Ecological Archives E093-153-D1

Daniel L. Preston, Sarah A. Orlofske, John P. McLaughlin, and Pieter T. J. Johnson. 2012. Food web including infectious agents for a California freshwater pond. Ecology 93:1760. http://dx.doi.org/10.1890/11-2194.1


METADATA CONTENTS

  1. Data Set Descriptors
    1. Data Set Title
    2. Data Set Identification Code
    3. Data Updates
    4. Authors
    5. Abstract
    6. Key Words
  2. Research Origin Descriptors
    1. Overall Project Description
    2. Research Motivation
    3. General Methodology
    4. Data Limitations and Potential Enhancements
  3. Data Set Status and Accessibility
    1. Latest Data Update
    2. Latest Metadata Update
    3. Copyright or Proprietary Restrictions
  4. Data Set Structural Descriptors
    1. Data Files
    2. Metadata Tables
  5. Acknowledgements
  6. References

I. Data Set Descriptors

 

    1. Data Set Title
    2. Data Set Identification Code
    3. Data Updates
    4. Authors
    5. Abstract
    6. Key Words

I.A. Data Set Title: Food web including infectious agents for a California freshwater pond

I.B. Data Set Identification Code: PresEtAl2011-qpweb.

I.C. Data Updates: The data set may be periodically updated. For a record of previous versions and identification codes see Table 1.

I.D. Authors

Individual: Daniel L. Preston
Role: Owner, Corresponding Author
Organization: University of Colorado at Boulder
Position: Graduate Student
Address: Department of Ecology and Evolutionary Biology
University of Colorado
Ramaley N122, CB334
Boulder, CO 80309 USA
Phone: (303) 492-5623
Fax: (303) 492-8699
Email: daniel.preston@colorado.edu
Url: http://www.colorado.edu/eeb/facultysites/pieter/

 

Individual: Sarah A. Orlofske
Role: Content Provider
Organization: University of Colorado at Boulder
Position: Graduate Student
Address: Department of Ecology and Evolutionary Biology
University of Colorado
Ramaley N122, CB334
Boulder, CO 80309 USA
Phone: (303) 492-5623
Fax: (303) 492-8699
Email: sarah.orlofske@colorado.edu
Url: http://www.colorado.edu/ebio/gradstudents/orlofske/Sarahs_Website/Home.html

 

Individual: John P. McLaughlin
Role: Content Provider
Organization: University of California, Santa Barbara
Position: Graduate Student
Address: Department of Ecology, Evolution and Marine Biology
University of California
Santa Barbara, CA 93106-9610
Phone: (805) 893-3998
Fax: (805) 893-4724
Email: mclaughlin@lifesci.ucsb.edu
Url: http://www.lifesci.ucsb.edu/eemb/labs/kuris/

 

Individual: Pieter T. J. Johnson
Role: Owner
Organization: University of Colorado at Boulder
Position: Assistant Professor
Address: Department of Ecology and Evolutionary Biology
University of Colorado
Ramaley N122, CB334
Boulder, CO 80309 USA
Phone: (303) 492-5623
Fax: (303) 492-8699
Email: pieter.johnson@colorado.edu
Url: http://www.colorado.edu/eeb/facultysites/pieter/

I.E. Abstract: This data set presents a comprehensive food web for Quick Pond, a northern California pond ecosystem. The web includes organisms from all regions of the pond (i.e., littoral, limnetic, profundal, and benthic zones) as well as terrestrial organisms that interact with the aquatic community or have aquatic life-stages. The food web has three attributes that are often omitted from freshwater food webs: inclusion of (1) parasites and other infectious agents, (2) ontogenetic stages of most animals with complex life cycles, and (3) biomass information for many animals. Data on species presence was obtained over three years using field sampling techniques (i.e., seine- and D-nets, stove-pipe samplers, and visual encounter surveys) and laboratory examinations of free-living organisms for infectious agents (primarily metazoan parasites, but also some microbes). We collected body size and biomass data for abundant aquatic animals >1 mm and for trematode parasites, which were the most abundant parasitic group. Information on trophic interactions was obtained from direct observations and published literature sources. Within the food-web data we include supporting information for each node on taxonomy, lifestyle, and residency; and for each link we include information on type of interaction and the source of evidence (e.g., direct observation, literature, or inferred). The food web contains 113 nodes, 1905 links, and 63 species. To facilitate comparisons between food webs from different ecosystems we present the data in a system-neutral format.

I.F. Key Words :biomass; complex life cycles; food webs, freshwater; infectious agents; parasites; pond; Quick Pond; trophic interactions; wetland.


II. Research Origin Descriptors

 

  1. Overall Project Description
  2. Research Motivation
  3. General Methodology
    1. System Definition
        1. Description
        2. Spatio-temporal Coverage
    2. Nodes
        1. Orientation
        1. Node Inclusion
        2. Node Resolution
        3. Additional Node Classifications
        4. Node Biomass Estimation
        5. Node Body Size Estimation
    1. Links
        1. Orientation
        2. Link Type
        3. Link Determination
  1. Data Limitations and Potential Enhancements
  2. General Note
  3. Nodes
  4. Links
  5. Body Size and Biomass
  6. Potential Enhancements

II.A. Overall Project Description: Not applicable, as this is a stand-alone project.

 

II.B. Research Motivation : The role of parasites in food webs has been investigated in a temperate lake Huxham et al. 1995), an artic lake (Amundsen et al. 2009), a temperate stream (Hernandez and Sukhdeo 2008) and intertidal estuaries or mudflats in Scotland (Huxham et al. 1995), New Zealand (Thompson et al. 2005) the western USA (Lafferty et al. 2006) and the eastern USA (Anderson and Sukhdeo 2011). The influence of parasites on network topology has varied across these ecosystems, although they tend to increase important metrics such as connectance, linkage density and food chain length. Parasites also contribute substantial biomass to some estuarine ecosystems, suggesting that they can play significant roles in energy flow (Kuris et al. 2008). Nonetheless, it's unclear whether the important ecological roles of parasites are ubiquitous across ecosystems, or whether they represent 'special cases' where parasites are particularly abundant. Furthermore, despite supporting a diversity of parasites and serving as model systems in food web ecology (e.g., Wilbur 1997), the ecosystem level roles of parasites in freshwater pond ecosystems remain largely unstudied. Our aim was to investigate how parasites influenced the network structure of a pond in northern California. A current project seeks to address how parasites contribute to the animal biomass and energy flow in the same pond ecosystem (Preston et al., in preparation). By constructing a food web for a novel system that is comparable to other published food web data sets (Hechinger et al. 2011, Mouritsen et al. 2011, Thieltges et al. 2011, Zander et al. 2011), we hope to facilitate analyses that will lead to a more general understanding of the role of parasites in ecosystems.

II.C. General Methodology

  1. System Definition
  2. Description
  3. Spatio-temporal Coverage
  4. Nodes
  5. Orientation
  6. Node Inclusion
  7. Node Resolution
  8. Additional Node Classifications
  9. Node Biomass Estimation
  10. Node Body Size Estimation
  11. Links
  12. Link Orientation
  13. Link Determination
  14. Link Type

 

II.C.1. System Definition

II.C.1.i. Description: We constructed a food web for Quick Pond, which is in Alameda County, east of the San Francisco Bay in California, USA (Fig. 1a). Quick Pond has a permanent hydroperiod, lies at an elevation of 435 m, has an early summer surface area of 2234 m² and has a maximum depth of approximately 2.5 m (Fig 1b). Nutrient concentrations in June of 2009 were 53 ug/L total dissolved phosphorus and 1779 ug/L total dissolved nitrogen. Quick Pond was heavily sampled in the summer of 2009, with additional sampling occurring in the summers of 2010 and 2011. We used a combination of visual encounter surveys, standardized net sweeps with D-nets (1.4 mm mesh, 2600 cm² opening), stove-pipe samplers (53 cm diameter × 74 cm height) and seine nets (4 mm mesh, 1 m tall by 2 m wide) to characterize the biotic community. We examined a subset of free-living hosts in the laboratory to detect infectious agents, and we amended our field survey efforts with additional information from the published literature. Additional research has occurred at Quick Pond involving macroinvertebrate communities and human impacts (Lunde and Resh, in Press) and consequences of trematode-induced amphibian malformations on host ecology (Goodman and Johnson 2011).

Fig1
 
   FIG. 1. The location of Quick Pond in Alameda County in northern California (A; map courtesy of K. Richgels) and Quick Pond in June of 2009 (B; photo by D. Preston).

 

II.C.1.ii. Spatio-temporal Coverage:

Geographic Description: Quick Pond

Coordinates: Latitude: 37.66

Longitude: -121.93

Temporal Coverage: Beginning Date: 2009

Ending Date: 2011

II.C.2. Nodes

  1. Orientation
  2. Node Inclusion
  3. Node Resolution
  4. Additional Node Classifications
  5. Node Biomass Estimation
  6. Node Body Size Estimation

 

II.C.2.i. Orientation: Nodes for the food web are listed in the Quick_Pond_Nodes data files. Two metadata tables describe the Nodes data files. Table 2A defines node data column headers. Table 2B defines node data column variables. Below, we provide additional background information on the nodes.

II.C.2.ii. Node Inclusion: The majority of the nodes were added based on data collected between 2009 and 2011. Some invertebrates were added based on data obtained by Lunde and Resh (in press). Most species with complex life cycles were disaggregated into a series of nodes, with each node representing a discrete life stage. We included nodes for some life stages that were not directly observed, but must be present for the organisms to complete their life cycle (e.g., adult acanthocephalan worms were added when only larval cystacanths were directly observed). For abundant organisms larger than 1 mm, we measured body size and determined biomass for all aquatic life stages (either with direct mass measurements or using length-to-mass regressions).

II.C.2.iii. Node Resolution: The “Node Resolution” column in the node data files indicates the degree of resolution for each node. Most of the nodes are species, or species-specific life stages. Study design constraints led us to classify some individuals to “morphospecies”. We often did this for rarer and small organisms. Thus, although such nodes are not identified below some higher taxonomic category, they generally do represent distinct species. Each node is unique, as indicated by its unique “NodeID”, “Species.StageID” and “WorkingName”.

In addition to providing a unique working name for each node, and indicating the general organismal “Group” to which each node belongs, the data sets also include a series of columns for the taxonomic hierarchy (i.e., Kingdom through Specific epithet). This is intended to aid users in understanding node identity and to facilitate taxonomic diversity analyses, not to promote the adoption of a particular taxonomic schema.

II.C.2.iv. Additional Node Classifications: To facilitate analyses and interpretation, we have additionally classified nodes by several different schemes. The node metadata tables list and define all such categories and variables (Tables 2A, 2B). For example, we indicate each node’s “Feeding type” (feeding, non-feeding, autotrophic), “Lifestyle” (e.g., free-living, infectious, commensal), “Consumer Strategy” (e.g., predator, macroparasite, pathogen, detritivore), and “Native” or non-native status. Additionally, the columns “Mobility” and “Residency” indicate for each node the general degree of vagility characterizing individuals on daily and seasonal time scales. Mobility and Residency also impact the expected proportion of a node’s links that the web captures. For example, a migrant has low linkage completeness because a substantial number of an individual’s interactions occur outside of the system.

II.C.2.v. Node Biomass Estimation: The biomass estimates encompass most abundant aquatic organisms larger than 1 mm and aquatic life stages of complex life cycle organisms. We also include biomass estimates for trematode parasites. Biomass estimates represent mid-summer 'snap-shots' and we recognize that the biomass of each taxon is likely to vary over the duration of the year. For most invertebrates, we utilized published length-to-mass regressions to convert length measurements into dry mass estimates (see the nodes data file for all sources of length-to-mass regressions). We developed our own length-to-mass regressions for some organisms that were abundant and for which there were no published regressions (e.g., amphibian larvae). Biomass of different trematode parasite life stages was estimated based on a combination of field data on infection prevalence, direct measurements of trematode mass and published estimates of trematode biomass per host individual (Bernot and Lamberti 2008, Hechinger et al. 2008). The Quick_Pond_Nodes data tables indicate the particular biomass estimation method used for each node, and metadata Table 2B lists and defines each method.

II.C.2.vi. Node Body Size Estimation: Most body sizes were directly measured during field sampling. Body size represents individual dry body mass characterizing a species or stage in the local population. As with biomass, we only provide estimates for aquatic life stages that were directly measured. The Quick_Pond_Nodes data tables indicate the particular body size estimation technique used for each node and metadata Table 2B lists and defines each method.

II.C.3. Links

  1. Link Orientation
  2. Link Determination
  3. Link Type

II.C.3.i. Link Orientation: Consumer-resource links are listed in the Quick_Pond_Links data files. Two metadata tables describe the links data files. Table 3A defines all column headers. Table 3B defines all column variables, except for the Link Types, which are indicated in Table 3C. Below, we provide additional background information.

II.C.3.ii. Link Determination: Consumer-resource links for the food web were obtained from direct observations, published literature and expert knowledge. Most parasitic consumer-resource links for aquatic life stages were based on direct observations. Exceptions occurred when we logically inferred the presence of undetected or unquantified stages of parasites that were quantified at other life stages (e.g., many adult helminths are designated as consumers of a bird species when the bird preys on an intermediate host containing detected parasite stages infectious to birds). The Quick_Pond_Links data set includes columns (“Evidence” and “EvidenceNotes”) that indicate the general evidence or rationale for each link. See metadata Table 3B for explicit definitions.

II.C.3.iii. Link Type: We provide information on the nature of the individual consumer-resource interactions based on the consumer-resource node classifications and other information. A total of 21 different link types are recognized. Given the importance of link types, we have pulled this information from the metadata link variable table and placed it in Table 3C, which provides definitions of all link types. Understanding link types is essential prior to conducting analyses of the network. For instance, links defined as Predation involve predators as consumers, whereas links defined as Parasitic Castration involve parasitic castrators as consumers. Also, several of the link types that are not typically included in food webs do not represent resource dependencies (i.e., Concurrent Predation on Symbionts, Trophic Transmission, Commensalism). For this reason, such links should be excluded from some analyses. However, Concurrent Predation on Symbionts represents mortality sources for symbionts, Trophic Transmission is important to understand parasite transmission and Commensalism indicates a dependency, but not a trophic interaction.

II.D. Data Limitations and Potential Enhancements

  1. General Note
  2. Nodes
  3. Links>
  4. Body Size and Biomass
  5. Potential Enhancements

II.D.1. General Note: Although the web is well resolved, there is uncertainty in link assignment and in the resolution of some nodes. We welcome any input from colleagues allowing improvement of the web, and will periodically update these data sets if we acquire substantial new data (please check for the latest update before using).

II.D.2. Nodes: The clearest limitation to the data set is the underrepresentation and absence of some groups. Table 4 lists missing, underrepresented groups and severely aggregated nodes. The most aggregated nodes are phytoplankton, benthic microalgae and periphyton, vascular plants and bacteria. These groups were aggregated because detecting individual species was either beyond the scope of the present work (i.e., bacteria) or they were likely to share consumer-resource links with the same set of species (i.e., benthic microalgae/periphyton and vascular plants). Many meiofauna and zooplankton species were given individual nodes, but these groups were likely under-sampled and were therefore also given an aggregated node to represent missing species. The parasites of these groups are also underrepresented. We also omitted nodes for many entirely terrestrial species that are likely to have short-term interactions with other species in the pond food web (e.g., some native birds and mammals that were not directly observed at the pond). Terrestrial species were only included when they were directly observed or when their presence was necessary to complete the life cycle of an observed parasite species.

II.D.3. Links: The assigned links came primarily from direct observations and literature sources, with some being inferred from expert opinion. As such, incorrect links may have been included, but we feel this approach is favorable to only including links that are directly observed (which will miss many links in a complex food web). The Quick_Pond_Links data file provides information on the evidence for each link.

II.D.4. Body size and Biomass : We only include estimates of body size and biomass for aquatic organisms larger than 1 mm and we omit certain rare groups. The biomass estimates were also taken during mid-summer, and the biomass of most groups is likely to vary seasonally.


III. Data Set Status and Accessibility

III.A. Latest Data Update: The data set may be periodically updated. For a record of previous versions and identification codes see Table 1.

III.B. Latest Metadata Update: There have been no alterations to the metadata subsequent to first publication.

III.C. Copyright or Proprietary Restrictions: These data sets are freely available for non-commercial scientific use, given the appropriate scholarly citation.


IV. Data Set Structural Descriptors

  1. Data Files
  2. Metadata Tables

IV.A. Data Files: Below are the files for the Quick Pond food web, consisting of a Quick_Pond_Nodes file that provides information on all of the species and/or life stages present in the web and a Quick_Pond_Links file that contains information on the trophic interactions. A third file contains all of the data in one single file. Detailed information on column headers and variables is presented in the Metadata Tables below.

Quick_Pond_Nodes.csv – The node information for the Quick Pond food web. File includes 113 rows (not including the header row) and 39 columns, formatted as comma separated values. No compression scheme was used. Blank cells indicate that information has not been collected or is not applicable.

Quick_Pond_Links.csv – The trophic link information for the compiled Metaweb. File includes 1905 rows (not including the header row) and 18 columns, formatted as comma separated values. No compression scheme was used. Blank cells indicate that information has not been collected or is not applicable.

All_Quick_Pond_Data_Files.zip - A zip file containing all the above data files.

IV.B. Metadata Tables

Below are the metadata tables, which describe the column header and variable information contained in the above data files. These are the same set of tables linked to in the methods section.

There are six metadata tables (click here to download all six tables) organized into two groups: Tables 2A-B refer to the Node data sheets, while Tables 3A-C refer to the Links data sheets. There are two types of tables: the A tables describe the information contained within each column; the B tables define the variables found in each column. Specific variable definitions can also be accessed by clicking on the header for any particular column in the A tables. Table 3C describes the various consumer strategies. Table 4 details the missing and underrepresented groups and severely aggregated nodes.

Table 2A: Column header descriptions for Nodes data file: Column headers are taken directly from the Quick_Pond_Nodes.csv data file and are followed directly by their descriptions. To obtain a list of the variables in a column, as well as their definition, click on the column header.

Table 2B: Column variable descriptions for Nodes data file: Definitions of variables are organized by column headers from Table 2A.

Table 3A: Column header descriptions for Links data files: Column headers are taken directly from the Quick_Pond_Links.csv data file and are followed directly by their descriptions. To obtain a list of the variables and their definitions present in any column click on the column header.

Table 3B: Column variable descriptions for Links data file: Definitions of variables are organized by column headers from Table 3A. Link-type variables are defined in Table 3C.

Table 3C: Link-type definitions for Links data file: Definitions of Link-type variables are organized for this column header from Table 3A.

Table 4: Missing, under-represented groups and severely aggregated nodes.

All_Quick_Pond_Metadata_Tables.zip – A zipped file containing Tables 2A, 2B, 3A, 3B, 3C, and 4.


V. Acknowledgments

We thank K. Richgels, M. Baragona, and B. Goodman for assistance in collecting field data. East Bay Regional Parks, D. Rocha, S. Bobzien and S. Quick facilitated access to the field site. We thank K. Lafferty and D. Thieltges for helpful discussion. Funding has come from an NSF grant (DEB-0841758), a David and Lucile Packard Foundation Fellowship to P. Johnson, NSF Fellowships to D. Preston and S. Orlofske, the Society of Wetland Scientists Student Grant and the University of Colorado.


VI. Literature cited

Amundsen, P. A., K. D. Lafferty, R. Knudsen, R. Primicerio, A. Klemetsen, and A. M. Kuris. 2009. Food web topology and parasites in the pelagic zone of a subarctic lake. Journal of Animal Ecology 78:563–572.

Anderson, T. K., and M. V. K. Sukhdeo. 2011. Host centrality in food web networks determines parasite diversity. PLoS ONE 6:e26798.

Bernot, R. J., and G. A. Lamberti. 2008. Indirect effects of a parasite on a benthic community: and experiment with trematodes, snails and periphyton. Freshwater Biology 53:322–329.

Goodman, B. A., and P. T. J. Johnson. 2011. Ecomorphology and disease: cryptic effects of parasitism on host habitat use, thermoregulation and predator avoidance. Ecology 92:542–548.

Hechinger, R. F., K. D. Lafferty, F. T. Mancini III, R. R. Warner, and A. M. Kuris. 2008. How large is the hand in the puppet? Ecological and evolutionary factors affecting body mass of 15 trematode parasitic castrators in their snail host. Evolutionary Ecology 23:651–667.

Hechinger, R. F., K. D. Lafferty, J. P. McLaughlin, B. L. Fredensborg, T. C. Huspeni, J. Lorda, P. K. Sandhu, J. C. Shaw, M. E. Torchin, K. L. Whitney, and A. M. Kuris. 2011. Food webs including parasites, biomass, body sizes, and life stages for three California/Baja California estuaries. Ecology 92:791.

Hernandez, A. D., and M. V. K. Sukhdeo. 2008. Parasites alter the topology of a stream food web across seasons. Oecologia 156:613–624.

Huxham, M., D. Raffaelli, and A. Pike. 1995. Parasites and food webs patterns. Journal of Animal Ecology 64:168–176.

Kuris, A. M., R. F. Hechinger, J. C. Shaw, K. L. Whitney, L. Aguirre-Macedo, C. A. Boch, A. P. Dobson, E. J. Dunham, B. L. Fredensborg, T. C. Huspeni, J. Lorda, L. Mababa, F. T. Mancini, A. B. Mora, M. Pickering, N. L. Talhouk, M. E. Torchin, and K. D. Lafferty. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454:515–518.

Lafferty, K. D., A. P. Dobson, and A. M. Kuris. 2006. Parasites dominate food web links. Proceedings of the National Academy of Sciences of the United States of America 103:11211–11216.

Lunde, K. B., and V. H. Resh. In Press. Development and validation of a macroinvertebrate index of biotic integrity (IBI) for assessing urban impacts to Northern California freshwater wetlands. Environmental Monitoring and Assessment.

Mouritsen, K. N., R. Poulin, J. P. McLaughlin, and D. W. Thieltges. 2011. Food web including metazoan parasites for an intertidal ecosystem in New Zealand. Ecology 92:2006.

Thieltges, D. W., K. Reise, K. N. Mouritsen, J. P. McLaughlin, and R. Poulin. 2011. Food web including metazoan parasites for a tidal basin in Germany and Denmark. Ecology 92:2005.

Thompson, R. M., K. N. Mouritsen, and R. Poulin. 2005. Importance of parasites and their life cycle characteristics in determining the structure of a large marine food web. Journal of Animal Ecology 74:77–75.

Wilbur, H. M. 1997. Experimental ecology of food webs: complex systems in temporary ponds. Ecology 78:2279–2302.

Zander, C. D., N. Josten, K. C. Detloff, R. Poulin, J. P. McLaughlin, and D. W. Thieltges. 2011. Food web including metazoan parasites for a brackish shallow water ecosystem in Germany and Denmark. Ecology 92:2007.


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