The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry?

The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics.

Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions.

Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae and across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations.

Halophilic bacteria in a Lake Michigan drainage basin as potential biological indicators of chloride-impacted freshwaters.

There are few biological indicators for freshwater systems subjected to high chloride levels. Freshwater systems receive many forms of chloride such as road salts (e.g.

fliA, flrB, and fliR regulate adhesion by controlling the expression of critical virulence genes in Vibrio harveyi.

Bacteria adhesion to fish mucus is a crucial virulence mechanism. As the initial step of bacterial infection, adhesion is impacted by bacterial motility and environmental conditions. However, its molecular mechanism is yet unclear.

Storage, patterns and influencing factors for soil organic carbon in coastal wetlands of China.

Soil organic carbon (SOC) in coastal wetlands, also known as "blue C," is an essential component of the global C cycles. To gain a detailed insight into blue C storage and controlling factors, we studied 142 sites across ca. 5000 km of coastal wetlands, covering temperate, subtropical, and tropical climates in China.

Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.

Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored.

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States.

Wastewater microbiome research often relies on sequencing of hypervariable regions of 16S rRNA genes, which are difficult to classify at refined taxonomic levels. Here, we introduce a data set of near-full-length 16S rRNA genes from samples designed to capture known geographic and seasonal variations in municipal wastewater microbial communities.

Comprehensive understanding the impacts of dietary exposure to polyethylene microplastics on genetically improved farmed tilapia (Oreochromis niloticus): tracking from growth, microbiota, metabolism to gene expressions.

Microplastics (MPs) pollution has been recognized as a threat to sustainable fisheries due to the risks of MPs contamination in the process of feed production and susceptibility of fish to ingest MPs from the aquatic environment. In this study, we applied comprehensive approaches to investigate the impacts of polyethylene microplastics (PE-MPs) on juvenile genetically improved farmed tilapia (GIFT, Oreochromis niloticus) through 9-week dietary exposure based on growth performance, gut microbiota, liver metabolism, and gene expressions in brain and liver tissues. Dietary exposure to two kinds of PE-MPs with different median size (27 μm and 63 μm, respectively) concentration-dependently decreased weight gain (WG), while increased feed conversion ratio (FCR) and hepatosomatic index (HSI) of the tilapia.

Linking Water Quality to Drinking Water Treatment Costs Using Time Series Analysis: Examining the Effect of a Treatment Plant Upgrade in Ohio.

We estimate a cost function for a water treatment plant in Ohio to assess the avoided-treatment costs resulting from improved source water quality. Regulations and source water concerns motivated the treatment plant to upgrade its treatment process by adding a granular activated carbon building in 2012. The cost function uses daily observations from 2013 to 2016; this allows us to compare the results to a cost function estimated for 2007-2011 for the same plant.

Chronic exposure to high-density polyethylene microplastic through feeding alters the nutrient metabolism of juvenile yellow perch ().

Microplastics are emergent contaminants threatening aquatic organisms including aquacultured fish. This study investigated the effects of high-density polyethylene (HDPE, 100 to 125 μm) on yellow perch () based on integrative evaluation including growth performance, nutritional status, nutrient metabolism, fish health, and gut microbial community. Five test diets (0, 1, 2, 4, or 8 g HDPE/100 g diet) containing 41% protein and 10.

Redesign of hydrophobic quantum dots mitigates ligand-dependent toxicity in the nematode C. elegans.

Surface properties of engineered nanomaterials (ENMs) have been shown to influence their interaction with biological systems. However, studies to date have largely focused on hydrophilic materials, likely due to biocompatibility concerns and aqueous exposure conditions necessary for many model systems. Therefore, a knowledge gap exists in nanotoxicity literature for impacts of hydrophobic ENMs, with studies of hydrophobic materials largely limited to carbon ENMs.

Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes.

Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulate traits.

Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.

Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth's largest lakes.

SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works.

Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction.

Cross-species transcriptomic signatures identify mechanisms related to species sensitivity and common responses to nanomaterials.

Physico-chemical characteristics of engineered nanomaterials are known to be important in determining the impact on organisms but effects are equally dependent upon the characteristics of the organism exposed. Species sensitivity may vary by orders of magnitude, which could be due to differences in the type or magnitude of the biochemical response, exposure or uptake of nanomaterials. Synthesizing conclusions across studies and species is difficult as multiple species are not often included in a study, and differences in batches of nanomaterials, the exposure duration and media across experiments confound comparisons.

Bacterial Recruitment to Carnivorous Pitcher Plant Communities: Identifying Sources Influencing Plant Microbiome Composition and Function.

Processes influencing recruitment of diverse bacteria to plant microbiomes remain poorly understood. In the carnivorous pitcher plant model system, individual pitchers open to collect rainwater, invertebrates and a diverse microbial community, and this detrital food web is sustained by captured insect prey. This study examined how potential sources of bacteria affect the development of the bacterial community within pitchers, how the host plant tissue affects community development and how established vs.

Altered Larval Yellow Perch Swimming Behavior Due to Methylmercury and PCB126 Detected Using Hidden Markov Chain Models.

Fish swimming behavior is a commonly measured response in aquatic ecotoxicology because behavior is considered a whole organism-level effect that integrates many sensory systems. Recent advancements in animal behavior models, such as hidden Markov chain models (HMM), suggest an improved analytical approach for toxicology. Using both new and traditional approaches, we examined the sublethal effects of PCB126 and methylmercury on yellow perch (YP) larvae () using three doses.

Single-Well Injection-Drift Test to Estimate Groundwater Velocity.

A simple algebraic equation is presented here to estimate the magnitude of groundwater velocity based on data from a single-well injection-drift test thereby eliminating the time-consuming and costly extraction phase. A volume of tracer-amended water was injected by forced-gradient into a single well followed by monitoring of the conservative solute tracers under natural-gradient conditions as their upgradient portions drifted back through the well. The breakthrough curve data from the single well during the drift phase was analyzed to determine the mean travel times of the tracers.

Measuring flow speeds in natural waters by training an artificial neural network to analyze high-frequency flow-induced vibrations of tethered floats.

Measuring water currents in natural waters is limited by the cost of sensors. Standard sonar-based acoustic current Doppler profilers (ADCPs) are high cost, about $10-20 K per unit. Tilt current meters (TCMs) are much cheaper.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance.

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly.

Energy Starvation in from Exposure to a Lithium Cobalt Oxide Nanomaterial.

Growing evidence across organisms points to altered energy metabolism as an adverse outcome of metal oxide nanomaterial toxicity, with a mechanism of toxicity potentially related to the redox chemistry of processes involved in energy production. Despite this evidence, the significance of this mechanism has gone unrecognized in nanotoxicology due to the field's focus on oxidative stress as a universal─but nonspecific─nanotoxicity mechanism. To further explore metabolic impacts, we determined lithium cobalt oxide's (LCO's) effects on these pathways in the model organism through global gene-expression analysis using RNA-Seq and untargeted metabolomics by direct-injection mass spectrometry.