Evaluation of Daphnid Grazing on Microscopic Zoosporic Fungi by Using Comparative Threshold Cycle Quantitative PCR

ABSTRACTLethal parasitism of large phytoplankton by chytrids (microscopic zoosporic fungi) may play an important role in organic matter and nutrient cycling in aquatic environments by shunting carbon away from hosts and into much smaller zoospores, which are more readily consumed by zooplankton. This pathway provides a mechanism to more efficiently retain carbon within food webs and reduce export losses. However, challenges in accurate identification and quantification of chytrids have prevented a robust assessment of the relative importance of parasitism for carbon and energy flows within aquatic systems. The use of molecular techniques has greatly advanced our ability to detect small, nondescript microorganisms in aquatic environments in recent years, including chytrids. We used quantitative PCR (qPCR) to quantify the consumption of zoospores byDaphniain laboratory experiments using a culture-based comparative threshold cycle (CT) method. We successfully quantified the reduction of zoospores in water samples duringDaphniagrazing and confirmed the presence of chytrid DNA inside the daphnid gut. We demonstrate that comparativeCTqPCR is a robust and effective method to quantify zoospores and evaluate zoospore grazing by zooplankton and will aid in better understanding how chytrids contribute to organic matter cycling and trophic energy transfer within food webs.IMPORTANCEThe study of aquatic fungi is often complicated by the fact that they possess complex life cycles that include a variety of morphological forms. Studies that rely on morphological characteristics to quantify the abundances of all stages of the fungal life cycle face the challenge of correctly identifying and enumerating the nondescript zoospores. These zoospores, however, provide an important trophic link between large colonial phytoplankton and zooplankton: that is, once the carbon is liberated from phytoplankton into the parasitic zoospores, the latter are consumed by zooplankton and carbon is retained in the aquatic food web rather than exported from the system. This study provides a tool to quantify zoospores and evaluate the consumption of zoospores by zooplankton in order to further our understanding of their role in food web dynamics.

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Flotsam and jetsam: a global review of the role of inputs of marine organic matter in sandy beach ecosystems

10.32942/osf.io/68as7 ◽

2021 ◽

Author(s):

Glenn A. Hyndes ◽

Emma Berdan ◽

Cristian Duarte ◽

Jenifer E. Dugan ◽

Kyle A. Emery ◽

...

Keyword(s):

Organic Matter ◽

Food Webs ◽

Food Source ◽

Sandy Beach ◽

Morphological Characteristics ◽

Sandy Beaches ◽

Marine Animals ◽

Marine Organic Matter ◽

Beach Cast

Sandy beaches are iconic interfaces that functionally link the ocean with the land by the flow of marine organic matter. These cross-ecosystem fluxes often comprise uprooted seagrass and dislodged macroalgae that can form substantial accumulations of detritus, termed ‘wrack’, on sandy beaches. In addition, the tissue of the carcasses of marine animals that regularly wash up on beaches form a rich food source (‘carrion’) for a diversity of scavenging animals. Here, we provide a global review of how wrack and carrion provide spatial subsidies that shape the structure and functioning of sandy beach ecosystems (sandy beaches and adjacent surf zones), which typically have little in situ primary production. We also examime the spatial scaling of the influence of these processes across the broader seascape and landscape, and identify key gaps in our knowledge to guide future research directions and priorities. Globally, large quantities of detrital kelp and seagrass can flow into sandy beach ecosystems, where microbial decomposers and animals remineralise and consume the imported organic matter. The supply and retention of wrack are influenced by the oceanographic processes that transport it, the geomorphology and landscape context of the recipient beaches, and the condition, life history and morphological characteristics of the taxa that are the ultimate source of wrack. When retained in beach ecosystems, wrack often creates hotspots of microbial metabolism, secondary productivity, biodiversity, and nutrient remineralization. Nutrients are produced during wrack break-down, and these can return to coastal waters in surface flows (swash) and the aquifier discharging into the subtidal surf. Beach-cast kelp often plays a key trophic role, being an abundant and preferred food source for mobile, semi-aquatic invertebrates that channel imported algal matter to predatory invertebrates, fish, and birds. The role of beach-cast marine carrion is likely to be underestimated, as it can be consumed rapidly by highly mobile scavengers (e.g. foxes, coyotes, raptors, vultures). These consumers become important vectors in transferring marine productivity inland, thereby linking marine and terrestrial ecosystems. Whilst deposits of organic matter on sandy beach ecosystems underpin a range of ecosystem functions and services, these can be at variance with aesthetic perceptions resulting in widespread activities, such ‘beach cleaning and grooming’. This practice diminishes the energetic base of food webs, intertidal fauna, and biodiversity. Global declines in seagrass beds and kelp forests (linked to global warming) are predicted to cause substantial reductions in the amounts of marine organic matter reaching many beach ecosystems, likely causing flow-on effects on food webs and biodiversity. Similarly, future sea-level rise and stormier seas are likely to profoundly alter the physical attributes of beaches, which in turn can change the rates at which beaches retain and process the influxes of wrack and animal carcasses. Conservation of the multi-faceted ecosystem services that sandy beaches provide will increasingly need to encompass a greater societal appreciation and the safeguarding of ecological functions reliant on beach-cast organic matter on innumerable ocean shores worldwide.

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Cryptic Cycling of Complexes Containing Fe(III) and Organic Matter by Phototrophic Fe(II)-Oxidizing Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02826-18 ◽

2019 ◽

Vol 85 (8) ◽

Cited By ~ 4

Author(s):

Chao Peng ◽

Casey Bryce ◽

Anneli Sundman ◽

Andreas Kappler

Keyword(s):

Organic Matter ◽

Anoxygenic Phototrophic Bacteria ◽

Aquatic Environments ◽

Photic Zone ◽

Iron Cycling ◽

Microbial Oxidation ◽

Photochemical Reduction ◽

Content Type ◽

Dissolved Iron ◽

New Type

ABSTRACTFe-organic matter (Fe-OM) complexes are abundant in the environment and, due to their mobility, reactivity, and bioavailability, play a significant role in the biogeochemical Fe cycle. In photic zones of aquatic environments, Fe-OM complexes can potentially be reduced and oxidized, and thus cycled, by light-dependent processes, including abiotic photoreduction of Fe(III)-OM complexes and microbial oxidation of Fe(II)-OM complexes, by anoxygenic phototrophic bacteria. This could lead to a cryptic iron cycle in which continuous oxidation and rereduction of Fe could result in a low and steady-state Fe(II) concentration despite rapid Fe turnover. However, the coupling of these processes has never been demonstrated experimentally. In this study, we grew a model anoxygenic phototrophic Fe(II) oxidizer,Rhodobacter ferrooxidansSW2, with either citrate, Fe(II)-citrate, or Fe(III)-citrate. We found that strain SW2 was capable of reoxidizing Fe(II)-citrate produced by photochemical reduction of Fe(III)-citrate, which kept the dissolved Fe(II)-citrate concentration at low (<10 μM) and stable concentrations, with a concomitant increase in cell numbers. Cell suspension incubations with strain SW2 showed that it can also oxidize Fe(II)-EDTA, Fe(II)-humic acid, and Fe(II)-fulvic acid complexes. This work demonstrates the potential for active cryptic Fe cycling in the photic zone of anoxic aquatic environments, despite low measurable Fe(II) concentrations which are controlled by the rate of microbial Fe(II) oxidation and the identity of the Fe-OM complexes.IMPORTANCEIron cycling, including reduction of Fe(III) and oxidation of Fe(II), involves the formation, transformation, and dissolution of minerals and dissolved iron-organic matter compounds. It has been shown previously that Fe can be cycled so rapidly that no measurable changes in Fe(II) and Fe(III) concentrations occur, leading to a so-called cryptic cycle. Cryptic Fe cycles have been shown to be driven either abiotically by a combination of photochemical reduction of Fe(III)-OM complexes and reoxidation of Fe(II) by O2, or microbially by a combination of Fe(III)-reducing and Fe(II)-oxidizing bacteria. Our study demonstrates a new type of light-driven cryptic Fe cycle that is relevant for the photic zone of aquatic habitats involving abiotic photochemical reduction of Fe(III)-OM complexes and microbial phototrophic Fe(II) oxidation. This new type of cryptic Fe cycle has important implications for biogeochemical cycling of iron, carbon, nutrients, and heavy metals and can also influence the composition and activity of microbial communities.

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Application of Isothermal Amplification Techniques for Identification of Madurella mycetomatis, the Prevalent Agent of Human Mycetoma

Journal of Clinical Microbiology ◽

10.1128/jcm.01544-15 ◽

2015 ◽

Vol 53 (10) ◽

pp. 3280-3285 ◽

Cited By ~ 23

Author(s):

Sarah A. Ahmed ◽

Wendy W. J. van de Sande ◽

Marie Desnos-Ollivier ◽

Ahmed H. Fahal ◽

Najwa A. Mhmoud ◽

...

Keyword(s):

Morphological Characteristics ◽

High Specificity ◽

Its Region ◽

Molecular Techniques ◽

Isothermal Amplification ◽

Content Type ◽

Fungal Dna ◽

Madurella Mycetomatis ◽

Phenotypic Methods ◽

Species Specific

Appropriate diagnosis and treatment of eumycetoma may vary significantly depending on the causative agent. To date, the most common fungus causing mycetoma worldwide isMadurella mycetomatis. This species fails to express any recognizable morphological characteristics, and reliable identification can therefore only be achieved with the application of molecular techniques. Recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) are proposed as alternatives to phenotypic methods. Species-specific primers were developed to target the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region ofM. mycetomatis. Both isothermal amplification techniques showed high specificity and sufficient sensitivity to amplify fungal DNA and proved to be appropriate for detection ofM. mycetomatis. Diagnostic performance of the techniques was assessed in comparison to conventional PCR using biopsy specimens from eumycetoma patients. RPA is reliable and easy to operate and has the potential to be implemented in areas where mycetoma is endemic. The techniques may be expanded to detect fungal DNA from environmental samples.

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Complete Genomic Sequence of Pseudoalteromonas sp. Strain SAO4-4, a Protease-Producing Bacterium Isolated from Seawater of the Atlantic Ocean

Genome Announcements ◽

10.1128/genomea.00284-18 ◽

2018 ◽

Vol 6 (22) ◽

Cited By ~ 1

Author(s):

Bai-Lu Tang ◽

Jin-Cheng Rong ◽

Yan-Ru Dang ◽

Bin-Bin Xie ◽

Xiu-Lan Chen ◽

...

Keyword(s):

Organic Matter ◽

Atlantic Ocean ◽

Genome Sequence ◽

Complete Genome ◽

Genomic Sequence ◽

Aquatic Environments ◽

Complete Genomic Sequence ◽

Content Type ◽

Circular Chromosomes ◽

Complete Genomic

ABSTRACT The complete genome of Pseudoalteromonas sp. strain SAO4-4, a protease-producing bacterium from seawater, is composed of two circular chromosomes and one plasmid. This genome sequence will provide a better understanding of the ecological roles of protease-producing bacteria in the degradation of organic matter in marine aquatic environments.

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Biometry of neotropical invertebrates inhabiting floodplain rivers: unraveling bionomy

Iheringia Série Zoologia ◽

10.1590/1678-4766e2017014 ◽

2017 ◽

Vol 107 (0) ◽

Cited By ~ 1

Author(s):

Florencia Zilli ◽

Julia del Barco ◽

Agustín Vanzetti

Keyword(s):

Organic Matter ◽

Life History ◽

Food Webs ◽

Management Strategies ◽

Future Research ◽

Aquatic Environments ◽

Floodplain Wetlands ◽

Feeding Types ◽

Linearized Model ◽

Floodplain Rivers

ABSTRACT Currently, it is widely recognized that invertebrates play key roles in neotropical floodplains and in many other environments worldwide. However, little information has been published concerning their biometry, in spite that it represents an essential tool for many different studies. Here, we provided length-mass and length-length relationships by fitting the linearized model (log10 Y = log10a + b log10 X) and several mean biomass ratios ± SE for bivalves, gastropods, quironomids, ephemeropterans, oligochaetes and hirudineans. We measured, weighed, oven dried and incinerated to ashes specimens collected from 2005 to 2014 in the Paraná River, Argentina. The lineal equations had fit levels higher than 75% in most of the significant regressions. Hence, when slopes were compared, differences raised from ontogeny and phylogeny of taxa. Additionally, slopes resulted different from constants of other regions, types of environments and climates. In addition, organic matter ratios resulted significantly different among invertebrates according to their feeding types. The equations and ratios that we provided will facilitate future research on life history, productivity and energy transference in the food webs of invertebrates inhabiting floodplain wetlands and can be used as tools for planning management strategies and in restoration projects of aquatic environments.

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Comparison of Quantitative PCR and Droplet Digital PCR Multiplex Assays for Two Genera of Bloom-Forming Cyanobacteria, Cylindrospermopsis and Microcystis

Applied and Environmental Microbiology ◽

10.1128/aem.00931-15 ◽

2015 ◽

Vol 81 (15) ◽

pp. 5203-5211 ◽

Cited By ~ 33

Author(s):

Shu Harn Te ◽

Enid Yingru Chen ◽

Karina Yew-Hoong Gin

Keyword(s):

Quantitative Pcr ◽

Dynamic Range ◽

Digital Pcr ◽

Droplet Digital Pcr ◽

Molecular Techniques ◽

Cyanobacterial Blooms ◽

Accurate Analysis ◽

Content Type ◽

Cyanobacterial Species ◽

Pcr Multiplex

ABSTRACTThe increasing occurrence of harmful cyanobacterial blooms, often linked to deteriorated water quality and adverse public health effects, has become a worldwide concern in recent decades. The use of molecular techniques such as real-time quantitative PCR (qPCR) has become increasingly popular in the detection and monitoring of harmful cyanobacterial species. Multiplex qPCR assays that quantify several toxigenic cyanobacterial species have been established previously; however, there is no molecular assay that detects several bloom-forming species simultaneously.MicrocystisandCylindrospermopsisare the two most commonly found genera and are known to be able to produce microcystin and cylindrospermopsin hepatotoxins. In this study, we designed primers and probes which enable quantification of these genera based on the RNA polymerase C1 gene forCylindrospermopsisspecies and the c-phycocyanin beta subunit-like gene forMicrocystisspecies. Duplex assays were developed for two molecular techniques—qPCR and droplet digital PCR (ddPCR). After optimization, both qPCR and ddPCR assays have high linearity and quantitative correlations for standards. Comparisons of the two techniques showed that qPCR has higher sensitivity, a wider linear dynamic range, and shorter analysis time and that it was more cost-effective, making it a suitable method for initial screening. However, the ddPCR approach has lower variability and was able to handle the PCR inhibition and competitive effects found in duplex assays, thus providing more precise and accurate analysis for bloom samples.

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Stream Macroinvertebrates and Carbon Cycling in Tangled Food Webs

Ecosystems ◽

10.1007/s10021-021-00626-8 ◽

2021 ◽

Author(s):

Benoît O. L. Demars ◽

Joanna L. Kemp ◽

Baptiste Marteau ◽

Nikolai Friberg ◽

Barry Thornton

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Food Web ◽

Food Webs ◽

Carbon Sources ◽

Terrestrial Ecosystems ◽

Terrestrial Organic Matter ◽

Before And After ◽

Reference Stream ◽

Induced Changes

AbstractThe annual global loss of organic carbon from terrestrial ecosystems into rivers is similar to the organic carbon stored in soils each year. Dissolved organic matter (DOM) flows through the food web to macroinvertebrates, but little is known about the effect of DOM increase on stream food webs and how much macroinvertebrates may contribute to the regulation of carbon fluxes in rivers. Using a before and after control impact (BACI) experimental design, we increased by 12% (+ 0.52 mg C L−1) the concentration of DOM in a stream for three weeks by adding sucrose, with a distinctive δ13C signature, to simulate a pulse of natural DOM supply from soils. We partitioned the diet of macroinvertebrates from carbon sources according to the green pathway (autotrophs) and detrital pathways (bacteria and terrestrial organic matter). Our flow food web approach based on C fluxes, with bacteria as a key node, showed the dominant contribution of the detrital pathways for macroinvertebrates in the reference stream. DOM addition induced changes in the diets of individual taxa, but did not have any strong effects on the relative overall contribution of the detrital pathways versus the green pathway. Autotrophic uptake of CO2 respired by bacteria was much larger than bacterial C flux to invertebrates (that is, the classic microbial loop) and allowed a significant fraction of natural allochthonous organic carbon to make its way to macroinvertebrates via autotrophs fixing CO2 respired by bacteria. Overall macroinvertebrates did not regulate directly to any great extent the flux of stream DOM towards downstream ecosystems.

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Multifunctionality of belowground food webs: resource, size and spatial energy channels

10.1101/2021.06.06.447267 ◽

2021 ◽

Author(s):

Anton M. Potapov

Keyword(s):

Organic Matter ◽

Food Web ◽

Food Webs ◽

Terrestrial Ecosystems ◽

Feeding Preference ◽

Size Spectrum ◽

Soil Food Web ◽

Energy Fluxes ◽

Biogeochemical Models ◽

Web Reconstruction

The belowground compartment of terrestrial ecosystems drives nutrient cycling, the decomposition and stabilisation of organic matter, and supports aboveground life. Belowground consumers create complex food webs that regulate functioning, ensure stability and support biodiversity both below and above ground. However, existing soil food-web reconstructions do not match recently accumulated empirical evidence and there is no comprehensive reproducible approach that accounts for the complex resource, size and spatial structure of food webs in soil. Here I build on generic food-web organization principles and use multifunctional classification of soil protists, invertebrates and vertebrates, to reconstruct "multichannel" food-web across size classes of soil-associated consumers. This reconstruction is based on overlying feeding preference, prey protection, size spectrum and spatial distribution matrices combined with biomasses of trophic guilds to infer weighted trophic interactions. I then use food-web reconstruction, together with assimilation efficiencies, to calculate energy fluxes assuming a steady-state energetic system. Based on energy fluxes, I describe a number of indicators, related to stability, biodiversity and multiple ecosystem-level functions such as herbivory, top-down control, translocation and transformation of organic matter. I illustrate the approach with an empirical example, comparing it with traditional resource-focused soil food-web reconstruction. The multichannel reconstruction can be used to assess trophic multifunctionality (analogous to ecosystem multifunctionality), i.e. simultaneous support of multiple trophic functions by the food-web, and compare it across communities and ecosystems spanning beyond the soil. With further validation and parametrization, my multichannel reconstruction approach provides an effective tool for understanding and analysing soil food webs. I believe that having this tool will inspire more people to comprehensively describe soil communities and belowground-aboveground interactions. Such studies will provide informative indicators for including consumers as active agents in biogeochemical models, not only locally but also on regional and global scales.

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Food webs and the transmission of parasites to marine fish

Parasitology ◽

10.1017/s003118200200149x ◽

2002 ◽

Vol 124 (7) ◽

pp. 83-99 ◽

Cited By ~ 190

Author(s):

D. J. MARCOGLIESE

Keyword(s):

Food Web ◽

Food Webs ◽

Spatial Scales ◽

Sediment Quality ◽

Life Cycles ◽

Helminth Parasites ◽

Food Web Structure ◽

Marine Systems ◽

Parasite Communities ◽

Web Structure

Helminth parasites of fish in marine systems are often considered to be generalists, lacking host specificity for both intermediate and definitive hosts. In addition, many parasites in marine waters possess life cycles consisting of long-lived larval stages residing in intermediate and paratenic hosts. These properties are believed to be adaptations to the long food chains and the low densities of organisms distributed over broad spatial scales that are characteristic of open marine systems. Moreover, such properties are predicted to lead to the homogenization of parasite communities among fish species. Yet, these communities can be relatively distinct among marine fishes. For benthos, the heterogeneous horizontal distribution of invertebrates and fish with respect to sediment quality and water depth contributes to the formation of distinct parasite communities. Similarly, for the pelagic realm, vertical partitioning of animals with depth will lead to the segregation of parasites among fish hosts. Within each habitat, resource partitioning in terms of dietary preferences of fish further contributes to the establishment of distinct parasite assemblages. Parasite distributions are predicted to be superimposed on distributional patterns of free-living animals that participate as hosts in parasite life cycles. The purpose of this review is first, to summarize distribution patterns of invertebrates and fish in the marine environment and relate these patterns to helminth transmission. Second, patterns of transmission in marine systems are interpreted in the context of food web structure. Consideration of the structure and dynamics of food webs permits predictions about the distribution and abundance of parasites. Lastly, parasites that influence food web structure by regulating the abundance of dominant host species are briefly considered in addition to the effects of pollution and exploitation on food webs and parasite transmission.

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A Novel Triplex Quantitative PCR Strategy for Quantification of Toxigenic and Nontoxigenic Vibrio cholerae in Aquatic Environments

Applied and Environmental Microbiology ◽

10.1128/aem.03516-14 ◽

2015 ◽

Vol 81 (9) ◽

pp. 3077-3085 ◽

Cited By ~ 11

Author(s):

Rupert Bliem ◽

Sonja Schauer ◽

Helga Plicka ◽

Adelheid Obwaller ◽

Regina Sommer ◽

...

Keyword(s):

Risk Assessment ◽

Vibrio Cholerae ◽

Quantitative Pcr ◽

Water Samples ◽

Dynamic Range ◽

Environmental Water ◽

Environmental Water Samples ◽

Aquatic Environments ◽

Ecological Studies ◽

Content Type

ABSTRACTVibrio choleraeis a severe human pathogen and a frequent member of aquatic ecosystems. Quantification ofV. choleraein environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenicV. choleraein environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-correctedV. choleraeabundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6 × 102to 2.3 × 104cell equivalents liter−1, whereas GR-corrected abundances ranged from 4.7 × 103to 1.6 × 106cell equivalents liter−1. GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenicV. choleraein various aquatic environments for ecological studies as well as for risk assessment programs.

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