Actual Abundance Research Articles

LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors.

Mass spectrometry (MS) has become a predominant choice for large-scale absolute protein quantification, but its quantification accuracy still has substantial room for improvement. A crucial issue is the bias between the peptide MS intensity and the actual peptide abundance, i.e., the fact that peptides with equal abundance may have different MS intensities. This bias is mainly caused by the diverse physicochemical properties of peptides. Here, we propose an algorithm for label-free absolute protein quantification, LFAQ, which can correct the biased MS intensities by using the predicted peptide quantitative factors for all identified peptides. When validated on data sets produced by different MS instruments and data acquisition modes, LFAQ presented accuracy and precision superior to those of existing methods. In particular, it reduced the quantification error by an average of 46% for low-abundance proteins. The advantages of LFAQ were further confirmed using the data from published papers.

Neutrophilic Asthma Is Associated with Increased Airway Bacterial Burden and Disordered Community Composition.

Neutrophilic asthma (NA) is an important asthma inflammatory phenotype associated with disease severity, airflow limitation, and steroid resistance, and its mechanism is still uncertain. Evidences suggest a potential role for bacteria in its pathogenesis, but, so far, this remains poorly understood. We sought to investigate airway bacterial burden, community composition, and inflammatory response in NA. Fifty-four stable asthmatics without infection were enrolled and separated into either NA group (n = 20) or non-NA group (n = 34). Subject demographics, Asthma Control Test (ACT) scores, medications, and pulmonary functions were documented. Sputum cytology, airway bacterial burden, microbial community composition, and inflammatory cytokines were assessed. The total airway bacterial burden was significantly increased in subjects with NA versus non-NA and was positively correlated with the sputum neutrophil percentage. Airway neutrophilia was associated with less airway bacterial community richness and diversity, along with a distinct community composition. In patients with NA, bacteria in phylum Proteobacteria, especially Haemophilus spp. and Moraxella spp., showed significant increases in both actual loads and relative abundances, while bacteria in phyla Firmicutes, Actinobacteria, and Saccharibacteria showed decreased relative abundances compared with non-NA. Patients with NA demonstrated higher levels of interleukin-1β (IL-1β), IL-6, IL-8, IL-12, IL-17A, and tumor necrosis factor-α (TNF-α) in sputum samples compared with non-NA. Increased bacterial burden and distinct microbiota composition were the key characters of neutrophilic phenotype in asthma, accompanied by excessive airway inflammation. Understanding the relationship between airway microbiota and neutrophilic inflammation may help in treatment and management of asthma, such as targeting airway microbiota.

Which mosquitoes (Diptera: Culicidae) are candidates for DNA extraction in forensic practice?

Mosquitoes can be of importance in forensic context as a source of the perpretator's DNA. The aim of this study was to find how can we optimize the selection of appropriate mosquito individuals. The study was based on the data of 177833 trapped female mosquitoes and 105236 individuals which were collected directly from human skin. The mean human-specific biting willingness value of Aedes species was the highest (mean: 0.8). Significant differences were found between the human-specific biting willingness value variances of Aedes and Culex (p=0.0117) and barely significant differences between Anopheles and Culiseta (p = 0.5412), as well as between Aedes and Culiseta genera (p = 0.0562). Culiseta species showed the lowest human-specific biting willingness values (mean = 0.16). The mean of the human-specific biting willingness values of univoltine and multivoltine mosquitoes were 0.43 and 0.37 which means no significant difference between the variances of the two groups (p = 0.625). The mean of the human-specific biting willingness values of the predominantly mammal biting and non-mammal biting mosquitoes were 0.45 and 0.03 with a very significant difference (p<0.0001). Only five mosquito species have a relative biting risk index equal or more than 0.03 in Hungary, namely of Aedes vexans (0.43), Ochlerotatus cantans: (0.25), Ochlerotatus sticticus: (0.11), Culex modestus: (0.07) and Aedes cinereus: (0.03). It can be concluded that the mean human-specific biting willingness of mosquitoes depends on the genera, the host preference and it is independent of the annual number of generations or the breeding habitat preference. The relative biting risk index reflects the actual and annual relative abundances and the usefulness and availability of a mosquito for legal purposes reducing the financial and time requirements of the investigations.

Ionisation efficiencies can be predicted in complicated biological matrices: A proof of concept

The importance of metabolites is assessed based on their abundance. Most of the metabolites are at present identified based on ESI/MS measurements and the relative abundance is assessed from the relative peak areas of these metabolites. Unfortunately, relative intensities can be highly misleading as different compounds ionise with vastly different efficiency in the ESI source and matrix components may cause severe ionisation suppression. In order to reduce this inaccuracy, we propose predicting the ionisation efficiencies of the analytes in seven biological matrices (neat solvent, blood, plasma, urine, cerebrospinal fluid, brain and liver tissue homogenates). We demonstrate, that this approach may lead to an order of magnitude increase in accuracy even in complicated matrices. For the analyses of 10 compounds, mostly drugs, in negative electrospray ionisation mode we reduce the predicted abundance mismatch compared to the actual abundance on average from 660 to 8 times. The ionisation efficiencies were predicted based on i) the charge delocalisation parameter WAPS and ii) the degree of ionisation α, and the prediction model was subsequently validated based on the cross-validation method ‘leave-one-out’.

Models of Coupled Settlement and Habitat Networks for Biodiversity Conservation: Conceptual Framework, Implementation and Potential Applications

Worldwide, the expansion of settlement and transport infrastructure is one of the most important proximate as well as ultimate causes of biodiversity loss. As much as every modern human society depends on a network of settlements that is well-connected by transport infrastructure (i.e. settlement network), animal and plant species depend on networks of habitats between which they can move (i.e. habitat networks). However, changes to a settlement network in a region often threaten the integrity of the region’s habitat networks. Determining plans and policy to prevent these threats is made difficult by the numerous interactions and feedbacks that exist between and within the settlement and habitat networks. Mathematical models of coupled settlement and habitat networks can help us understand the dynamics of this social-ecological system. Yet, few attempts have been made to develop such mathematical models. In this paper, we promote the development of models of coupled settlement and habitat networks for biodiversity conservation. First, we present a conceptual framework of key variables that are ideally considered when operationalising the coupling of settlement and habitat networks. In this framework, we first describe important network-internal interactions by differentiating between the structural (i.e. relating to purely physical conditions determining the suitability of a location for living or movement) and functional (i.e. relating to the actual presence, abundance or movement of people or other organisms) properties of either network. We then describe the main one-way influences that a settlement network can exert on the habitat networks and vice versa. Second, we give several recommendations for the mathematical modelling of coupled settlement and habitat networks and present several existing modelling approaches (e.g. habitat network models and land-use transport interaction models) that could be used for this purpose. Lastly, we elaborate on potential application of models of coupled settlement and habitat networks in the development of complex network theory, in the assessment of system resilience and in conservation, transport and urban planning. The development of coupled settlement and habitat network models is important to gain a better system-level understanding of biodiversity conservation under a rapidly urbanising and growing human population.

Nitrate: An Environmental Endocrine Disruptor? A Review of Evidence and Research Needs.

Nitrate is heavily used as an agricultural fertilizer and is today a ubiquitous environmental pollutant. Environmental endocrine effects caused by nitrate have received increasing attention over the last 15 years. Nitrate is hypothesized to interfere with thyroid and steroid hormone homeostasis and developmental and reproductive end points. The current review focuses on aquatic ecotoxicology with emphasis on field and laboratory controlled in vitro and in vivo studies. Furthermore, nitrate is just one of several forms of nitrogen that is present in the environment and many of these are quickly interconvertible. Therefore, the focus is additionally confined to the oxidized nitrogen species (nitrate, nitrite and nitric oxide). We reviewed 26 environmental toxicology studies and our main findings are (1) nitrate has endocrine disrupting properties and hypotheses for mechanisms exist, which warrants for further investigations; (2) there are issues determining actual nitrate-speciation and abundance is not quantified in a number of studies, making links to speciation-specific effects difficult; and (3) more advanced analytical chemistry methodologies are needed both for exposure assessment and in the determination of endocrine biomarkers.

Application of a mixed modelling approach to standardize catch-per-unit-effort data for an abalone dive fishery in Western Victoria, Australia

Despite the prevalence of catch per unit effort (CPUE) as a key metric in fisheries assessments it can be fraught with inherent problems that often cause its use as an index of abundance to become contentious. This is particularly the case with abalone, a sedentary shellfish targeted by commercial dive fishers around the globe. It is common practice to standardize CPUE to at least partly address issues about how well it reflects the actual abundance of a stock. Differences between standardized and unstandardized trends may lead to controversy between scientists and stakeholders when standardized trends provide a less optimistic picture of stock status. It is within this context that we applied Linear Mixed Model (LMM) and Generalized Linear Mixed Model (GLMM) methods to standardize CPUE for the Western Zone blacklip abalone fishery in Victoria, Australia. This fishery was chosen for our evaluation because it included substantial population losses from a disease shock during the middle of the time series. The effects of diver, reef location, month and their interactions with year were included as random effects in these models and the results compared with nominal geometric means. The two standardization methods provided similar standardized CPUE trends and clearly demonstrated that a large proportion of the variance could be attributed to diver and spatial effects. The GLMM seemed to explain more variability in the data and produced better precision for standardized CPUEs than LMM. The temporal trend in variability attributed to divers and spatial scales reveals the impact of disease as well as any homo/heterogeneity effect. The CPUE trends responded to the impact of disease against a backdrop of declining stock, however when compared with the inter-annual pattern in nominal CPUE, the standardized trends showed that the decline immediately following the onset of disease was less precipitous. In contrast to what appeared to be an increase in the nominal series during the more recent post-disease period, there was only a slight non-significant increase observable in the standardized trends.

The "Tracked Roaming Transect" and distance sampling methods increase the efficiency of underwater visual censuses.

Underwater visual census (UVC) is the most common approach for estimating diversity, abundance and size of reef fishes in shallow and clear waters. Abundance estimation through UVC is particularly problematic in species occurring at low densities and/or highly aggregated because of their high variability at both spatial and temporal scales. The statistical power of experiments involving UVC techniques may be increased by augmenting the number of replicates or the area surveyed. In this work we present and test the efficiency of an UVC method based on diver towed GPS, the Tracked Roaming Transect (TRT), designed to maximize transect length (and thus the surveyed area) with respect to diving time invested in monitoring, as compared to Conventional Strip Transects (CST). Additionally, we analyze the effect of increasing transect width and length on the precision of density estimates by comparing TRT vs. CST methods using different fixed widths of 6 and 20 m (FW3 and FW10, respectively) and the Distance Sampling (DS) method, in which perpendicular distance of each fish or group of fishes to the transect line is estimated by divers up to 20 m from the transect line. The TRT was 74% more time and cost efficient than the CST (all transect widths considered together) and, for a given time, the use of TRT and/or increasing the transect width increased the precision of density estimates. In addition, since with the DS method distances of fishes to the transect line have to be estimated, and not measured directly as in terrestrial environments, errors in estimations of perpendicular distances can seriously affect DS density estimations. To assess the occurrence of distance estimation errors and their dependence on the observer’s experience, a field experiment using wooden fish models was performed. We tested the precision and accuracy of density estimators based on fixed widths and the DS method. The accuracy of the estimates was measured comparing the actual total abundance with those estimated by divers using FW3, FW10, and DS estimators. Density estimates differed by 13% (range 0.1–31%) from the actual values (average = 13.09%; median = 14.16%). Based on our results we encourage the use of the Tracked Roaming Transect with Distance Sampling (TRT+DS) method for improving density estimates of species occurring at low densities and/or highly aggregated, as well as for exploratory rapid-assessment surveys in which divers could gather spatial ecological and ecosystem information on large areas during UVC.

Impacts of the nonlinear relationship between abundance and its index in a tuned virtual population analysis

The abundance index used in a tuned virtual population analysis (VPA) is usually assumed to be proportional to actual abundance. However, the actual abundance and abundance index do not always have a linear relationship. Such nonlinearity can cause biases in abundance estimates as well as retrospective biases arising from systematic differences in abundance estimates when more data are successively added. Severe retrospective biases can damage the reliability of stock assessments. In this study, we use an approach to estimate an additional parameter that controls the nonlinearity in a tuned VPA. A performance test using simulated data revealed that the tuned VPA was able to accurately estimate the nonlinearity parameter and thus yielded less biased abundance estimates and smaller retrospective biases. We also found that estimating the nonlinearity parameters was effective even under other model misspecification scenarios, such as disregarding historical increases in catchability and time-varying natural mortality. Moreover, we applied this approach to some Japanese fish stocks and evaluated its validity. We found that estimating the nonlinearity parameters in the tuned VPA enhances the reliability of fisheries stock assessments.

Are Two Days Enough? Checking the Accuracy of the Survey Protocols Used in Common Bird Monitoring Schemes

Summary. Common bird monitoring schemes have become an important tool in conservation biology because they provide useful information for assessing spatial and temporal variations of bird populations. However, recorded data may suffer from several observational procedures that cause error. In recent years, a robust mathematical framework has been developed to control for potential confounding factors affecting the assessment of the actual spatial and temporal variability of bird populations. Surprisingly few attempts have been made to check the effectiveness of current methodology empirically and thus to determine to what extent monitoring scheme data can provide accurate estimates of actual bird abundances. To check the effect of intra-annual variability of bird counts, I conducted daily surveys of House Martin Delichon urbicum and Common Swift Apus apus populations along a 2-km transect line in Tres Cantos (Madrid, Spain) between March and September 2005. The data recorded perfectly mimicked the informa...

High-Resolution MaxEnt Modelling of Habitat Suitability for Maternity Colonies of the Barbastelle Bat Barbastella barbastellus (Schreber, 1774) in Rhineland-Palatinate, Germany

The barbastelle bat Barbastella barbastellus (Schreber, 1774), probably one of the rarest of western European bat species, has suffered from substantial population declines over the last several decades. In fact, it was believed to be extinct within the federal state of Rhineland-Palatinate (western Germany) until the discovery of a maternity colony in 2004. More reproduction sites have since been found, which demonstrates a substantial knowledge gap about the actual distribution and abundance of the species in Rhineland-Palatinate. Suitable habitats for maternity colonies are crucial for the survival of a population and knowledge of their location is critical for conservation. We modelled the suitability of habitats for use by maternity colonies in Rhineland-Palatinate based on high-resolution data of the forest structure and roosting sites of maternity colonies, using the presence-only machine learning approach MaxEnt. In addition to statistical tests of the model performance, we analysed general occurrence surveys from the last few years for evidence of barbastelle and conducted an in-situ survey on one of the sites identified as highly suitable by the model, but for which no occurrence records exist. On this site, we discovered a new maternity colony. Analysis of third-party surveys resulted in two recently discovered colonies, which shows the barbastelle's range is not restricted to the area south of the Moselle River. The results of our study along with the scattered pattern of potentially suitable locations for maternity colonies in the region challenge previous assumptions of the geographic distribution of barbastelle in Rhineland-Palatinate. This study demonstrates the potential of habitat suitability modelling in conservation ecology and the results may provide a basis for future preservation strategies in the region.

Persistence of marine fish environmental DNA and the influence of sunlight.

Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.

Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa

Understanding the abundance change of certain bacterial taxa is quite important for the study of soil microbiology. However, the observed differences of relative abundances by high-throughput techniques may not accurately reflect those of the actual taxon abundances. This study investigated whether soil microbial abundances coupling with microbial quantities can be more informative in describing the microbial population distribution under different locations. We analyzed relative abundances of the major species in soil microbial communities from Beijing and Tibet grasslands by using 16 S rRNA high-throughput sequencing technique, and quantified the absolute bacterial cell numbers directly or indirectly by multiple culture-independent measurements, including adenosine tri-phosphate (ATP), flow cytometry (FCM), quantitative real-time PCR (qPCR), phospholipid fatty acids (PLFA) and microbial biomass Carbon (MBC). By comparison of the relative abundance and the estimated absolute abundances (EAA) of the major components in soil microbial communities, several dominant phyla, including Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonates and Planctomycetes, showed significantly different trends. These results indicated that the change in EAA might be more informative in describing the dynamics of a population in a community. Further studies of soil microbes should combine the quantification and relative abundances of the microbial communities for the comparisons among various locations.

Realized trophic niche driven by apparent competition: an example with marsupials

AbstractAccording to apparent competition theory, the co‐occurrence of two species that share the same predators appears to affect each other's population growth and abundance. However, due to habitat loss and over‐hunting, top predators are being made rare worldwide. Considering that apparent competitors share similar resources, we would expect the absence of top predators to reflect in changes on prey realized trophic niches. To test our hypothesis, we developed a model to predict the abundance ratio of apparent competitor species based on changes in their realized trophic niches. We tested our model against field data on the Neotropical marsupials Didelphis aurita and Metachirus nudicaudatus. Our results revealed that D. aurita and M. nudicaudatus are two species under apparent competition and their realized trophic niche and diet overlap change according to the presence of top predators. The model was able to predict the actual relative abundances of D. aurita and M. nudicaudatus in the three empirical studies analyzed. Our study presents quantitative support to the apparent competition theory; however, the model's applications to other groups still need to be verified. Additionally, our study shows that the lack of top predators has consequences on the realized trophic niche of their prey, and therefore, we reinforce that conservation plans need to focus on the effects of top predator loss on ecosystems.

Grasshopper species composition shifts following a severe rangeland grasshopper outbreak

Little is known about how grasshopper species abundances shift during and following severe outbreaks, as sampling efforts usually end when outbreaks subside. Grasshopper densities, species composition and vegetation have infrequently been sampled during and after a severe outbreak in the western U.S., which is needed to better understand the cause of outbreaks and population declines. In this study, grasshopper densities, species composition and vegetation were monitored at a northern mixed rangeland site from 1999 to 2003 where densities reached 130 per m2 during a severe outbreak. Phoetaliotes nebrascensis (Acrididae: Melanoplinae) comprised 79% of the outbreak in 2000, but declined to 3% by 2003. The dramatic shifts in proportional and actual abundance of P. nebrascensis over a 5 year period illustrate that species dominance can change rapidly, even for a highly dominant outbreak species. The difficulty of fully understanding factors causing shifts in grasshopper populations is illustrated by population declines in all species observed in 2002 and 2003. The data can help predict the intensity and decline of outbreaks and points to the critical importance of long term simultaneous monitoring of grasshopper densities, species composition and vegetation for outbreak prediction.

Quantification, isolation and characterization of Bifidobacterium from the vaginal microbiomes of reproductive aged women

The vaginal microbiome plays an important role in women's reproductive health. Imbalances in this microbiota, such as the poorly defined condition of bacterial vaginosis, are associated with increased susceptibility to sexually transmitted infections and negative reproductive outcomes. Currently, a “healthy” vaginal microbiota in reproductive aged women is understood to be dominated by Lactobacillus, although “atypical” microbiomes, such as Bifidobacterium-dominated profiles, have been described. Despite these observations, vaginal bifidobacteria remain relatively poorly characterized, and questions remain regarding their actual abundance in the microbiome. In this study, we used quantitative PCR to confirm the relative abundance of Bifidobacterium in the vaginal microbiomes of healthy reproductive aged women (n = 42), previously determined by deep sequencing. We also isolated and phenotypically characterized vaginal bifidobacteria (n = 40) in the context of features thought to promote reproductive health. Most isolates were identified as B. breve or B. longum based on cpn60 barcode sequencing. Fermentation patterns of vaginal bifidobacteria did not differ substantially from corresponding type strains of gut or oral origin. Lactic acid was produced by all vaginal isolates, with B. longum strains producing the highest levels, but only 32% of isolates produced hydrogen peroxide. Most vaginal bifidobacteria were also able to tolerate high levels of lactic acid (100 mM) and low pH (4.5 or 3.9), conditions typical of vaginal fluid of healthy women. Most isolates were resistant to metronidazole but susceptible to clindamycin, the two most common antibiotics used to treat vaginal dysbiosis. These findings demonstrate that Bifidobacterium is the dominant member of some vaginal microbiomes and suggest that bifidobacteria have the potential to be as protective as lactobacilli according to the current understanding of a healthy vaginal microbiome.

CO concentration in the upper stratosphere and mesosphere of Titan from VIMS dayside limb observations at 4.7 µm

During the last 30 years, many works have focused on the determination of the CO abundance in Titan’s atmosphere, but no measurement above 300 km has been done yet due to the faint signal of CO. Nevertheless, such measurements are particularly awaited as a confirmation of photochemical models predictions that CO is uniformly mixed in the whole atmosphere. Moreover, since CO is the main atmospheric reservoir of oxygen, its actual abundance has implications on the origins of Titan’s atmosphere. In this work, we analyse a set of Cassini VIMS daytime limb observations of Titan at 4.7 µm, which is dominated by solar-pumped non-LTE (non-local thermodynamic equilibrium) emission of CO ro-vibrational bands. In order to retrieve the CO abundance from these observations, we developed a non-LTE model for the CO vibrational levels. The retrieval of the CO concentration is performed following a bayesian approach and using the calculated non-LTE populations. The data set analysed consists of 47 limb scanning sequences -about 1500 spectra- acquired by VIMS in 2006 and 2007. CO relative abundance profiles from 200 to 500 km are obtained, for each set analysed. The mean result shows no significant variations with altitude and is consistent with the prediction of a well-mixed vertical profile. However, if compared with Earth-based mm measurements, a small vertical gradient is plausible.

Relating trophic resources to community structure: a predictive index of food availability.

The abundance and the distribution of trophic resources available for consumers influence the productivity and the diversity of natural communities. Nevertheless, assessment of the actual abundance of food items available for individual trophic groups has been constrained by differences in methods and metrics used by various authors. Here we develop an index of food abundance, the framework of which can be adapted for different ecosystems. The relative available food index (RAFI) is computed by considering standard resource conditions of a habitat and the influence of various generalized anthropogenic and natural factors. RAFI was developed using published literature on food abundance and validated by comparison of predictions versus observed trophic resources across various marine sites. RAFI tables here proposed can be applied to a range of marine ecosystems for predictions of the potential abundance of food available for each trophic group, hence permitting exploration of ecological theories by focusing on the deviation from the observed to the expected.

Improved real-time PCR method for quantification of the abundance of all known ribotypes of the ichthyotoxic dinoflagellate Cochlodinium polykrikoides by comparing 4 different preparation methods

Red tides by the ichthyotoxic dinoflagellate Cochlodinium polykrikoides have caused large scaled mortality of fish and great loss in aquaculture industry in many countries. Detecting and quantifying the abundance of this species are the most critical step in minimizing the loss. The conventional quantitative real-time PCR (qPCR) method has been used for quantifying the abundance of this species. However, when analyzing >500 samples collected during huge C. polykrikoides red tides in South Sea of Korea in 2014, this conventional method and the previously developed specific primer and probe set for C. polykrikoides did not give reasonable abundances when compared with cell counting data. Thus improved qPCR methods and a new specific primer and probe set reflecting recent discovery of 2 new ribotypes have to be developed. A new species-specific primer and probe set for detecting all 3 ribotypes of C. polykrikoides was developed and provided in this study. Furthermore, because the standard curve between cell abundance and threshold cycle value (Ct) is critical, the efficiencies of 4 different preparation methods used to determine standard curves were comparatively evaluated. The standard curves were determined by using the following 4 different preparations: (1) extraction of DNA from a dense culture of C. polykrikoides followed by serial dilution of the extracted DNA (CDD method), (2) extraction of DNA from each of the serially diluted cultures with different concentrations of C. polykrikoides cultures (CCD method), (3) extraction of DNA from a dense field sample of C. polykrikoides collected from natural seawater and then dilution of the extracted DNA in serial (FDD method), and (4) extraction of DNA from each of the serially diluted field samples having different concentrations of C. polykrikoides (FCD method). These 4 methods yielded different results. The abundances of C. polykrikoides in the samples collected from the coastal waters of South Sea, Korea, in 2014–2015, obtained using the standard curves determined by the CCD and the FCD methods, were the most similar (0.93–1.03 times) and the second closest (1.16–1.33 times) to the actual cell abundances obtained by enumeration of cells. Thus, our results suggest that the CCD method is a more effective tool to quantify the abundance of C. polykrikoides than the conventional method, CDD, and the FDD and FCD methods.

Plant–soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo

AbstractWe investigated consequences of plant–soil feedbacks (PSFs) in a tropical montane forest on Mt. Kinabalu in Borneo by measurements of light and soil conditions, ecophysiological analyses of tree seedlings, a long‐term adult and seedling census, and a simple simulation model. The study plot (2.74 ha) is in a mixed conifer–broadleaf forest with 24% relative basal area of conifers. First, we investigated light and soil conditions beneath two dominant species, a conifer Dacrydium gracilis (Podocarpaceae, arbuscular mycorrhizal tree) and a broadleaf Lithocaprus clementianus (Fagaceae, ectomycorrhizal tree). The relative light intensity was marginally higher beneath Dacrydium tree crown than beneath Lithocarpus tree crown. The concentrations of inorganic nitrogen and labile phosphorus, and the nitrogen mineralization rate, were lower beneath Dacrydium than beneath Lithocarpus, suggesting that soils beneath Dacrydium were more nutrient deficient. Microscopic observations confirmed that conifer seedlings (including Dacrydium) harbored arbuscular mycorrhizal fungi. In addition, a molecular analysis showed that root‐associated mycorrhizal fungal communities were clearly different between conifer and broadleaf seedlings, and consequently, nutrient acquisition capacity of seedlings may be different between them. Indeed, stable isotopic evidence suggested that Dacrydium seedlings are more efficient in inorganic nitrogen acquisition than Lithocarpus seedlings. These results predicted that the conifer seedlings would out‐compete broadleaf seedlings and have a greater advantage beneath the conifer canopy. To test the possible advantage of conifer seedlings in performance, we developed hierarchical Bayesian models and estimated growth and mortality rates using the seedling census data during 2006–2012. We found that conifer seedlings performed better than broadleaf seedlings beneath Dacrydium canopy. On the other hand, broadleaf seedlings performed better than conifer seedlings beneath Lithocarpus canopy. The consequences of the PSFs for the tree community composition were investigated by developing a simple simulation model, and were compared with the results of a model without PSFs. After a 10 000‐year simulation, the relative abundance of conifers with PSFs converged to 22%, which was consistent with the actual abundance; the model without effects of PSFs predicted a relative abundance of only ~10%. The results suggested that PSFs contributed to the maintenance of the conifer dominance in the tropical montane forest.