Mining spatiotemporal co-occurrence patterns in solar datasets
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B. Aydin↗
SEARCH · Engineering Papers
Results for “co-occurrence patterns”
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Mining At Most Top-K% Spatiotemporal Co-occurrence Patterns in Datasets with Extended Spatial Representations
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Karthik Ganesan Pillai↗
Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere
Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.
59 BASIC BIOLOGICAL SCIENCES↗
Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery
Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Our results suggested soil microbial a-diversity decreased under high C10–C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10–C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.
59 BASIC BIOLOGICAL SCIENCES↗
Co-occurrence of native white-tailed deer and invasive wild pigs: Evidence for competition?
Understanding whether invasive and native species compete for shared resources where they co-occur is essential for mitigating the negative impacts of invasive species on native ecosystems. Here, we examined how the presence and density of an invasive species, wild pigs (Sus scrofa), affect native white-tailed deer (Odocoileus virginianus; hereafter, deer) on the Savannah River Site, SC, USA. We examined potential changes in deer areas of use, temporal overlap, and occupancy to evaluate the effects of wild pig occurrence and density on deer space use, diel activity, and co-occurrence with wild pigs across 9 months during 2018 and 2019. Wild pig density had the strongest effect on deer space use in high- and moderate-use areas. Declines in deer space use in response to wild pig density were most pronounced in March and October 2018 and April 2019 for females, while male space use declined in response to wild pig density in October and December 2018. Both species were largely nocturnal with high overlap in diel activity across months. Deer occupancy responses to wild pig density varied across months, with negative responses in May and October 2018 and positive responses in July 2018 and April 2019. Deer and wild pigs co-occurred at 30%–59% of camera stations across months, with broadscale co-occurrence patterns being unaffected by changes in shared cover or wild pig occurrence. Overall, our results suggest that deer make fine-scale behavioral adjustments to avoid wild pigs, providing evidence that competition is likely occurring even where wild pig density is relatively low. Such fine-scale behavioral plasticity in deer appears to mitigate the costs of competition with wild pigs and may be a mechanism enabling long-term co-existence of deer and wild pigs. Our study provides novel insight on the complexities of spatiotemporal relationships between invasive wild pigs and native deer and suggests that the negative effects of interactions between deer and wild pigs may be more pronounced when deer life history needs are particularly demanding. In areas where eradication of invasive wild pigs may be impossible, maintaining low wild pig densities may help mitigate, but may not eliminate, the negative effects of wild pigs on deer.
resource partitioning↗
A Bayesian model for multivariate discrete data using spatial and expert information with application to inferring building attributes
When modeling sparsely observed multivariate data, strong prior information elicited from experts can be used to bolster predictive accuracy and counteract sampling bias. Similarly, modeling autocorrelation in space can help make use of co-occurrence patterns present in many types of spatial data. To make use of both expert prior information and spatial structure, we propose a novel graphical model for a spatial Bayesian network developed specifically to address challenges in inferring the attributes of buildings from geographically sparse observational data. This model is implemented as the sum of a spatial multivariate Gaussian random field and a tabular conditional probability function in real-valued space prior to projection onto the probability simplex. This modeling form is especially suitable for the usage of prior information in the form of sets of atomic rules obtained from experts. To perform inference with missing data, we implement a Markov chain Monte Carlo scheme composed of alternating steps of Gibbs sampling of missing entries and Hamiltonian Monte Carlo for model parameters. A case study in building attribution is presented to highlight the advantages and limitations of this approach.
97 MATHEMATICS AND COMPUTING↗
Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning
Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.
60 APPLIED LIFE SCIENCES↗
Breeding of microbiomes conferring salt tolerance to plants
Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture.
59 BASIC BIOLOGICAL SCIENCES↗
Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase
The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families inArabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein–protein and co-occurrence interactions, informed by gene network patterns using the STRING database, inArabidopsis thalianaandChlamydomonas reinhardtiiunveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified inArabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue ‘The evolution of plant metabolism’.
Life Sciences & Biomedicine - Other Topics↗
Statistical relationships across epigenomes using large-scale hierarchical clustering
Recent advances in genomics and sequencing platforms have revolutionized our ability to create immense data sets, particularly for studying epigenetic regulation of gene expression. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given nonlinear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine learning for discerning infectivity and susceptibility. In this study, we explore over 3000 epigenomes of uninfected individuals and provide a framework to characterize the relationships among epigenetic modifiers, their modifiers, genetic loci, and specific immune cell types across all chromosomes using hierarchical clustering. Hierarchical clustering of epigenomic data revealed consistent epigenetic patterns across chromosomes, demonstrating that variation due to epigenetic modifiers is greater than variation between cell types. Gene Ontology and KEGG pathway analyses indicated significant enrichment of genes involved in chromatin remodeling, mRNA splicing, immune responses, and the regulation of microRNAs and snoRNAs. Epigenetic modifiers frequently formed biologically relevant clusters, including the cohesin complex, RNA Polymerase II transcription factors, and PRC2 complex members. These clustering behaviors remained consistent across all chromosomes, supported by entropy analysis and high Adjusted Rand Index scores, indicating robust cross-chromosomal similarity. Co-occurrence analysis further revealed specific sets of modifiers that consistently appeared together within clusters, reflecting shared biological functions and interactions. Validation using another dataset confirmed the reproducibility of these clustering patterns and modifier co-occurrence relationships, underscoring the reliability and generalizability of the methodology.
97 MATHEMATICS AND COMPUTING↗
Image Correlation Pattern Optimization for Micro-Scale In-Situ Strain Measurements
The accuracy and precision of digital image correlation (DIC) is a function of three primary ingredients: image acquisition, image analysis, and the subject of the image. Development of the first two (i.e. image acquisition techniques and image correlation algorithms) has led to widespread use of DIC; however, fewer developments have been focused on the third ingredient. Typically, subjects of DIC images are mechanical specimens with either a natural surface pattern or a pattern applied to the surface. Research in the area of DIC patterns has primarily been aimed at identifying which surface patterns are best suited for DIC, by comparing patterns to each other. Because the easiest and most widespread methods of applying patterns have a high degree of randomness associated with them (e.g., airbrush, spray paint, particle decoration, etc.), less effort has been spent on exact construction of ideal patterns. With the development of patterning techniques such as microstamping and lithography, patterns can be applied to a specimen pixel by pixel from a patterned image. In these cases, especially because the patterns are reused many times, an optimal pattern is sought such that error introduced into DIC from the pattern is minimized. DIC consists of tracking the motion of an array of nodes from a reference image to a deformed image. Every pixel in the images has an associated intensity (grayscale) value, with discretization depending on the bit depth of the image. Because individual pixel matching by intensity value yields a non-unique scale-dependent problem, subsets around each node are used for identification. A correlation criteria is used to find the best match of a particular subset of a reference image within a deformed image. The reader is referred to references for enumerations of typical correlation criteria. As illustrated by Schreier and Sutton and Lu and Cary systematic errors can be introduced by representing the underlying deformation with under-matched shape functions. An important implication, as discussed by Sutton et al., is that in the presence of highly localized deformations (e.g., crack fronts), error can be reduced by minimizing the subset size. In other words, smaller subsets allow the more accurate resolution of localized deformations. Contrarily, the choice of optimal subset size has been widely studied and a general consensus is that larger subsets with more information content are less prone to random error. Thus, an optimal subset size balances the systematic error from under matched deformations with random error from measurement noise. The alternative approach pursued in the current work is to choose a small subset size and optimize the information content within (i.e., optimizing an applied DIC pattern), rather than finding an optimal subset size. In the literature, many pattern quality metrics have been proposed, e.g., sum of square intensity gradient (SSSIG), mean subset fluctuation, gray level co-occurrence, autocorrelation-based metrics, and speckle-based metrics. The majority of these metrics were developed to quantify the quality of common pseudo-random patterns after they have been applied, and were not created with the intent of pattern generation. As such, it is found that none of the metrics examined in this study are fit to be the objective function of a pattern generation optimization. In some cases, such as with speckle-based metrics, application to pixel by pixel patterns is ill-conditioned and requires somewhat arbitrary extensions. In other cases, such as with the SSSIG, it is shown that trivial solutions exist for the optimum of the metric which are ill-suited for DIC (such as a checkerboard pattern). In the current work, a multi-metric optimization method is proposed whereby quality is viewed as a combination of individual quality metrics. Specifically, SSSIG and two auto-correlation metrics are used which have generally competitive objectives. Thus, each metric could be viewed as a constraint imposed upon the others, thereby precluding the achievement of their trivial solutions. In this way, optimization produces a pattern which balances the benefits of multiple quality metrics. The resulting pattern, along with randomly generated patterns, is subjected to numerical deformations and analyzed with DIC software. The optimal pattern is shown to outperform randomly generated patterns.
Bomarito, G. F.↗
Relationship between circum-Arctic atmospheric wave patterns and large-scale wildfires in boreal summer
Long-term assessment of severe wildfires and associated air pollution and related climate patterns in and around the Arctic is essential for assessing healthy human life status. To examine the relationships, we analyzed the National Aeronautics and Space Administration (NASA) modern-era retrospective analysis for research and applications, version 2 (MERRA-2). Our investigation based on this state-of-the-art atmospheric reanalysis data reveals that 13 out of the 20 months with the highest PM2.5 (corresponding to the highly elevated organic carbon in the particulate organic matter [POM] form) monthly mean mass concentration over the Arctic for 2003–2017 were all in summer (July and August), during which POM of ⩾0.5 μg/cu. m and PM2.5 were positively correlated. This correlation suggests that high PM2.5 in the Arctic is linked to large wildfire contributions and characterized by significant anticyclonic anomalies (i.e. clockwise atmospheric circulation) with anomalous surface warmth and drier conditions over Siberia and subpolar North America, in addition to Europe. A similar climate pattern was also identified through an independent regression analysis for the July and August mean data between the same atmospheric variables and the sign-reversed Scandinavian pattern index. We named this pattern of recent atmospheric circulation anomalies the circum-Arctic wave (CAW) pattern as a manifestation of eastward group-velocity propagation of stationary Rossby waves (i.e. large-scale atmospheric waves). The CAW induces concomitant development of warm anticyclonic anomalies over Europe, Siberia, Alaska, and Canada, as observed in late June 2019. Surprisingly, the extended regression analysis of the 1980–2017 period revealed that the CAW pattern was not prominent before 2003. Understanding the CAW pattern under future climate change and global warming would lead to better prediction of co-occurrences of European heatwaves and large-scale wildfires with air pollution over Siberia, Alaska, and Canada in and around the Arctic in summer.
wildfire↗
Use of feature extraction techniques for the texture and context information in ERTS imagery: Spectral and textural processing of ERTS imagery
The author has identified the following significant results. A procedure was developed to extract cross-band textural features from ERTS MSS imagery. Evolving from a single image texture extraction procedure which uses spatial dependence matrices to measure relative co-occurrence of nearest neighbor grey tones, the cross-band texture procedure uses the distribution of neighboring grey tone N-tuple differences to measure the spatial interrelationships, or co-occurrences, of the grey tone N-tuples present in a texture pattern. In both procedures, texture is characterized in such a way as to be invariant under linear grey tone transformations. However, the cross-band procedure complements the single image procedure by extracting texture information and spectral information contained in ERTS multi-images. Classification experiments show that when used alone, without spectral processing, the cross-band texture procedure extracts more information than the single image texture analysis. Results show an improvement in average correct classification from 86.2% to 88.8% for ERTS image no. 1021-16333 with the cross-band texture procedure. However, when used together with spectral features, the single image texture plus spectral features perform better than the cross-band texture plus spectral features, with an average correct classification of 93.8% and 91.6%, respectively.
Haralick, R. H.↗
Advances in Hyperspectral Image Classification Methods for Vegetation and Agricultural Cropland Studies
Hyperspectral data are becoming more widely available via sensors on airborne and unmanned aerial vehicle (UAV) platforms, as well as proximal platforms. While space-based hyperspectral data continue to be limited in availability, multiple spaceborne Earth-observing missions on traditional platforms are scheduled for launch, and companies are experimenting with small satellites for constellations to observe the Earth, as well as for planetary missions. Land cover mapping via classification is one of the most important applications of hyperspectral remote sensing and will increase in significance as time series of imagery are more readily available. However, while the narrow bands of hyperspectral data provide new opportunities for chemistry-based modeling and mapping, challenges remain. Hyperspectral data are high dimensional, and many bands are highly correlated or irrelevant for a given classification problem. For supervised classification methods, the quantity of training data is typically limited relative to the dimension of the input space. The resulting Hughes phenomenon, often referred to as the curse of dimensionality, increases potential for unstable parameter estimates, overfitting, and poor generalization of classifiers. This is particularly problematic for parametric approaches such as Gaussian maximum likelihood–based classifiers that have been the backbone of pixel-based multispectral classification methods. This issue has motivated investigation of alternatives, including regularization of the class covariance matrices, ensembles of weak classifiers, development of feature selection and extraction methods, adoption of nonparametric classifiers, and exploration of methods to exploit unlabeled samples via semi-supervised and active learning. Data sets are also quite large, motivating computationally efficient algorithms and implementations. This chapter provides an overview of the recent advances in classification methods for mapping vegetation using hyperspectral data. Three data sets that are used in the hyperspectral classification literature (e.g., Botswana Hyperion satellite data and AVIRIS airborne data over both Kennedy Space Center and Indian Pines) are described in Section 3.2 and used to illustrate methods described in the chapter. An additional high-resolution hyperspectral data set acquired by a SpecTIR sensor on an airborne platform over the Indian Pines area is included to exemplify the use of new deep learning approaches, and a multiplatform example of airborne hyperspectral data is provided to demonstrate transfer learning in hyperspectral image classification. Classical approaches for supervised and unsupervised feature selection and extraction are reviewed in Section 3.3. In particular, nonlinearities exhibited in hyperspectral imagery have motivated development of nonlinear feature extraction methods in manifold learning, which are outlined in Section 3.3.1.4. Spatial context is also important in classification of both natural vegetation with complex textural patterns and large agricultural fields with significant local variability within fields. Approaches to exploit spatial features at both the pixel level (e.g., co-occurrence–based texture and extended morphological attribute profiles [EMAPs]) and integration of segmentation approaches (e.g., HSeg) are discussed in this context in Section 3.3.2. Recently, classification methods that leverage nonparametric methods originating in the machine learning community have grown in popularity. An overview of both widely used and newly emerging approaches, including support vector machines (SVMs), Gaussian mixture models, and deep learning based on convolutional neural networks is provided in Section 3.4. Strategies to exploit unlabeled samples, including active learning and metric learning, which combine feature extraction and augmentation of the pool of training samples in an active learning framework, are outlined in Section 3.5. Integration of image segmentation with classification to accommodate spatial coherence typically observed in vegetation is also explored, including as an integrated active learning system. Exploitation of multisensor strategies for augmenting the pool of training samples is investigated via a transfer learning framework in Section 3.5.1.2. Finally, we look to the future, considering opportunities soon to be provided by new paradigms, as hyperspectral sensing is becoming common at multiple scales from ground-based and airborne autonomous vehicles to manned aircraft and space-based platforms.
Pasolli, Edoardo↗
Cloud field classification based upon high spatial resolution textural features. I - Gray level co-occurrence matrix approach
Stratocumulus, cumulus, and cirrus clouds were identified on the basis of cloud textural features which were derived from a single high-resolution Landsat MSS NIR channel using a stepwise linear discriminant analysis. It is shown that, using this method, it is possible to distinguish high cirrus clouds from low clouds with high accuracy on the basis of spatial brightness patterns. The largest probability of misclassification is associated with confusion between the stratocumulus breakup regions and the fair-weather cumulus.
Welch, R. M.↗
Spatial and Temporal Analysis of a Global Landslide Catalog
Landslide inventories are critical to support investigations ofwhere andwhen landslides have happened andmay occur in the future; however, there is surprisingly little information on the historical occurrence of landslides at the global scale. This paper presents a new publicly available global landslide catalog (GLC), which is based on media reports, online databases, and other sources. This database is currently available at http://ojo-streamer. herokuapp.com/. The 5741 points in the GLC provide a foundation for evaluating spatial and temporal trends in landslide activity from 2007 to 2013. Globally, landslideswere reportedmost frequently from July to September. Most events occurred in Asia, North America and Southeast Asia. In contrast, fewer than 5% of the fatalities were reported in North America, suggesting a significant amount of under-reporting in other regions as well as potential discrepancies between developing and developed regions. Reported landslide events were also compared to satellite-based precipitation estimates fromthe Tropical RainfallMeasuring Mission (TRMM) to evaluate the co-occurrence of extreme precipitation and landslide activity. Of the 3550 points considered in a subset of the GLC, approximately 60% of the reported landslides have daily precipitation exceeding the 95th percentile of precipitation calculated over a 14-year TRMMrecord for the same location. This study also investigated how the recurrence interval of extreme precipitation corresponded to some of the most catastrophic landslide events. In spite of several reporting and cataloging biases, spatial and temporal analysis of the GLC suggests that it is a valuable database for characterizing global patterns of landslide occurrence and evaluating relationships with extreme precipitation at regional and global scales.
Analysis↗
The influence of natural variability on extreme monsoons in Pakistan
The monsoons in Pakistan have been exceptionally harsh in recent decades, resulting in extraordinary drought conditions and record flooding events. The changing characteristics of extreme events are widely attributed to climate change. However, given this region’s long history of floods and droughts, the role of natural climate variability cannot be rejected without a careful diagnosis. Here, we examine how oceanic and atmospheric variability has contributed to unusual precipitation distributions in West South Asia. Variations in sea surface temperatures in the tropical Pacific and northern Arabian Sea, and internal atmospheric variability related to the circumglobal teleconnection pattern and the subtropical westerly jet stream, explain more than 70% of monthly summer precipitation variability in the 21st century. Several of these forcings have co-occurred with record strength during episodes of extreme monsoons, which have exacerbated the overall effect. Climate change may have contributed to increased variability and the in-phase co-occurrences of the identified mechanisms, but further research is required to confirm any such connection.
54 ENVIRONMENTAL SCIENCES↗
Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake
Abstract Background Protists, 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. Results Based 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. Conclusions We 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.
59 BASIC BIOLOGICAL SCIENCES↗