Relative Abundance Measurements Research Articles

Comparative assessment of eDNA metabarcoding and longline deployments for elasmobranch surveying across a large tropical marine park network

Abstract Medium‐ to large‐scale marine protected areas (MPAs) are playing an increasingly important role in global marine biodiversity conservation. A key question is “how do we collect relevant data on biodiversity and population trends to inform their design and measure success?” This question is particularly relevant for marine taxa that are difficult to survey, such as sharks and rays, and where populations may occur over vast areas. Environmental DNA (eDNA) metabarcoding has proven to be an effective sampling method and may provide a solution to these challenges; however, it remains unclear how its sampling effectiveness compares with traditionally used methods for elasmobranch surveying. Here, we directly compared the efficacy of eDNA metabarcoding and demersal longline deployments to survey elasmobranchs across 31 sites over a 55,000 km2 area of the Kimberley and Roebuck Australian Marine Parks in Australia's North‐west Marine Parks Network. In total, we documented 49 unique elasmobranch taxa, 36 of which were detected by eDNA and 32 (from a total of 815 captured sharks) by longline. A combined approach yielded over 34% more elasmobranch taxa than either method alone. Site community compositions varied between the two survey methods; notably eDNA was able to detect species from outside of the immediate sampling area, although this was still consistent with a detection radius of a few kilometres, highlighting a particular use in rugose reef habitats where it is difficult to deploy longlines. In investigating the quantitative use of eDNA data, we report that eDNA metabarcoding read abundance (count) data was poorly correlated with longline aggregate catch (count and biomass) data across raw, relative and rank abundance measures. However, we found that in multivariate analyses, both binary (presence–absence) and abundance (after square‐root transformation) datasets produced highly similar ordination patterns, largely segregating method (eDNA vs. longline), followed by latitude and depth. Lastly, we identified required levels of eDNA replication and longline deployments to maximize captured elasmobranch diversity. This study sets an integrated, georeferenced baseline and long‐term monitoring approach for the management and conservation of elasmobranch diversity within this unique marine park network.

A five-gene qPCR signature can classify type 2 asthma comparably to microscopy of induced sputum from severe asthma patients

ABSTRACT Asthma is a heterogenous disease characterized by airway inflammation and variable expiratory airflow limitation resulting in variable respiratory symptoms. Characterization of airway inflammation is important to choose the optimal treatment for severe asthma patients eligible for biological treatment. However, counting cells in induced sputum samples are a time-consuming process, highly dependent on personal skills. Replacing eosinophil and neutrophil cell counting with qPCR for transcripts of selected mast cell, and basophil genes may provide more reproducible results. Aims The objective of this study was to compare qPCR with microscopy in asthma endotyping. Methods A qPCR method measuring five mast cell/basophil genes was applied on induced sputum samples from 30 severe asthma patients and compared with microscopy. Target gene Ct-values (CPA3, GATA2, HDC, MS4A2, TPSAB1/TPSB2) were referenced to household β-actin Ct values as a measure of relative mRNA abundance of the target in each sample. Target/β-actin-ratios in eosinophilic and non-eosinophilic groups determined by microscopy with an eosinophil threshold of 3% in 400 cells were compared using Mann–Whitney U Test. Spearman´s correlations were used to test for correlation between targets vs. FENO and targets vs. blood eosinophil counts. Results The study demonstrated a statistical difference in relative mRNA abundance for four mast cell/basophil specific genes. CPA3, GATA2, HDC and MS4A2 were elevated in eosinophilic asthma versus non-eosinophilic asthma patients. The study found that GATA2, CPA3, MS4A2 and TPSAB1/TPSB2 transcripts are positively correlated with FENO. Neither the five mast cell genes nor the five-gene signature correlated with blood eosinophils. The five-gene signature with a target/β-actin-ratio cut-off ≥2 generated sensitivity = 87%, specificity = 94%, NPV = 88% and PPV = 92% compared to microscopy. Conclusion This study confirms the contribution of mast cells in the pathogenesis of EA and suggests that mast cell mRNA markers could be one of the biomarkers used to identify EA

Comparison of advanced methodologies for diatom identification within dynamic coastal communities

AbstractDiatom community composition has a critical influence on global ocean health and ecological processes. Developing accurate and efficient methods for diatom identification under dynamic environmental conditions is essential to understanding the implications of diatom community changes. Two developing methods for identifying and enumerating phytoplankton, cell imaging and molecular sequencing, are experiencing rapid advancements. This study aims to compare diatom taxonomic composition results within natural assemblages derived from rapidly advancing methods, FlowCam imaging and metabarcoding of the V4 region of the 18S rRNA gene, with traditional light microscopy cell counting techniques. All three methods were implemented in tandem to analyze changes in dynamic diatom assemblages within simulated upwelling experiments conducted in the California upwelling zone. The results of this study indicate that, summed across all samples, DNA sequencing detected four times as many genera as morphology‐based methods, thus supporting previous findings that DNA sequencing is the most powerful method for analyzing species richness. Results indicate that all three methods returned comparable relative abundance for the most abundant genera. However, the three methods did not return comparable absolute abundance, primarily due to barriers in deriving quantities in equal units. Overall, this study indicates that at the semi‐quantitative level of relative abundance measurements, FlowCam imaging and metabarcoding of the V4 region of the 18S rRNA gene yield comparable results with light microscopy but at the qualitative and quantitative levels, enumeration metrics diverge, and thus method selection and cross‐method comparison should be performed with caution.

Integrating assemblage structure and habitat mapping data into the design of a multispecies reef fish survey

AbstractObjectiveSince 2010, three spatially disjunct reef fish video surveys have provided fishery‐independent data critical to the assessment and management of reef fishes in the Gulf of Mexico. Although analytical approaches have recently been developed to integrate data from these surveys into a single measure of relative abundance and size composition, a more parsimonious approach would be to integrate survey efforts under a single Gulf‐wide survey design. Accordingly, we conducted a retrospective analysis of historical video‐ and habitat‐mapping data to develop a novel stratified random sampling design for conducting surveys of natural and artificial reef habitats.MethodsWe conducted a series of classification and regression tree analyses to delineate both spatial and habitat strata, and conducted simulations to assess the performance of an optimized survey design.ResultSpatially, classification and regression tree results identified three depth strata (10–25 m, >25–50 m, >50–180 m) and three regional strata (north‐central Gulf, Big Bend, southwest Florida) in the eastern Gulf. For both natural and artificial reefs, habitat strata were delineated based on a combination of relative relief (low, medium, high) and size of the individual reef feature, although reef scale differed markedly between natural (<100 m2, 100–1000 m2, >1000 m2) and artificial habitats (<25 m2, 25–100 m2, >100 m2). To optimize effort among sampling strata, effort was allocated proportionally based on a combination of habitat availability and managed‐species richness for each stratum. Simulation results indicated that relative median biases were <10% and relative median absolute deviations <30% on estimates of abundance for most species examined on natural reefs under the optimal design, except Greater Amberjack Seriola dumerili. These measures of bias and imprecision were similar or higher for most species simulated using simple random and stratified random survey designs. Estimated relative median bias and relative median absolute deviations were notably higher for artificial reef surveys.ConclusionBased on these results, survey efforts were integrated as the Gulf Fishery Independent Survey of Habitat and Ecosystem Resources (G‐FISHER) in 2020.

A High-Resolution Mass Spectrometer for the Experimental Study of the Gas Composition in Planetary Environments: First Laboratory Results

A new laboratory OrbitrapTM cell-based mass spectrometer, OLYMPIA (Orbitrap anaLYseur MultiPle IonisAtion), without a C-trap module, has been developed and constructed. The first operation of the OrbitrapTM cell-based device with the continuous ion source and without the C-trap module is reported. OLYMPIA is being developed and used as a workbench platform to test and develop technologies for the next generation of spaceborne mass spectrometers and as a laboratory instrument to perform high-resolution studies of space-relevant chemical processes. This instrument has been used to measure the quantitative composition of CO/N2/C2H4 mixtures of the same nominal mass using an electron ionization ion source. The relative abundance of ions has been measured using a short acquisition time (up to 250 ms) with a precision of better than 10% (for most abundant ions) and a mass resolution of 30,000–50,000 (full width at half maximum) over the mass range of m/z 28–86. The achieved mass accuracy of measurements is better than 20 ppm. This performance level is sufficient to resolve and identify the CO/N2/C2H4 components of the mixtures. The dynamic range and relative ion abundance measurements have been evaluated using a reference normal isotopic distribution of krypton gas. The measurement accuracy is about 10% for the 4 most abundant isotopes; 6 isotopes are detectable.

Drawdown, Habitat, and Kokanee Populations in a Western U.S. Reservoir

AbstractGreater drought frequency and severity due to climate change will result in greater drawdown of water storage reservoirs. However, changes to oxythermal regimes due to drawdown are reservoir specific and interface with fish species‐specific habitat requirements, producing varying effects on coldwater fish populations. We examined the effect of drawdown on the oxythermal habitat and relative abundance of kokanee Oncorhynchus nerka, a coldwater salmonid, in Island Park Reservoir on the Henrys Fork of the Snake River, Idaho. A measure of relative kokanee abundance was negatively, exponentially related to drawdown. Oxythermal patterns measured in the reservoir during 2021, a severe drought year, revealed that drawdown reduced kokanee habitat by increasing water temperatures and decreasing dissolved oxygen concentrations. Oxythermal refugia for kokanee appeared to relate to inflow from the spring‐fed Henrys Fork and other groundwater inflows. However, we did not quantify groundwater flow or connections, and we did not study kokanee population demographics or mortality. Reducing these sources of uncertainty is a priority for future study. Still, our study highlights a potential mechanism connecting reservoir drawdown to fish populations and the unique yet predictable mechanisms by which reservoir drawdown interacts with reservoir morphometry to affect fish habitat availability.

Geochemical changes in Eastern Canadian lake sediment cores spanning the last ∼150 years highlight a relative shift towards increased metals and erosive materials

Since the start of the Industrial Revolution, the chemical cycling of numerous elements has been fundamentally altered. Using 210Pb-dated sediment cores from 37 Eastern Canadian lakes situated in 4 ecozones, we quantified the geochemical change experienced across this region since ca. 1850 CE using high-resolution computed X-ray Tomography and micro-X-ray fluorescence (µ-XRF) ITRAX scanners. Independent calibrations of µ-XRF ITRAX intensities using ICP-MS and -AES found strong correlations for numerous elements. Using relative abundance measures and absolute concentration estimates, we observed that most of our study lakes recorded temporal enrichments of metals, with several sites exceeding Canadian sediment quality guidelines. Using principal component analysis, we identified that parameters commonly associated with erosion (strontium and titanium), organic matter (molybdenum incoherence to coherence scattering ratio), and metals (zinc and lead) were key variables structuring within and among-lake variation since ca. 1850 CE. Calcium was identified as an additional variable, particularly for lakes in the Mixedwood Plains (MWP) ecozone, which may be linked to catchment activities including land-use changes. Temporally, many lakes shifted towards greater accumulation of inorganic sediment, coeval with higher Pb and Zn concentrations, reaching maxima ca. 1970 CE before decreasing rapidly. These results suggest that most lakes in the region were subjected to environmental pollution but that controls on key atmospheric pollutants in North America were effective across a large part of the country.

Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes.

South Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors. The gut microbiota and gut permeability, as assessed through circulating lipopolysaccharide binding protein (LBP), may underlie the link between chronic inflammation and type 2 diabetes (T2D). The composition of the gut microbiota varies according to multiple factors including demographics, migration, and dietary patterns, particularly fiber intake. However, there is no evidence on the composition of the gut microbiota and its relationship with metabolic health in refugee populations, including those migrating to the United States from Bhutan. The objective of this study was to examine glycemic status in relation to LBP, systemic inflammation fiber intake, and gut microbiota composition in Bhutanese refugee adults residing in New Hampshire (n = 50). This cross-sectional study included a convenience sample of Bhutanese refugee adults (N = 50) in NH. Established bioinformatics pipelines for metagenomic analysis were used to determine relative genus abundance, species richness, and alpha diversity measures from shallow shotgun sequences. The relationships between inflammatory markers, gut microbiota composition, dietary fiber, and glycemic status were analyzed. We identified a substantial chronic disease burden in this study population, and observed a correlation between glycemic status, LBP, and inflammation, and a correlation between glycemic status and gut microbiome alpha diversity. Further, we identified a significant correlation between proinflammatory taxa and inflammatory cytokines. SCFA-producing taxa were found to be inversely correlated with age. To date, this is the most comprehensive examination of metabolic health and the gut microbiome in a Bhutanese refugee population in NH. The findings highlight areas for future investigations of inflammation and glycemic impairment, in addition to informing potential interventions targeting this vulnerable population.

SynDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing.

Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (r = 0.96; R2 ≥ 0.94) and significance (P < 0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. IMPORTANCE The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.

Observation of juvenile Eastern Blue Groper (Achoerodus viridis) on remnant oyster reefs in New South Wales, Australia.

Observation of juvenile Eastern Blue Groper (Achoerodus viridis) on remnant oyster reefs in New South Wales, Australia.

Shallow-water hydrothermal vent system as an extreme proxy for discovery of microbiome significance in a crustacean holobiont

The shallow-water hydrothermal vent (HV) system off Kueishan Island lies at the end of the Okinawa Trough to the northeast of Taiwan. Near its submarine vent openings, aperiodic vent discharges generate a dynamic acidic (pH 5.5-8.1) and sulfidic (9-3000 μM) ecosystem. The dominant metazoan in this unique environment is the brachyuran vent crab, Xenograpsus testudinatus, which has developed robust metabolic strategies and highly adaptive acid-base regulatory mechanisms to maintain its physiological homeostasis. X. testudinatus is considered a holobiont, but the symbiotic mechanisms underlying acid and sulfur tolerance in the host-microbe system remain largely unclear. In this study, we used LoopSeq long-read sequencing of the full-length 16S rRNA gene to identify the bacterial communities present in the gills and carapace surface of X. testudinatus. The alpha diversity analysis, Venn diagram, and principal coordinate analysis (PCoA) indicated that the gills and carapace surface exhibit different bacterial constituents. Further measurements of relative abundance, coupled with functional predictions and fluorescence in situ hybridization (FISH), revealed a predominance of Sulfurovum sp. NBC37-1, a key bacterium that can perform sulfur and hydrogen oxidation to support denitrification processes. Consequently, our findings suggest that the symbiotic bacteria may play a critical role in conferring the extraordinary acid and sulfur tolerances of X. testudinatus, allowing the crustacean holobiont to thrive in its ecological niche within one of the most extreme marine habitats on Earth.

Longitudinal Changes in the Composition of the Penile Microbiome Are Associated With Circumcision Status, HIV and HSV-2 Status, Sexual Practices, and Female Partner Microbiome Composition.

BackgroundPenile microbiome composition has been associated with HSV-2 and HIV in men and with bacterial vaginosis (BV) and HSV-2 in female sex partners. This study sought to 1) characterize penile microbiome composition over a 1-year period and 2) identify factors associated with penile microbiome composition over time.MethodsThis prospective study of community-recruited heterosexual couples in Kenya measured penile and vaginal microbiomes via 16S ribosomal RNA gene amplicon sequencing at 4 time points over 1 year (1, 6, and 12 months after baseline). We used longitudinal mixed-effects modeling to assess associated demographic, behavioral, and disease factors and changes in community type, meatal taxa with the highest mean relative abundance, and alpha and beta diversity measures. We estimated group-based trajectories to elucidate compositional trends.ResultsAmong 218 men with 740 observations, men had a median age of 26 years, 11.6% were living with HIV, and 46.1% were HSV-2 seropositive. We identified 7 penile community types that varied with circumcision status, female partner vaginal microbiome community state type (CST), condom use, and penile washing. Across varying analytic approaches, 50%–60% of men had stable penile microbiome compositions. Alpha diversity measures were lower for circumcised men and those who reported condom use; they were stable over time but higher if female partners had diverse CSTs or BV. BV was positively associated with the relative abundance of numerous individual penile taxa. The decreased Bray–Curtis similarity was more common for men with HSV-2, and HSV-2 was also associated with a lower relative abundance of Corynebacterium and Staphylococcus.ConclusionsOver a 1-year period, penile microbiome composition was stable for a substantial proportion of men and was influenced by men’s circumcision status, sexual practices, female partner’s vaginal CST and BV status, and men’s HSV-2 status. In the female genital tract, a diverse CST is often associated with poorer health outcomes. Our results contribute toward understanding whether this framework extends to the penile microbiome and whether diversity and the associated penile microbiome compositions influence susceptibility or resilience to poorer health outcomes in men. Focusing on understanding how these factors influence the penile microbiome may lead to therapeutic avenues for reduced HSV-2 and BV infections in men and their female sex partners.

SuperTIGER instrument abundances of galactic cosmic rays for the charge interval [formula omitted

We report preliminary elemental abundance results from the 55-day long-duration-balloon flight of SuperTIGER (Super Trans-Iron Galactic Element Recorder) during the 2012–2013 austral summer. SuperTIGER measured the relative abundances of Galactic cosmic-ray (GCR) nuclei with high statistical precision and well resolved individual element peaks from 10Ne to 40Zr. SuperTIGER also made exploratory measurements of the relative abundances up to 56Ba. Although the statistics are low for elements heavier than 40Zr, we present, for the first time, relative abundance measurements of charges Z=41-56 with individual element resolution. GCR measurements up to 40Zr support a source acceleration model where supernovae in OB associations preferentially accelerate refractory elements that are more readily embedded in interstellar dust grains than volatiles. In addition, injection into the GCR for both refractory and volatile elements appears to follow a charge dependence consistent with their grain sputtering cross sections. By extending the GCR measurement range past 40Zr, we can begin to further constrain these models.

Elevational patterns in tropical bryophyte diversity differ among substrates: A case study on Baru volcano, Panama

AbstractQuestionsBryophytes attain their highest diversity in tropical mountain forests. Although distribution patterns have been described, little emphasis has been placed on comparing patterns among substrates (e.g., terrestrial, epiphytic). Understanding these patterns is important, because they determine not only the pool of genetic resources, but also the functioning of these forest ecosystems. Therefore, we studied how bryophyte species diversity changes with elevation, how elevational patterns differ between substrate types, and how elevational trends relate to environmental drivers.LocationBaru volcano, Panama.MethodsAt each of eight elevations, between 1900 and 3300 m, bryophytes were collected in 600‐cm2 plots from six substrate types with four replicates. Species cover was registered as a measure of relative abundance. Species richness and community structure were determined and related to elevation, substrate types, and environmental drivers at three scales (plots, sets of four replicate plots per substrate per elevation, and all plots at each elevation).ResultsBryophyte species richness decreased towards higher elevations, at all three scales and on all substrates except bryophytes on soil, for which, at the plot scale, richness peaked at higher elevations than on the other substrates. Relative humidity explained richness slightly better than elevation. Communities at the lowest elevations had the most uneven compositions, due to the presence of many small species with low abundance.ConclusionsIn studies on the spatial distribution of bryophyte diversity, it is essential to consider different substrates and spatial scales separately. If substrates differ in their elevational species richness patterns, climate and land‐use change may affect bryophyte diversity patterns not only directly, but also indirectly via changes in substrate availability. Therefore, a better understanding of the spatial variation in bryophyte diversity in mountains is essential to elucidate the effects of environmental change on this important group of plants and their implications for ecosystem functioning.

Absolute Carbon Stable Isotope Ratio in the Vienna Peedee Belemnite Isotope Reference Determined by 1H NMR Spectroscopy.

The Vienna Peedee Belemnite (VPDB) isotope reference defines the zero point of the carbon stable isotope scale that is used to describe the relative abundance of 13C and 12C. An accurate and precise characterization of this isotope reference is valuable for interlaboratory comparisons and conducting robust carbon stable isotope analyses in a vast array of fields, such as chemical forensics, (bio)geochemistry, ecology, or (astro)biology. Here, we report an absolute 13C/12C ratio for VPDB that has been obtained, for the first time, using proton nuclear magnetic resonance spectroscopy (1H NMR). Four different NMR instruments were used to determine 13C/12C ratios in a set of glycine reference materials from the US Geological Survey (USGS64, USGS65, and USGS66) and a set of formate samples that were characterized by isotope ratios mass spectrometry (IRMS). Intercalibration of the NMR-derived 13C/12C ratios with relative abundance (δ13CVPDB) measurements from IRMS yields a value of 0.011100 for the absolute 13C/12C ratio in VPDB, with an expanded uncertainty of ±0.000026 (2σ, n = 114). This is significantly different from the value of 0.011180 that is commonly used but falls within the range of values recently revised using IRMS and infrared absorption measurements. 1H NMR was found to be an effective method for measuring absolute 13C/12C ratios due to its ability to simultaneously detect signals associated with 12C and 13C. Results provide a new and independent measure of the carbon isotope composition of VPDB, improving our understanding of this important isotope reference.

Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics.

Accurate and precise measurement of the relative protein content of blood-based samples using mass spectrometry is challenging due to the large number of circulating proteins and the dynamic range of their abundances. Traditional spectral processing methods often struggle with accurately detecting overlapping peaks that are observed in these samples. In this work, we develop a novel spectral processing algorithm that effectively detects over 1650 peaks with over 3.5 orders of magnitude in intensity in the 3 to 30 kD m/z range. The algorithm utilizes a convolution of the peak shape to enhance peak detection, and accurate peak fitting to provide highly reproducible relative abundance estimates for both isolated peaks and overlapping peaks. We demonstrate a substantial increase in the reproducibility of the measurements of relative protein abundance when comparing this processing method to a traditional processing method for sample sets run on multiple matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) instruments. By utilizing protein set enrichment analysis, we find a sizable increase in the number of features associated with biological processes compared to previously reported results. The new processing method could be very beneficial when developing high-performance molecular diagnostic tests in disease indications.

Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition

BackgroundNew technologies like next-generation sequencing have led to a proliferation of studies investigating the role of the gut microbiome in human health, particularly population-based studies that rely upon participant self-collection of samples. However, the impact of methodological differences in sample shipping, storage, and processing are not well-characterized for these types of studies, especially when transit times may exceed 24 h. The aim of this study was to experimentally assess microbiota stability in stool samples stored at 4 °C for durations of 6, 24, 48, 72, and 96 h with no additives to better understand effects of variable shipping times in population-based studies. These data were compared to a baseline sample that was immediately stored at − 80 °C after stool production.ResultsCompared to the baseline sample, we found that the alpha-diversity metrics Shannon’s and Inverse Simpson’s had excellent intra-class correlations (ICC) for all storage durations. Chao1 richness had good to excellent ICC. We found that the relative abundances of bacteria in the phyla Verrucomicrobia, Actinobacteria, and Proteobacteria had excellent ICC with baseline for all storage durations, while Firmicutes and Bacteroidetes ranged from moderate to good. We interpreted the ICCs as follows: poor: ICC < 0.50, moderate: 0.50 < ICC < 0.75, good: 0.75 < ICC < 0.90, and excellent: ICC > 0.90. Using the Bray–Curtis dissimilarity index, we found that the greatest change in community composition occurred between 0 and 24 h of storage, while community composition remained relatively stable for subsequent storage durations. Samples showed strong clustering by individual, indicating that inter-individual variability was greater than the variability associated with storage time.ConclusionsThe results of this analysis suggest that several measures of alpha diversity, relative abundance, and overall community composition are robust to storage at 4 °C for up to 96 h. We found that the overall community richness was influenced by storage duration in addition to the relative abundances of sequences within the Firmicutes and Bacteroidetes phyla. Finally, we demonstrate that inter-individual variability in microbiota composition was greater than the variability due to changing storage durations.

Seasonal Dynamics of Methanotrophic Bacteria in a Boreal Oil Sands End Pit Lake.

Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for 5 years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 104 cells mL-1 of water (median 0.5 × 103) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH4/O2 microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH4 and O2. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. IMPORTANCE The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multiseason and multiyear data set is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end pit lakes, but we propose that the dynamics are typical of boreal stratified lakes and widely applicable in microbial ecology and limnology. Methane-oxidizing bacteria are important model organisms in microbial ecology and have implications for global climate change.

Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales.

In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S-50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.

Measuring titanium isotope ratios in exoplanet atmospheres

Context. Measurements of relative isotope abundances can provide unique insights into the formation and evolution histories of celestial bodies, tracing various radiative, chemical, nuclear, and physical processes. In this regard, the five stable isotopes of titanium are particularly interesting. They are used to study the early history of the Solar System, and their different nucleosynthetic origins help constrain Galactic chemical models. Additionally, titanium’s minor isotopes are relatively abundant compared to those of other elements, making them more accessible for challenging observations, such as those of exoplanet atmospheres. Aims. We aim to assess the feasibility of performing titanium isotope measurements in exoplanet atmospheres. Specifically, we are interested in understanding whether processing techniques used for high-resolution spectroscopy, which remove continuum information about the planet spectrum, affect the derived isotope ratios. We also want to estimate the signal-to-noise requirements for future observations. Methods. We used an archival high-dispersion CARMENES spectrum of the M-dwarf GJ 1002 as a proxy for an exoplanet observed at very high signal-to-noise. Both a narrow (7045–7090 Å) and wide (7045–7500 Å) wavelength region were defined for which spectral retrievals were performed using petitRADTRANS models, resulting in isotope ratios and uncertainties. These retrievals were repeated on the spectrum with its continuum removed to mimic typical high-dispersion exoplanet observations. The CARMENES spectrum was subsequently degraded by adding varying levels of Gaussian noise to estimate the signal-to-noise requirements for future exoplanet atmospheric observations. Results. The relative abundances of all minor Ti isotopes are found to be slightly enhanced compared to terrestrial values. A loss of continuum information from broadband filtering of the stellar spectrum has little effect on the isotope ratios. For the wide wavelength range, a spectrum with a signal-to-noise of 5 is required to determine the isotope ratios with relative errors ≲10%. Super Jupiters at large angular separations from their host star are the most accessible exoplanets, requiring about an hour of observing time on 8-meter-class telescopes, and less than a minute of observing time with the future Extremely Large Telescope.