Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the ...presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within ~ 24 h.
Summary
Microcystis is a cyanobacterium that forms toxic blooms in freshwater ecosystems around the world. Biological variation among taxa within the genus is apparent through genetic and phenotypic ...differences between strains and via the spatial and temporal distribution of strains in the environment, and this fine‐scale diversity exerts strong influence over bloom toxicity. Yet we do not know how varying traits of Microcystis strains govern their environmental distribution, the tradeoffs and links between these traits, or how they are encoded at the genomic level. Here we synthesize current knowledge on the importance of diversity within Microcystis and on the genes and traits that likely underpin ecological differentiation of taxa. We briefly review spatial and environmental patterns of Microcystis diversity in the field and genetic evidence for cohesive groups within Microcystis. We then compile data on strain‐level diversity regarding growth responses to environmental conditions and explore evidence for variation of community interactions across Microcystis strains. Potential links and tradeoffs between traits are identified and discussed. The resulting picture, while incomplete, highlights key knowledge gaps that need to be filled to enable new models for predicting strain‐level dynamics, which influence the development, toxicity and cosmopolitan nature of Microcystis blooms.
Changes in seasonal cycles (i.e., phenology), can cause mismatches throughout aquatic food webs and often are used as the primary indicator of zooplankton response to environmental changes. However, ...zooplankton phenology has been largely overlooked in Lake Michigan despite the altered phenology of phytoplankton, including the disappearance of the offshore spring phytoplankton bloom following Dreissena mussel invasions.
Multiple measures of phenology were evaluated for the major zooplankton groups in offshore southeastern Lake Michigan both before the loss of the spring bloom (1983–2003), and after the spring bloom had disappeared (2007–2019). Water temperatures in spring did not differ between time periods.
Standardised biomass declined between time periods for all zooplankton groups in spring and for total zooplankton and the cladoceran Daphnia in the summer. Changes in zooplankton phenology varied across groups and depended on the phenological measures used. Month of peak biomass shifted later for all groups, but the central point of the growing season did not change for any group between time periods. The onset of population development was delayed only for the copepod Limnocalanus.
Spring chlorophyll concentrations combined with spring water temperatures provided the best predictions of population onset for Limnocalanus and Daphnia. The central point of the growing season varied with spring chlorophyll concentrations for Limnocalanus, but with spring water temperature for Daphnia.
Changes in zooplankton phenology were relatively subtle compared to the large changes observed for spring chlorophyll concentrations. By contrast, there were fairly consistent declines in zooplankton biomass across groups that were associated with the declines in spring chlorophyll either alone or in combination with spring water temperature. This may mean that food limitation has a stronger influence on zooplankton biomass or production than on zooplankton phenology in offshore Lake Michigan.
Based on our results from Lake Michigan, alterations such as nutrient reduction or invasive dreissenid mussel filtering that lead to declines in spring phytoplankton blooms in other large freshwater lakes could result in subtle delays in zooplankton phenology for some groups along with stronger declines in zooplankton biomass.
Whether bottom hypoxia has long-lasting consequences for pelagic fish populations remains speculative for most ecosystems. We explored hypoxia’s influence on two pelagic zooplanktivores in Lake Erie ...that have different thermal preferences: cold-water rainbow smelt (Osmerus mordax) and warm-water emerald shiners (Notropis atherinoides). To assess acute effects, we combined predictive bioenergetics-based modeling with field collections made across the hypoxic season in central Lake Erie during 2005 and 2007. To assess chronic effects, we related fishery-independent and fishery-dependent catches with hypoxia severity and top predator (walleye, Sander vitreus) abundance during 1986–2014. As our modeling predicted, hypoxia altered rainbow smelt movement and distributions, leading to avoidance of cold, hypoxic bottom waters. In response, diets shifted from benthic to pelagic organisms, and consumption and energetic condition declined. These changes were lacking in emerald shiners. Our long-term analyses showed rainbow smelt abundance and hypoxia to be negatively related and suggested that hypoxia avoidance increases susceptibility to commercial fishing and walleye predation. Collectively, our findings indicate that hypoxia can negatively affect pelagic fish populations over the long term, especially those requiring cold water.
Abstract
Bacteria represent most of the biodiversity and play key roles in virtually every ecosystem. In doing so, bacteria act as part of complex communities shaped by interactions across all ...domains of life. Here, we report on direct interactions between bacteria and dreissenid mussels, a group of invasive filter-feeders threatening global aquatic systems due to high filtration rates. Previous studies showed that dreissenids can impact bacterial community structure by changing trait distributions and abundances of specific taxa. However, studies on bacterial community effects were conducted using water from Lake Michigan (an oligotrophic lake) only, and it is unknown whether similar patterns are observed in systems with differing nutrient regimes. We conducted ten short-term dreissenid grazing experiments in 2019 using water from two eutrophic lake regions—the western basin of Lake Erie and Saginaw Bay in Lake Huron. Predation by dreissenids led to decline in overall bacterial abundance and diversity in both lakes. However, feeding on bacteria was not observed during every experiment. We also found that traits related to feeding resistance are less phylogenetically conserved than previously thought. Our results highlight the role of temporal, spatial, and genomic heterogeneity in bacterial response dynamics to a globally important invasive filter feeder.
Impacts of an invasive filter-feeder on bacterial biodiversity are context dependent.
We applied a three-dimensional biophysical model to Lake Michigan for the years 2000, 2005, and 2010 to consider the mechanisms controlling spatial and temporal patterns of phytoplankton abundance ...(chlorophyll a) and lake-wide productivity. Model skill was assessed by comparison to satellite-derived Chl a and field-measured water quality variables. We evaluated model sensitivity to scenarios of varying mussel filter feeding intensity, tributary phosphorus loads, and warm vs. cool winter-spring climate scenarios. During the winter-spring phytoplankton bloom, spatial patterns of Chl a were controlled by variables that influenced surface mixed layer depth: deep mixing reduced net phytoplankton growth through light limitation and by exposing the full water column to mussel filter feeding. Onset of summer and winter stratification promoted higher surface Chl a initially by increasing mean light exposure and by separating the euphotic zone from mussels. During the summer stratified period, areas of relatively high Chl a were associated with coastal plumes influenced by tributary-derived nutrients and coastal upwelling-downwelling. While mussels influenced spatial and temporal distribution of Chl a, lake-wide, annual mean primary production was more sensitive to phosphorus and warm/cool meteorology scenarios than to mussel filter feeding scenarios. Although Chl a and primary production declined over the quagga mussel invasion, our results suggest that increased nutrient loads would increase lake-wide productivity even in the presence of mussels; however, altered spatial and temporal patterns of productivity caused by mussel filter feeding would likely persist.
Summary
Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we ...simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake‐specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states.
The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA ...studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis.
Demographic differences in
Bythotrephes longimanus
populations are often used to infer the prevalence of different environmental conditions that regulate their population. We collected seasonal data ...on
Bythotrephes
abundance and life history at a nearshore (15 m), transitional (45 m) and offshore site (110 m) in Lake Michigan during 2007–2016. Due to higher fish predation requirements and the small size of zooplankton prey at the nearshore site, we expected life-history attributes of
Bythotrephes
would differ compared to the deeper sites, but body and spine length, percent of growth allocated to the spine, and brood size were similar among depths. Owing to higher abundances in the offshore, the ratio of consumption requirements: prey production (C:P) was relatively high throughout the growing season at the deepest site compared to the two shallower sites, where C:P was generally only high in the fall. However, reproductive characteristics of
Bythotrephes
at the offshore site did not reflect a food-limited population compared to the other two sites. Rather the proportion of barren females was higher at the nearshore site than those at the deeper sites, leading to much lower birth rates and abundance of
Bythotrephes
at the shallow site compared to the deeper sites.
The Chloroflexi CL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world's largest freshwater system, the ...Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that a CL500-11 population was present mostly in offshore waters along a transect in ultraoligotrophic Lake Michigan (a Laurentian Great Lake). It occurred throughout the water column in spring and only in the hypolimnion during summer stratification, contributing up to 18.1% of all cells. Genome reconstruction from metagenomic data suggested an aerobic, motile, heterotrophic lifestyle, with additional energy being gained through carboxidovory and methylovory. Comparisons to other available streamlined freshwater genomes revealed that the CL500-11 genome contained a disproportionate number of cell wall/capsule biosynthesis genes and the most diverse spectrum of genes involved in the uptake of dissolved organic matter (DOM) substrates, particularly peptides. In situ expression patterns indicated the importance of DOM uptake and protein/peptide turnover, as well as type I and type II carbon monoxide dehydrogenase and flagellar motility. Its location in the water column influenced its gene expression patterns the most. We observed increased bacteriorhodopsin gene expression and a response to oxidative stress in surface waters compared to its response in deep waters. While CL500-11 carries multiple adaptations to an oligotrophic lifestyle, its investment in motility, its large cell size, and its distribution in both oligotrophic and mesotrophic lakes indicate its ability to thrive under conditions where resources are more plentiful. Our data indicate that CL500-11 plays an important role in nitrogen-rich DOM mineralization in the extensive deep-lake hypolimnion habitat.
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