scholarly journals Mixoplankton interferences in dilution grazing experiments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guilherme Duarte Ferreira ◽  
Filomena Romano ◽  
Nikola Medić ◽  
Paraskevi Pitta ◽  
Per Juel Hansen ◽  
...  

AbstractIt remains unclear as to how mixoplankton (coupled phototrophy and phagotrophy in one cell) affects the estimation of grazing rates obtained from the widely used dilution grazing technique. To address this issue, we prepared laboratory-controlled dilution experiments with known mixtures of phyto-, protozoo-, and mixoplankton, operated under different light regimes and species combinations. Our results evidenced that chlorophyll is an inadequate proxy for phytoplankton when mixoplankton are present. Conversely, species-specific cellular counts could assist (although not fully solve) in the integration of mixoplanktonic activity in a dilution experiment. Moreover, cell counts can expose prey selectivity patterns and intraguild interactions among grazers. Our results also demonstrated that whole community approaches mimic reality better than single-species laboratory experiments. We also confirmed that light is required for protozoo- and mixoplankton to correctly express their feeding activity, and that overall diurnal grazing is higher than nocturnal. Thus, we recommend that a detailed examination of initial and final plankton communities should become routine in dilution experiments, and that incubations should preferably be started at the beginning of both day and night periods. Finally, we hypothesize that in silico approaches may help disentangle the contribution of mixoplankton to the community grazing of a given system.

2010 ◽  
Vol 134 (6) ◽  
pp. 964-969 ◽  
Author(s):  
Joseph D. Khoury ◽  
Dorothy M. Adcock ◽  
Fanny Chan ◽  
James T. Symanowski ◽  
Stefan Tiefenbacher ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhichao Wu ◽  
Felipe A. Medeiros

AbstractGlaucomatous damage results in characteristics structural and functional changes on optical coherence tomography (OCT) imaging and standard automated perimetry (SAP) testing. The clinical utility of these measures differs based on disease severity, as they are evaluated along different measurement scales. This study therefore sought to examine if a simplified combined structure–function index (sCSFI) could improve the detection and staging of glaucomatous damage, compared to the use of average retinal nerve fiber layer thickness (RNFL) measurements from OCT and mean deviation (MD) values from SAP alone, and also an estimated retinal ganglion cell counts (eRGC) measure derived using empirical formulas described previously. Examining 577 eyes from 354 participants with perimetric glaucoma and 241 normal eyes from 138 healthy participants, we found that the sCSFI performed significantly better than average RNFL, MD and eRGC count for discriminating between glaucoma and healthy eyes (P ≤ 0.008 for all). The sCSFI also performed significantly better than RNFL and eRGC count at discriminating between different levels of visual field damage in glaucoma eyes (P < 0.001 for both). These findings highlight the clinical utility of combining structural and functional information for detecting and staging glaucomatous damage using the simplified index developed in this study.


2005 ◽  
Vol 68 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
PAVEL KRCMAR ◽  
EVA RENCOVA

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species–derived material in concentrate feed mixtures and fish meals.


mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Marta Turon ◽  
Maria J. Uriz ◽  
Daniel Martin

ABSTRACTSponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllisspp.) and their host sponges (Clathria reinwardti,Amphimedon paraviridis,Neofibularia hartmani, andAaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of sixHaplosyllisspecies (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabitedA. paraviridisand was different from the single species that inhabitedA. suberitoides. Conversely, two different polychaete species were found inC. reinwardtiandN. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCEThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.


AoB Plants ◽  
2019 ◽  
Vol 11 (2) ◽  
Author(s):  
Clare Aslan ◽  
Noelle G Beckman ◽  
Haldre S Rogers ◽  
Judie Bronstein ◽  
Damaris Zurell ◽  
...  

Abstract Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.


2004 ◽  
Vol 70 (1) ◽  
pp. 167-173 ◽  
Author(s):  
Takahiro Matsuki ◽  
Koichi Watanabe ◽  
Junji Fujimoto ◽  
Yukiko Kado ◽  
Toshihiko Takada ◽  
...  

ABSTRACT A highly sensitive quantitative PCR detection method has been developed and applied to the distribution analysis of human intestinal bifidobacteria by combining real-time PCR with Bifidobacterium genus- and species-specific primers. Real-time PCR detection of serially diluted DNA extracted from cultured bifidobacteria was linear for cell counts ranging from 106 to 10 cells per PCR assay. It was also found that the method was applicable to the detection of Bifidobacterium in feces when it was present at concentrations of >106 cells per g of feces. Concerning the distribution of Bifidobacterium species in intestinal flora, the Bifidobacterium adolescentis group, the Bifidobacterium catenulatum group, and Bifidobacterium longum were found to be the three predominant species by examination of DNA extracted from the feces of 46 healthy adults. We also examined changes in the population and composition of Bifidobacterium species in human intestinal flora of six healthy adults over an 8-month period. The results showed that the composition of bifidobacterial flora was basically stable throughout the test period.


2020 ◽  
Author(s):  
Patricia Kaye Tahura Dumandan

Understanding the mechanisms driving biodiversity patterns amidst an era of global environmental change is the core of modern ecological research. The magnitude of biodiversity losses associated with anthropogenic activities has prompted resource managers and ecologists alike to identify strategies to address conservation issues. Broadly, two types of approaches are employed to answer ecological research questions: 1) single-species and 2) ecosystem-based approach. Single-species approaches are often useful to elucidate mechanisms driving population trajectories of individual species. On the other hand, ecosystem-based approaches can help in identifying general patterns that may be useful for multi-species management. Here, I used both approaches in assessing broad-scale patterns and mechanisms driving count trends of migrating raptors recorded at Hawk Mountain Sanctuary (HMS), Pennsylvania. In the first chapter, I used a hierarchical breakpoint model to identify the assemblage-wide and species-specific timing of the shifts in count trends. Then I evaluated if changes in trend directionality of counts were linked to species’ traits (body size, population size, migratory behavior, tolerance to human presence, DDT (dichlorodiphenyltrichlorethane) susceptibility, habitat or dietary specialization). I found that an assemblage-wide shift in counts occurred around 1974, and this timing was common among 14 of the 16 species in the assemblage. Moreover, I found that habitat specialization appeared to explain the synchronous positive and negative count trends of multiple species. Other traits that I evaluated were not consistently associated with either types of trends. The temporal shift in trends in 1974 emphasized the relative importance of DDT, an organochlorine known to have adversely influenced several wildlife species and was banned in the US around the 1970s, in driving population dynamics of raptor species. However, because the counts of species susceptible to DDT were highly variable after 1974, this may suggest that a suite of additional factors, acting together, affected the recovery of species from DDT-associated declines. Additionally, the potential role of habitat specialization in count trends may suggest important linkages between habitat use and demography. In the second chapter, I used a generalized linear mixed-effects model to assess the relationships between changes in the count totals and total proportional cover of major land-use types in nine states located in the northeastern US (Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, Vermont). The hierarchical modelling approach that I used allowed me to identify average and species-specific responses to the proportional cover of forested and urban area. These land-use variables were not associated with overall raptor counts. However, species-specific responses were variable and significant. I found that counts of Northern Goshawk, American Kestrel, Rough-legged Hawk, Sharp-shinned Hawk, and Red-tailed Hawk were positively associated with forest cover. On the other hand, Turkey and Black Vultures, Bald Eagle, and Peregrine Falcon were positively associated with urban cover. Moreover, Red-shouldered Hawk, Broad-winged Hawk, and Northern Harrier were not significantly associated with forest cover but were negatively associated with urban cover. Merlin and Cooper’s Hawk exhibited similar non-significant associations to forest but positive associations with urban cover. Finally, Golden Eagle and Osprey were not significantly associated with either land-use variables. These results provided insights on the potential influence of land-use changes on the demography of migrating raptors. Thus, these findings may be useful in improving our predictions of the population trajectories of these species in future landscape scenarios. These results illustrate the utility of evaluating species-level and assemblage-wide patterns in long-term count data. In this case, it allowed me to identify general patterns in counts of migrating raptors and gain detailed insights on the responses of individual species to land-use changes. In doing so, I was able to better understand the potential drivers of their ecological dynamics. By integrating information from these two approaches, we can expect to obtain a better understanding of natural systems and consequently, increase the probability of successful conservation outcomes.


2010 ◽  
Vol 61 (12) ◽  
pp. 1399 ◽  
Author(s):  
Marina Dolbeth ◽  
Filipe Martinho ◽  
Vânia Freitas ◽  
Sérgia Costa-Dias ◽  
Joana Campos ◽  
...  

Climate extremes, such as drought and floods, are increasing and should be considered in ecosystem management plans. The effects of an extreme drought were studied in two estuaries of the Iberian coast, Minho and Mondego, by exploring fish recruitment, growth and production over four years. The two estuaries are located within an area with transitional climate, and differ considerably in size, availability of freshwater wetlands and freshwater inflow. Fishes from the Minho estuary, at higher latitude, generally had lower growth rates and later timing of recruitment. During the drought, freshwater inflow was severely reduced in both estuaries. The overall fish assemblage production in the Minho estuary decreased considerably, whereas in the Mondego estuary it showed an increase. However, the drought effects seemed highly species‐specific and dependent on local geomorphology; the increase in the Mondego estuary was a result of an increase in a single species, whereas other species decreased or maintained similar production levels. Decreases in production in both estuaries were attributed to direct and indirect effects of changes in the freshwater inflow during the study period. This parameter should therefore be considered when undertaking management plans for transitional waters.


2009 ◽  
Vol 191 (22) ◽  
pp. 6804-6811 ◽  
Author(s):  
Saravanan Periasamy ◽  
Paul E. Kolenbrander

ABSTRACT Porphyromonas gingivalis is present in dental plaque as early as 4 h after tooth cleaning, but it is also associated with periodontal disease, a late-developing event in the microbial successions that characterize daily plaque development. We report here that P. gingivalis ATCC 33277 is remarkable in its ability to interact with a variety of initial, early, middle, and late colonizers growing solely on saliva. Integration of P. gingivalis into multispecies communities was investigated by using two in vitro biofilm models. In flow cells, bacterial growth was quantified using fluorescently conjugated antibodies against each species, and static biofilm growth on saliva-submerged polystyrene pegs was analyzed by quantitative real-time PCR using species-specific primers. P. gingivalis could not grow as a single species or together with initial colonizer Streptococcus oralis but showed mutualistic growth when paired with two other initial colonizers, Streptococcus gordonii and Actinomyces oris, as well as with Veillonella sp. (early colonizer), Fusobacterium nucleatum (middle colonizer), and Aggregatibacter actinomycetemcomitans (late colonizer). In three-species flow cells, P. gingivalis grew with Veillonella sp. and A. actinomycetemcomitans but not with S. oralis and A. actinomycetemcomitans. Also, it grew with Veillonella sp. and F. nucleatum but not with S. oralis and F. nucleatum, indicating that P. gingivalis and S. oralis are not compatible. However, P. gingivalis grew in combination with S. gordonii and S. oralis, demonstrating its ability to overcome the incompatibility when cultured with a second initially colonizing species. Collectively, these data help explain the observed presence of P. gingivalis at all stages of dental plaque development.


Cell nuclei have been isolated from various types of tissues. Evidence is presented which indicates that no appreciable loss of their major components occurs during isolation. Nuclei from normal cells of a particular type possess a constant composition characteristic of that type. The basic proteins extracted from such nuclei are not homogeneous. When they are of the histone type they can be separated into two parts conveniently described as a main histone and a subsidiary histone fraction respectively. A subsidiary product has also been obtained from protamins. A study of the chemical composition of the main histones and the protamins has shown that some of these are unquestionably species-specific. The phenomenon of cell specificity of these basic proteins has also been established in a number of instances. One case of cell specificity has also been found among the subsidiary histones. The difficulty of purification has prevented the detailed examination of others. The possible physiological significance of cell specificity of the basic proteins of cell nuclei is discussed.


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