Optimal Diet as a Function of Absolute Abundance, Relative Abundance, and Relative Value of Available Prey

Prey selection by a predatory leech, Nephelopsis obscura, was examined in a series of laboratory experiments. Two chironomids, Glyptotendipes paripes and Chironomus riparius, and the tubificid worm, Tubifex tubifex, were used as alternative prey. These three prey are all tube dwellers found in the same microhabit at the mud–water interface. The quality of each of the three prey types was estimated by their ability to promote the growth of the leeches. The two chironomids were much superior prey than Tubifex. Mixed diets did not improve growth. The selectivity of starved leeches offered equal densities of the two chironomids was not affected by the absolute abundance of prey. After 72 h the selectivity was biased toward Chironomous, the more mobile prey, and this bias increased with prey density. Varying the relative abundance of these two prey did not alter the selectivity of the leeches with a single exception. When Chironomus was the more abundant prey, selectivity was biased towards it, but this disappeared after 72 h. There were no significant effects of absolute abundance, relative abundance, or feeding history on the selectivity of leeches offered a choice between Glyptotendipes and Tubifex. Tubifex was rarely captured in any of the treatments tested. It was concluded that a description of prey choice by Nephelopsis does not require explanations based in optimal diet theory or frequency-dependent foraging. Differences in capture rates of different prey species may be related to their motility or vulnerability rather than any active choice on the part of Nephelopsis.

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Abundance of Boeckella gracilis (Daday, 1902) (Copepoda, Calanoida) in seasonal coastal pools in the Araucania region (38°S, Chile)

Crustaceana ◽

10.1163/15685403-00003814 ◽

2018 ◽

Vol 91 (10) ◽

pp. 1211-1217

Author(s):

Patricio De los Ríos

Keyword(s):

Correlation Analysis ◽

Environmental Stress ◽

Relative Abundance ◽

Calanoid Copepod ◽

Inverse Correlation ◽

Inland Waters ◽

Absolute Abundance ◽

Significant Inverse Correlation

Abstract The presence of the calanoid copepod Boeckella gracilis (Daday, 1902) in Chilean seasonal pools has been only poorly studied as yet. The aim of the present study thus is to investigate the role of conductivity and temperature on the relative and absolute abundance of B. gracilis in seasonal coastal pools in the Araucania region (38°S, Chile). The results of correlation analysis revealed the presence of a significant inverse correlation between conductivity and relative abundance, whereas no significant correlations were found between conductivity and absolute abundance, between temperature and absolute abundance, and between temperature and relative abundance. These results agree partially with similar observations for mountain pools in the same region, but they would not agree with observations for calanoids of saline and subsaline inland waters in the northern and southern extremes of Chile. Considering this scenario, the species would show different populational responses to environmental stress in different situations, which phenomenon deserves to be studied more extensively and in more detail.

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Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

Microorganisms ◽

10.3390/microorganisms9091797 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1797

Author(s):

Xiaofan Wang ◽

Samantha Howe ◽

Feilong Deng ◽

Jiangchao Zhao

Keyword(s):

Decision Making ◽

Relative Abundance ◽

Quantitative Methods ◽

High Throughput Sequencing ◽

Bacterial Load ◽

Data Interpretation ◽

Absolute Quantification ◽

Large Sample Size ◽

Absolute Abundance ◽

Host Interactions

High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.

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Distribution of antibiotic-resistant bacteria in aerobic composting of swine manure with different antibiotics

Environmental Sciences Europe ◽

10.1186/s12302-021-00535-6 ◽

2021 ◽

Vol 33 (1) ◽

Author(s):

Tingting Song ◽

Hongna Li ◽

Binxu Li ◽

Jiaxun Yang ◽

Muhammad Fahad Sardar ◽

...

Keyword(s):

Antibiotic Resistance ◽

Community Structure ◽

Bacterial Community ◽

Relative Abundance ◽

Bacterial Community Structure ◽

Swine Manure ◽

Resistant Bacteria ◽

Absolute Abundance ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant

Abstract Background Livestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting. Results The absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments. Conclusion Among the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.

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Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry

The Analyst ◽

10.1039/c4an00567h ◽

2014 ◽

Vol 139 (21) ◽

pp. 5439-5450 ◽

Cited By ~ 7

Author(s):

Philip L. Loziuk ◽

Ronald R. Sederoff ◽

Vincent L. Chiang ◽

David C. Muddiman

Keyword(s):

Mass Spectrometry ◽

Relative Abundance ◽

Isotope Dilution ◽

Isotope Dilution Mass Spectrometry ◽

Protein Quantification ◽

Protein Cleavage ◽

Absolute Abundance

Relative abundance values and their associated variability are dynamic and dependent on absolute abundance.

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Dynamics of Microbial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus Minor)

10.21203/rs.3.rs-585254/v1 ◽

2021 ◽

Author(s):

Hokyung Song ◽

Keesan Lee ◽

Injae Hwang ◽

Eunjeong Yang ◽

Jungmoon Ha ◽

...

Keyword(s):

Microbial Communities ◽

Relative Abundance ◽

Direct Contact ◽

Turnover Rate ◽

Hatching Success ◽

Nest Material ◽

Absolute Abundance ◽

Future Studies ◽

Parus Minor ◽

Nest Materials

Abstract Eggshell microbial communities may affect hatching success and nestling’s condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest-material microbial communities and their changes during incubation in the Oriental Tit (Parus minor). Microbial communities on the nest material were relatively stable and remained distinct from the eggshell communities, and had higher diversity and greater phylogenetic clustering compared to the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of microbial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics between the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird’s skin, feathers or cloaca/intestine, which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials and the incubating bird’s body.

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The quest for absolute abundance: the use of internal standards for DNA-based microbial and community ecology

10.32942/osf.io/q7gy6 ◽

2020 ◽

Cited By ~ 1

Author(s):

Joshua Harrison ◽

W. John Calder ◽

Bryan N. Shuman ◽

C. Alex Buerkle

Keyword(s):

Community Ecology ◽

Relative Abundance ◽

Compositional Data ◽

Direct Measure ◽

Absolute Abundance ◽

Internal Standards ◽

Integral Component ◽

Dna Pools ◽

Relative Abundances ◽

Sequencing Process

To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as ``spike-ins'') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.

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Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽

10.7717/peerj.4514 ◽

2018 ◽

Vol 6 ◽

pp. e4514 ◽

Cited By ~ 25

Author(s):

Jun Lou ◽

Li Yang ◽

Haizhen Wang ◽

Laosheng Wu ◽

Jianming Xu

Keyword(s):

Bacterial Community ◽

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Laboratory Strain ◽

Soil Bacterial Community ◽

Absolute Abundance ◽

Internal Reference ◽

Biodegradation Study ◽

Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

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Contemporary fisheries stock assessment: many issues still remain

ICES Journal of Marine Science ◽

10.1093/icesjms/fsu015 ◽

2014 ◽

Vol 72 (1) ◽

pp. 7-18 ◽

Cited By ~ 84

Author(s):

Mark N. Maunder ◽

Kevin R. Piner

Keyword(s):

Information Content ◽

Relative Abundance ◽

Stock Assessment ◽

Diagnostic Methods ◽

Natural Mortality ◽

Absolute Abundance ◽

Substantial Impact ◽

Composition Data ◽

The Absolute ◽

Management Advice

Abstract Interpretation of data used in fisheries assessment and management requires knowledge of population (e.g. growth, natural mortality, and recruitment), fisheries (e.g. selectivity), and sampling processes. Without this knowledge, assumptions need to be made, either implicitly or explicitly based on the methods used. Incorrect assumptions can have a substantial impact on stock assessment results and management advice. Unfortunately, there is a lack of understanding of these processes for most, if not all, stocks and even for processes that have traditionally been assumed to be well understood (e.g. growth and selectivity). We use information content of typical fisheries data that is informative about absolute abundance to illustrate some of the main issues in fisheries stock assessment. We concentrate on information about absolute abundance from indices of relative abundance combined with catch, and age and length-composition data and how the information depends on knowledge of population, fishing, and sampling processes. We also illustrate two recently developed diagnostic methods that can be used to evaluate the absolute abundance information content of the data. Finally, we discuss some of the reasons for the slowness of progress in fisheries stock assessment.

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A standardised monitoring protocol for the black caiman (Melanosuchus niger)

Wildlife Research ◽

10.1071/wr19135 ◽

2020 ◽

Vol 47 (4) ◽

pp. 317

Author(s):

Adrián Naveda-Rodríguez ◽

Víctor Utreras B. ◽

Galo Zapata-Ríos

Keyword(s):

Relative Abundance ◽

Survey Design ◽

Conservation Status ◽

Absolute Abundance ◽

Imperfect Detection ◽

Monitoring Protocol ◽

Abundance Estimates ◽

Consistent Manner ◽

Status Assessment ◽

The Individual

Abstract ContextEstimating population abundance can be plagued by the violation of methodological assumptions, which can be overcome with standardised protocols. The black caiman (BC) is considered a conservation-dependent species, and previous abundance estimates are surrounded by uncertainty and flaws in the survey (e.g. different survey design and efforts) and analytical approach used (e.g. relative abundance index, which ignores imperfect detection). Its conservation status assessment demands the implementation of a standardised monitoring protocol. AimsThe protocol provides guidelines to collect and analyse data in a consistent manner to survey BC. Besides accounting for imperfect detection to produce reliable abundance estimates, the protocol aimed to be easily implemented by park rangers, and to fit field observations into a hierarchical modelling approach to assess how environmental variables affects detectability and abundance. MethodsThe protocol subdivides a 20-km transect into 10 2-km segments; each transect is surveyed four consecutive nights, starting at 1900 hours and finishing when the 20km are completed. For each caiman detected, the observers estimated head size to classify the individual by age. We tested the protocol in Ecuador during January and December 2017, and field data were analysed using N-mixture models. We compared abundance estimates derived with this protocol with commonly used relative abundance indexes. Key resultsWe surveyed 460km that resulted in 177 detections. Percentage of moonlight and distance from human settlement best explained detectability and abundance respectively. Mean detection probability was 0.14 (95% BCI: 0.1–0.18), whereas absolute abundance was 196 (95% BCI: 147–370). The overall adult to immature ratio was 1:1.3. ConclusionsThis is the first estimate of detectability and absolute abundance for BC by using a standardised survey with a clearly defined and repeatable survey and analysis methods. Relative abundance indexes did not reflect absolute abundance estimates. We recommend the use of this protocol in future surveys across the Amazon region to effectively evaluate BC conservation status. ImplicationsPopulation size cannot be estimated from relative abundance indexes; they lead to bias estimates for ignoring imperfect detection. We discourage the use of relative abundance indexes to evaluate the conservation status of this species.

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