to evaluate current practices and highlight areas that need improvement. From each of the 18 review papers that evaluated the quality of meta-analyses, we calculated the percentage of meta-analyses that met criteria related to specific steps taken in the meta-analysis process (i.e., execution) and the clarity with which those steps were articulated (i.e., reporting). We also re-evaluated all the meta-analyses available from Pappalardo et al. to extract new information on ten additional criteria and to assess how the meta-analyses recognized and addressed non-independence. In general, we observed better performance for criteria related to reporting than for criteria related to execution; however, there was a wide variation among criteria and meta-analyses. Meta-analyses had low compliance with regard to correcting for phylogenetic non-independence, exploring temporal trends in effect sizes, and conducting a multifactorial analysis of moderators (i.e., explanatory variables). In addition, although most meta-analyses included multiple effect sizes per study, only 66% acknowledged some type of non-independence. The types of non-independence reported were most often related to the design of the original experiment (e.g., the use of a shared control) than to other sources (e.g., phylogeny). We suggest that providing specific training and encouraging authors to follow the PRISMA EcoEvo checklist recently developed by O’Dea et al. can improve the quality of ecological meta-analyses.
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.
Quantification of Dissolved O 2 in Bulk Aqueous Solutions and Porous Media Using NMR Relaxometry
Effects of dissolved paramagnetic oxygen (O 2 ) in water on 1 H nuclear magnetic resonance (NMR) Carr-Purcell-Meiboom-Gill (CPMG) experiments is evaluated at a 1 H Larmor frequency of 2 MHz. Dissolution of O 2 into water significantly reduces the 1 H transverse relaxation coefficient (T 2 ). For deoxygenated water, T 2 is 3388 ms, water at ambient atmospheric conditions (7.4 mg/L O2) exhibits a T2 of 2465 ms, and dissolution of 2710 mg/L O 2 further reduces T 2 to 36 ms. The results were fit with an empirical model to facilitate prediction of T 2 times for bulk water as a function of paramagnetic oxygen concentrations in solution. Dissolved O 2 also greatly influences 1 H NMR CPMG experiments of confined water in a model system composed of Berea sandstone. For this system, 90 mg/L O 2 in H 2 O enhances T 2 relaxation of bulk water such that the relaxation time is comparable to physically confined water in the sandstone pores. Given the sensitivity of NMR T 2 coefficients to paramagnetic oxygen, low-field NMR-based characterization of fluid and porous media structure requires control of dissolved oxygen, as geospatial variation in the partial pressure of O 2 alone is expected to perturb fluid and pore relaxation times by up to 60 and 36%, respectively.
Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States
Abstract Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E ( mcyE ) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis . Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.
Artificial light at night outweighs temperature in lengthening urban growing seasons
Plant growing seasons are largely regulated by light and temperature. Cities are increasingly hot (higher air temperature), from the urban heat island effect, and bright (artificial light at night, ALAN). However, the relative effect of heat and light on the timing of plant growth events, called phenology, is unclear, limiting our understanding under climate change and urbanization. Here we used multiple satellite observations of 428 Northern Hemisphere cities from 2014 to 2020 to analyze phenological patterns along a gradient from rural to urban. We found that ALAN increased exponentially toward urban centers, and exerted stronger influence than air temperature in lengthening the urban growing season, especially by delaying its end, although the effects varied across climate zones. Our findings demonstrate that ALAN is a critical driver of vegetation dynamics in cities, one we should consider during urban management and development.
Taxonomic and Functional Diversity of Aquatic Macroinvertebrate Assemblages and Water Quality in Rivers of the Dry Tropics of Costa Rica
One of Costa Rica’s driest areas is the province of Guanacaste, in the Pacific Northwest, with almost no rain during the dry season from November to April. Due to this marked seasonality, the area is covered by dry tropical deciduous forest, considered the most threatened and least known tropical ecosystem in this area. This study analyzes and characterizes the assemblages of aquatic macroinvertebrates in water bodies within the Tempisque basin. Biological water quality was measured using the BMWP′-CR index. Macroinvertebrate assemblages were analyzed using abundance, richness, and functional feeding group approaches (FFG). Partial least square (PLS) analyses were performed, and the relationships between environmental factors and macroinvertebrate assemblages are also discussed. Macroinvertebrate assemblages were dominated numerically by mayflies, caddisflies, flies, and beetles. The BWMP′-CR index showed varying biological water quality, ranging from “very bad” to “excellent,” depending on rainfall and site management. Results suggest that tropical Mesoamerican rivers contradict the “river continuum concept” because predators and scrapers displace shredders in numbers. On the other hand, the study area shows a notable high richness of the Coleoptera genera. The class Rhynchocoela (Nemertea) is reported for the first time in Central America. The results indicate that the dry forest river ecosystem shows staggering biodiversity despite the surrounding agricultural land use, probably because of their older origin concerning tropical rain forests in Central America.
The Zooplankton International Geospatial (ZIG) dataset: A global repository of spatiotemporal freshwater zooplankton community composition data to support ecological research
Zooplankton play critical roles in aquatic ecosystem function and food webs. Nevertheless, global syntheses of their abundance and community dynamics are challenging due to methodological differences across monitoring programs, taxonomic inconsistencies, and a lack of standardized metadata. To reconcile these challenges, we assembled, curated, validated, and harmonized the Zooplankton International Geospatial (ZIG) dataset, which includes co-located and contemporaneous zooplankton, water chemistry, and limnological data from 307 lakes and reservoirs. ZIG includes waterbodies from each major lake thermal region and range in size from 0.8-2,805,8600 hectares. Temporal coverage for individual waterbodies ranges between 1-60 years of data (median = 4 years) with sampling from once annually to weekly. ZIG is publicly available and can be used to understand freshwater biodiversity change and its drivers at unprecedented scales, and we consider it to be a cornerstone for future investigations of freshwater biology, chemistry, and ecology.
The Zooplankton International Geospatial dataset: A global repository of spatiotemporal freshwater zooplankton community composition data from lakes and reservoirs to support ecological research
Zooplankton transfer substantial energy in aquatic food webs and are used as indicators of environmental change. Syntheses of zooplankton community dynamics globally require datasets that span a wide range of environmental gradients; however, these datasets are limited due to methodological differences across programs, taxonomic inconsistencies, and a lack of standardized metadata. To reconcile these challenges, we created the Zooplankton International Geospatial (ZIG) dataset, which includes original zooplankton, water physical and chemical variables, and lake morphometric data from 311 inland lakes and reservoirs. ZIG includes waterbodies ranging in size from 0.005 to 82,100 km2 and spanning broad latitudinal (−47.26 to 64.90) and longitudinal ranges (−165.04 to 176.53). Temporal coverage for individual waterbodies ranges between 1 and 60 yr with sampling frequency ranging from annually to weekly. With its extensive coverage and content, we consider ZIG to be a cornerstone for future investigations of global scale lake biodiversity change.
TEMPEST3 surface runoff water chemistry and organic matter composition
Coastal flooding, driven by storm surges and sea level rise, can mobilize organic matter (OM) via runoff, while introducing compositionally distinct OM (e.g., estuarine OM) into the system. To understand event-scale OM dynamics, we monitored source waters and surface runoff during an ecosystem-scale field manipulation experiment, TEMPEST (Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments), in June 2024. The TEMPEST experiment is part of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales – Field, Measurements, and Experiments) project and designed to investigate biogeochemical and ecological impacts of freshwater and seawater flooding on coastal terrestrial-aquatic interface ecosystems by simulating freshwater and seawater storm events in two 2000m2 coastal upland forest plots (freshwater and brackish seawater plots). The temporal coverage of this dataset is during the TEMPESTⅢ event (June 11-13, 2024). This dataset contains: - Surface runoff discharge measured by flumes - Sensor data (specific conductivity, salinity, dissolved oxygen, and temperature) - Particle size distribution - Total suspended sediment concentrations (TSS), particulate and dissolved organic carbon (POC, DOC) concentrations, total nitrogen and total dissolved nitrogen (TN, TDN) concentrations - Bulk particulate and dissolved OM compositions (stable C and N isotopes of particulates and optical measurements of chromophoric dissolved OM) - High resolution mass spectrometry analysis data - Water isotope data All data files are plain-text CSV (comma-separated value), and no special software is required to read them.
Predator mass mortality events restructure food webs through trophic decoupling
Predators have a key role in structuring ecosystems. However, predator loss is accelerating globally, and predator mass-mortality events (MMEs)—rapid large-scale die-offs—are now emblematic of the Anthropocene epoch. Owing to their rare and unpredictable nature, we lack an understanding of how MMEs immediately impact ecosystems. Past predator-removal studies may be insufficient to understand the ecological consequences of MMEs because, in nature, dead predators decompose in situ and generate a resource pulse, which could alter ensuing ecosystem dynamics by temporarily enhancing productivity. Here we experimentally induce MMEs in tritrophic, freshwater lake food webs and report ecological dynamics that are distinct from predator losses or resource pulses alone, but that can be predicted from theory. MMEs led to the proliferation of diverse consumer and producer communities resulting from weakened top-down predator control and stronger bottom-up effects through predator decomposition. In contrast to predator removals alone, enhanced primary production after MMEs dampened the consumer community response. As a consequence, MMEs generated biomass dynamics that were most similar to those of undisturbed systems, indicating that they may be cryptic disturbances in nature. These biomass dynamics led to trophic decoupling, whereby the indirect beneficial effects of predators on primary producers are lost and later materialize as direct bottom-up effects that stimulate primary production amid intensified herbivory. Furthermore, these results reveal ecological signatures of MMEs and demonstrate the feasibility of forecasting novel ecological dynamics arising with intensifying global change.