Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to
CHARACTERIZING NEMATODE BIODIVERSITY AND ABUNDANCE THROUGH NEXT-GENERATION SEQUENCING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
1008067
Grant No.
(N/A)
Project No.
CA-D-ENM-6851-H
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 29, 2015
Project End Date
Sep 30, 2020
Grant Year
(N/A)
Project Director
Nadler, S.
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Entomology and Nematology
Non Technical Summary
Increasing the efficiency and effectiveness of identifying nematodes in soil samples through development of new methods and applications is essential to solving basic and applied problems in agriculture. This research will use a model system and next-generation genetic methods to characterize the nematode species present in soil samples and estimate their abundance. These new methods have important applications in basic and applied research in soil ecology and agricultural systems.
Animal Health Component
0%
Research Effort Categories
Basic
35%
Applied
25%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
10131301120100%
Knowledge Area
101 - Appraisal of Soil Resources;

Subject Of Investigation
3130 - Nematodes;

Field Of Science
1120 - Nematology;
Goals / Objectives
1. Improve protocols for routine methods to photo-document nematodes by through-focus digital image capture and amplification and sequencing DNA from the same individual specimens. Imaged and sequenced nematodes must have microscopic resolution equal to that obtainable from standard (fixed) permanent slide specimens and be suitable for morphological description. The purpose of this objective is to produce digital morphological vouchers of the entire specimen that link together diagnostic sequence data with morphology.2. Move from traditional molecular systematic approaches for DNA extraction, PCR and sequencing to higher throughput 96-well methods. Characterize nematode biodiversity and abundance in soil samples based on random sampling of individual nematodes. Refine these methods for rapid-throughput determination and verification of sequences representing hundreds of individuals per sample. Use this methodology to estimate nematode species diversity and abundance in nine samples from the model desert system (three replicates of three different plant rhizospheres: Larrea tridentata, Parkinsonia florida, and Justicia californica).3. Use bulk-extracted nematodes from the same nine soil samples (see objective 2) and bulk DNA extractions to conduct metagenetic PCR amplifications and 454 sequencing. Use 454 sequences to assess nematode species diversity, and read frequencies to estimate the abundance of different species. Screen for chimeric sequences. Compare species diversity and abundance results to findings from objective 2.
Project Methods
Collection Sites. The collection site is Deep Canyon Reserve (DCR), part of the UC Reserve system located in Palm Desert California. Species-level inventory of nematodes at DCR will include replicate sampling of the rhizospheres of 3 perennial plant species that are co-located but discretely spaced at DCR. We target these "nematode high abundance" soils, rhizospheres of L. tridentata or creosote bush, P. florida or Blue Palo Verde, and J. californica or hummingbird bush. These soils are suitable for the comparison using standard approaches and metagenetics and will yield data on spatial/habitat variation in species richness and abundance.Development of Living Cultures. We will attempt to establish in vitro cultures of species for which we have some likelihood of success. Traditionally this has been done using Petri plate cultures with NGM agar (supplemented with bacteria). These cultures are grown at 15-25 C, depending on requirements of the species. Cultures will also be cryopreserved by standard techniques (Sulston and Hodgkin, 1988, Demeure and Freckman, 1981), although some species have very poor re-establishment success from cryopreservation. These cultures represent a value added component that can be used in related research.LM and digital imaging for linking gene sequence identifiers with morphology. Technical advances have facilitated linkages between morphology and nematode sequences. The relatively high-throughput Reverse Taxonomy (RT) approach combines high-resolution images of features and an overall through-focus image to link information from individuals (that are destructively sampled) with sequences and other individuals. Following acquisition of sequence data for individuals, standard measurement data can be acquired from specimen images as needed. The strategy of combining digital images of specimens sequenced in large numbers preserves maximal information, while permitting the throughput required for species-level systematics and providing the baseline data for assessment of metagenetics.Standard molecular methods (for RT and species delimitation). Following digital imaging, individual nematodes are cut with a micro-scalpel (Bioquip) and DNA made available using PrepGem. Samples are processed in 96-well plates for DNA extraction, PCR and sequencing. This facilitates tracking samples, and reduces labeling and handling errors. PrepGem extractions yield DNA for 10 PCRs/nematode. In preliminary work, individual nematode extractions had high PCR and sequence success (~90%) using the proofreading DNA polymerase KOD XL. PCR will be performed using custom primers designed from previous research. A 450-bp sequence of the D2-D3 LSU rDNA domain works well for molecular prospecting and diagnosis and this length is also compatible with Titanium 454. Despite known caveats of rDNA for phylogenetics (Smythe et al., 2006), these genes provide a readily obtainable source of sequence data from individual soil nematodes that currently has no substitute for prospecting and identification. Metagenetics. The choice of 454 Titanium (GS Jr) is based on the length of our cephalob-prospecting LSU region (~450 bp), the utility of which was verified in previous research. 454 NGS permits comparing the near full-length diagnostic sequence we obtain by RT (standard 3730 sequencing) in many 454 sequences; however, the primary diagnostic sites are within the first 300 bp of this fragment, such that even less than full length 454 reads will be useful. Stringent quality control measures can mitigate 454 sequence errors (454 is prone to misreading homopolymers), and our study has the advantage of independent characterization of the same samples by standard sequencing. Four independent PCRs (22-24 cycles) using 500 ng DNA template/PCR will be performed (then pooled) on each sample extract to reduce amplification artifacts and bias. For tracking, each sample will be tagged using MID linkers (differing by >2 bases) that reside between the PCR primers and Roche fusion adapters (Binladen et al., 2007). PCR products will be cleaned using AMPure (or gel isolated if required), quantified and standardized, and pooled for emPCR and pyrosequencing (Titanium kits). The Mothur package will be used for management and analysis of metagenetics data.Data analysis of species richness. Rarefaction analysis will be used to compare observed richness among samples, and with bootstrap resampling, estimates of confidence surrounding observed richness comparisons can be evaluated. Rarefaction does not provide estimates of total richness from the sample; this requires richness estimators that extrapolate from data. For nematodes, non-parametric richness estimators will likely violate fewer assumptions than parametric or accumulation-curve type methods (Hughes et al., 2001). The nonparametric Chao1 richness estimator will be compared across samples, and 95% C.I.s will be calculated so that differences between samples can be evaluated. Both rarefaction and the Chao1 estimator will be used (EstimateS software package, R. Colwell) to: 1) monitor progress in discovery of diversity by molecular prospecting, and 2) to compare species richness estimates between samples. Comparisons of nematode species show that most have >1% rDNA sequence divergence between variable domains of rDNA (Blaxter et al., 2005). Other investigations based on rDNA have found that grouping all individuals with ≥95% sequence similarity as species failed to discriminate among all species in the sample. These results suggest that a cutoff of <99% and >95% is necessary, but within this range any threshold can only be regarded as a heuristic estimator, and defining nematode species by molecular similarity alone is inadvisable (Adams, 1998; Nadler et. al., 2000; Nadler, 2002). For monitoring progress of species discovery based on molecular prospecting, a range of similarity cutoff values (96-99%) can be used. This approach estimates how the number of putative species compares by rarefaction or richness estimate to evaluate sampling progress, and to develop hypotheses of lineages to be tested with additional loci. In contrast, for final calculation of Chao1 richness (e.g., comparisons of samples), species will derive from formal delimitation based on phylogenetic analysis of multiple loci and evaluation of morphology.

Progress 10/29/15 to 09/30/20

Outputs
Target Audience:This project target audience includes a wide range of scientists including ecologists, nematologists, parasitologists, soil scientists, and plant pathologists. What is of interest is in the form of refined methods and protocols for biodiversity assessments and DNA sequences for nematode identification. DNA sequences of nematodes can be used for nematode identification by experts and non-experts, phylogenetic analysis, and estimating nematode relative abundance of taxa in samples. Sequences determined in this project have been published in open public databases (GenBank) where they form one basis for identification and also references for species diagnostics and ecological studies. In addition, sequence databases can be used to increase understanding of the phylogenetic (evolutionary) relationships of nematodes, including pathogens of plants and animals. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One Ph.D. student completed his training (worked on nematode associates of walnut twig beetle) and degree in 2020. Another Ph.D. student is continuing research on nematode metagenetics with anticipated graduation in 2022. Several undergraduates participated in nematode biodiversity research during this period. Two former undergraduates (K. Davies, C. Carlson) are first authors on journal publications. Even during the pandemic, one undergraduate student has continued some research. How have the results been disseminated to communities of interest?During the project period, results were reported at the annual meeting of the Society of Nematologists. This past year scientific societies cancelled their meetings due to the pandemic. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The main objectives of the project were to: 1) discover and describe new nematode biodiversity, and 2) use soil samples to characterize nematode biodiversity through use of metagenetic tools developed and refined in the laboratory. The lab used molecular tools to compare diversity and relative abundance of nematode species from the rhizosphere soil of three different desert plant species. First, Sanger sequencing of individual nematodes was used to characterize these samples. Next, the lab developed metagenetic methods for use with these same samples. Metagenetics using Illumina sequencing revealed a greater diversity of nematode species in these samples than Sanger sequencing, which is predicted based on the larger sample size (~ 10x greater nematodes) used for each metagenetic sample. Comparing the Sanger and metagenetic results, there was no correlation between the relative abundance of individuals of each nematode species as estimated by direct Sanger sequencing versus the relative abundance of sequence reads for corresponding taxa as assessed by Illumina metagenetics for the same samples. The best explanation for this result involves differences that would effect read number in metagenetics but not assessments based on sequencing individual nematodes. These include nematode size differences (both species differences and differences between different life stages within a species) and differences in rDNA repeat copy number characteristic of different species. Although the individual (Sanger) approach can provide estimates of relative abundance of individual nematode species, it is not efficient, whereas metagenetics is much more efficient for estimating nematode biodiversity of samples. Unfortunately, information on abundance of particular species is important for estimating agriculturally important parameters such as economic thresholds for plant parasites. During the project period, a new study of soil nematode biodiversity was initiated but not yet completed. It involves a metagenetics sampling protocol designed to evaluate within and between plant rhizosphere variation in diversity, with two samples taken per rhizosphere, and six samples taken per sampling site (three plants per site). Approximately 75 samples were collected across California deserts; desert soils are particularly useful for this exploratory research because the nematodes are anhydrobiotic, permitting collection of samples without the need for immediate processing without degradation. These samples will be used to test for correlations between particular species and soil characteristics (e.g., organic matter, salinity, pH), and also species diversity and soil characteristics. The sampling protocol also permits investigation of species patchiness. Metagenetics with these samples is being performed using long-read technology rather Illumina. This permits use of a longer nuclear ribosomal DNA barcode identifier. One unexpected finding to date is high variation in the abundance of nematodes between samples from individual rhizospheres, which has important implications for nematode sampling generally. Other accomplishments during the reporting period include discovery of a new nematode species (Bursaphelenchus juglandis n. sp.) that is associated with Walnut Twig beetle (Pityophthorus juglandis), a species that is part of the disease complex (along with a fungal pathogen) that is known as Thousand Cankers Disease of walnut. This species description has now been published. It is unknown if the nematode plays a role in disseminating the fungal pathogen.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Davies, K., C. Pagan, and S. A. Nadler. Host population expansion and the genetic architecture of the pinniped hookworm Uncinaria lucasi. Journal of Parasitology, 106: 383-391.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Ryss, A. Y., C. Parker, S. Alvarez-Ortega, S. A. Nadler, and S. A. Subbotin. 2020. Bursaphelenchus juglandis n. sp. (Nematoda: Aphelenchoididae), an associate of walnut twig beetle, Pityophthorus juglandis, the vector of thousand cankers disease. Nematology, 0:1-30.
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Carlson, C., C. Schutz, C. Pagan, L. E. Camp, and S. A. Nadler. Phylogeography of Baylisascaris procyonis (raccoon roundworm) in North America.


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:DNA sequences of nematodes can be used for nematode identification, phylogenetic analysis, and estimating their relative abundance in samples. Therefore, the project is of value to a wide range of scientists (ecologists, nematologists, parasitologists, soil scientists, plant pathologists) in the form of refined methods and protocols and through yielding DNA sequences for nematode identification. These sequences are published in open public databases (GenBank) where they form one basis (along with type specimens) for species diagnostics and comparisons of species. In addition, this activity increases understanding of the phylogenetic (evolutionary) relationships of nematodes, including pathogens of plants and animals. The field research provides a systematic foundation for more detailed studies of trophic relationships between nematodes and other soil organisms that inhabit the rhizospheres of plants. These findings will be of interest to a broad range of ecologists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?During the reporting period, training has been provided for two graduate students and six undergraduates. Most of the undergraduates were completing research required for their degree programs. One undergraduate research project has been submitted for publication (accepted, pending revision). How have the results been disseminated to communities of interest?New publications are forthcoming in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?Prepare publications from completed research comparing metagenetics with Sanger-based sequencing of individual nematodes. Collect metagenetic data on broad-based sampling of desert soil. Complete species description of a new Bursaphelenchus species and other ongoing nematode biodiversity studies.

Impacts
What was accomplished under these goals? A main objective of these studies is to: 1) discover and describe new nematode biodiversity, and 2) use soil samples to characterize nematode biodiversity through use of metagenetic tools that are being developed and refined. Previously the lab used metagenetics to compare diversity and relative abundance of taxa from the rhizospheres of three different desert plant species. Sanger sequencing of individual nematodes was also used to characterize these samples. Metagenetics revealed a greater diversity of nematodes in these samples than Sanger sequencing, which is predicted based on the larger sample size (~ 10x greater) of nematodes used for each metagenetic sample. Comparing the Sanger versus metagenetic results, there was no correlation between the relative abundance of the taxa in the Sanger results and the relative abundance of sequence reads for corresponding taxa as assessed by metagenetics for the same samples. The best explanation for this result involves differences that would effect read number in metagenetics but not assessments based on sequencing individual nematodes. These include nematode size differences and differences in rDNA repeat copy number per genome between taxa. Although the individual (Sanger) approach can provide estimates of relative abundance of species, metagenetics is much more efficient for estimating nematode biodiversity of samples. During the reporting period, a new study of soil nematode biodiversity was initiated. This research involves a new sampling protocol designed to evaluate within and between plant rhizosphere variation in diversity, with two samples taken per rhizosphere and six samples taken per sampling site (three plants per site, creosote bush). Approximately 75 samples were collected across California deserts, from far Southern CA near the border, to as far North as Death Valley. These samples will permit tests of correlation between particular species and soil characteristics (e.g., organic matter, salinity, pH), and also species diversity and soil characteristics. The sampling protocol also permits investigation of species patchiness. These samples have been extracted and are being prepared for metagenetics using long-read technology rather than more typical short read (300 base) methods. This will permit use of a longer barcode identifier. One unexpected finding to date is high variation in the abundance of nematodes between soil samples from individual creosote bushes. Other accomplishments during the reporting period include discovery of a new nematode species (Bursaphelenchus) that is associated with Walnut Twig beetle, a species that is part of the disease complex that is known as Thousand Cankers Disease of walnut. Description of this new species is in progress.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Feiner, N., S. de Souza-Lima, F. Jorge, S. Naem, F. Aubret, T. Uller, and S. A. Nadler. Vertical transmission of a nematode from female lizards to the brains of their offspring. American Naturalist.
  • Type: Journal Articles Status: Under Review Year Published: 2020 Citation: Davies, K., C. Pagan, and S. A. Nadler. Host population expansion and the genetic architecture of the pinniped hookworm Uncinaria lucasi.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:DNA sequences of nematodes can be used for both nematode identification and estimating their relative abundance in samples. Therefore, the project is of value to a wide group of scientists (ecologists, nematologists, parasitologists, soil scientists) in the form of refined methods and protocols and resulting DNA sequences for nematode identification. These sequences will be published in open public databases (GenBank) where they form the basis (references, along with type specimens) for species diagnostics and comparisons of species, and increased phylogenetic understanding of nematodes, including pathogens of plants and animals. In addition, the field research done at desert fields sites provides a systematic foundation for more detailed studies of trophic relationships between nematodes and other soil organisms that inhabit the rhizospheres of plants. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?During the reporting period, training has been provided for two graduate students, five undergraduates, and one visiting scientist from Iran. All of the undergraduates were completing research required for their degree programs. One visiting scientist (sabbatical visitor) participated in these research projects, including both morphological and genetic methods. How have the results been disseminated to communities of interest?During the reporting period, through publication of two scientific papers (as listed) and a presentation on nematode metagenetics at a scientific meeting by one of the graduate students. What do you plan to do during the next reporting period to accomplish the goals?Complete additional bioinformatic analyses in preparation for publication of one manuscript. We will conduct a broader biodiversity assessment based on replicate soil samples from a single host plant species collected throughout a broad sampling of California deserts. This sampling will permit distinguishing between within-sample versus among sample variation in species diversity.

Impacts
What was accomplished under these goals? A main objective of these studies is to compare results from Sanger sequencing of individual nematodes from soil samples (estimates of biodiversity and community composition based on individuals) with results obtained by metagenetic characterization of pooled nematodes from the same soil samples (extracted pools of 3-12,000 nematodes per sample). These methods were used to characterize nematode biodiversity, and to compare diversity and relative abundance of taxa from the rhizospheres of three different plant species sampled from the same collecting site -- versus samples from the same plant species collected from three different sites along a 600 meter transect (total of nine samples: three sites times three plant species). Sanger sequencing of hundreds of randomly selected individual nematodes per soil sample revealed that the predominant nematode taxa in this desert ecosystem are species of Cephalobidae and Panagrolaimidae. These microbivores were expected to be abundant in desert soil based on previous investigations. Other trophic groups detected included plant parasites and fungal feeders (Tylenchida) and omnivores (Dorylaimida). Metagenetics revealed a greater diversity of nematodes in these nine samples (approximately 27% more on average) than Sanger sequencing, which is predicted based on the larger sample size (~ 10x greater) of nematodes used for each metagenetic sample. The metagenetics approach also yielded non-nematode sequences, although nematodes represented 73% of the sequence reads. As expected there were few non-nematode sequences in the Sanger-based dataset because these sequences were based on DNA extractions of individual nematodes. In one metagenetic experiment, ten replicates of the same field-sampled DNA preparation were used for ten separate PCRs prior to library construction (each replicate uniquely indexed). There was no variation in taxa detected across the ten replicates, and very little variation in relative abundance of sequence reads representing distinct taxa across replicates. This uniformity in results indicates that stochastic elements of PCR are not likely to be contributors to variation in the metagenetic results. In comparing the Sanger versus metagenetic results, there was no correlation between the relative abundance of the taxa in the Sanger results and the relative abundance of sequence reads for corresponding taxa as assessed by metagenetics for the same samples. Given the control PCR experiment reported previously, the most likely explanations involve differences that would effect read number in metagenetics but not assessments based on sequencing individual nematodes (Sanger). The most obvious of these include nematode size differences (leading to variation in DNA/nematode) and differences in rDNA repeat copy number per genome between taxa. It would be difficult to devise a correction factor for the former because pools of nematodes used for metagenetics include unknown mixtures of larval stages and adults, which vary substantially in size within species. We regard the Sanger individual-based dataset as our best estimate of the relative abundance of taxa. All samples were dominated by microbivores, with minor component taxa including plant parasites and omnivores. Predominant nematode species recorded from samples by the Sanger method include Cephalobidae (Acrobeles, Acrobeloides, Chiloplacus, Zeldia) and Panagrolaimidae (e.g., Panagrolaimus). Considering these predominant taxa, there was no apparent correlation with host plant species (rhizosphere) or locality. That is, the relative abundance of nematode taxa from replicates of the same plant species (rhizosphere) showed substantial variation. Likewise, soil samples from the same locality (but different species of plants) also showed substantial variation in relative abundance of taxa. These results suggest that these nematode communities are non-equilibrium, perhaps dominated by disturbance and patchiness. However, we have not sampled appropriately to investigate this pattern in detail.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Hoberg, E. P., K. Burek-Huntington, K. Beckmen , L. Camp, and S. A. Nadler. 2018. Transuterine infection by Baylisascaris transfuga: Neurological migration and fatal debilitation in sibling moose calves (Alces alces gigas) from Alaska. International Journal for Parasitology: Parasites and Wildlife, 7: 280-288.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Camp, L. E., M. R. Radke, D. M. Shihabi, C. Pagan, G. Yang, and S. A. Nadler. 2018. Molecular phylogenetics and species-level systematics of Baylisascaris. International Journal for Parasitology: Parasites and Wildlife, 7: 450-462.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Pagan, C., S. A. Nadler, and J. G. Baldwin, 2018. Characterization of soil nematode communities in a Sonoran Desert study system. Society of Nematologists Annual Meeting, Albuquerque, New Mexico, July 2018.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:This research is designed to be of value to a large community of scientists (ecologists, nematologists, parasitologists, soil scientists) in the form of DNA sequences useful for nematode identification. These sequences are published in open public databases (GenBank) where they form the reference basis (along with type specimens) for species diagnostics and comparisons of species, providing evolutionary context for understanding nematodes, including pathogens of plants and animals. In addition, the field research done at Deep Canyon Reserve provides a systematic foundation for more detailed studies of trophic and other ecological relationships between nematodes and other soil organisms that inhabit the rhizosphere of plants. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?During the reporting period, training has been provided for two graduate students, five undergraduates, and one visiting scientist. Three of the undergraduates are undertaking research required for their degree programs in Animal Biology or Global Disease Biology. One visiting scientist (sabbatical visitor) participated in these research projects, including both morphology and genetic methods. How have the results been disseminated to communities of interest?During the reporting period, through publication of scientific papers (as listed) and a presentation at a scientific meeting. What do you plan to do during the next reporting period to accomplish the goals?We have completed the metagenetic data collection. The main emphasis during the next reporting period is to complete the bioinformatic analyses and submit the findings for publication. Other, separate projects will also be pursued. One involves a broader-scale geographic sampling of soil nematodes to These involve diagnostics for certain animal parasites that have been submitted to the lab for morphological and genetic analysis.

Impacts
What was accomplished under these goals? Identifying new species of nematodes, understanding how many species are found in particular hosts or soil environments, and characterizing the evolutionary relationships among known species are important activities for advancing research in agricultural and environmental nematology. Accomplishments included growth in systematic and taxonomic knowledge resulting from the generation and analysis of new sequence data. During the project period, this research has focused mainly on biodiversity, phylogenetics, and molecular diagnostic research for different groups of nematodes, including plant and animal parasites, soil microbe feeders, and species that prey on other organisms. Journal publications during the project reflect new detailed hypotheses for relationships of certain nematode groups. Hatch funds have been used to leverage federal funding in the form of a NSF grant that permits investigations of nematode biodiversity through support for equipment and supplies, and undergraduate and graduate student funding. Most recently the lab has focused its efforts on biodiversity research involving soil nematodes from a University of California reserve site, Boyd Deep Canyon Reserve. This desert soil environment was selected to serve as a model system for investigating new higher-throughput methodologies for understanding nematode diversity and diagnosing species. These soil nematodes are dominated by microbe-feeding nematodes, but also include plant parasites and predatory species that feed on other nematodes. The main research activities have involved documenting morphological diversity by through-focus microscopy and image capture, with correlated molecular sequence identifiers for these individual nematodes. Molecular investigations of these nematodes were conducted using large-scale sampling of individual nematodes (hundreds of individuals per sample) with sequencing of ribosomal RNA identifiers, and metagenetic tools. These approaches permit accurate identifications of species and more rapid diagnostics of the species present in samples. Metagenetic sequencing has been completed on nine soil samples that were also characterized using traditional sequencing methods (non high-throughput). Preliminary analysis reveals no correlation between the read abundance from metagenetic datasets and the abundance of individual species as determined by direct sequencing of individuals. However, the metagenetic analysis, which is based on bulk extraction of nematodes isolated from soil, shows a greater number of species, consistent with the greater number of nematodes characterized per sample. These results indicate that ecological analyses of soil nematodes that require estimates of the relative abundance of individual species are incompatible with current metagenetic methods. In contrast, given their relative ease of application compared to Sanger sequencing of individual nematodes, metagenetic approaches are preferred for ecological analyses that only require estimates of the number of different species present in a sample.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Osten-Sacken, N., M. Heddergott, A. Schleimer, H. E. Anheyer-Behmenburg, M. Runge, G. J. Horsburgh, L. Camp, S. A. Nadler, A. C. Frantz. 2017. Similar yet different: co-analysis of the genetic diversity and structure of an invasive nematode parasite and its invasive mammalian host. International Journal for Parasitology, in press.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Kim, T., E. Kern, H. Kwak, J. Kim, C. Park, S. A. Nadler, Y. J. Bae, and J. K. Park. The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha: Nematoda). Scientific Reports, submitted.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Liang, L., L. Lu?, S. A. Nadler, D. I. Gibson, L.-P. Zhang, H.-X. Chen, W-T Zhao, and Y-N. Guo. Molecular phylogeny and dating reveal a terrestrial origin for Ascaridoid nematodes in the early Carboniferous. Submitted, Systematic Biology.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Seguel, M., S. Nadler, C. Field, and P. Duignan. Vasculitis and thrombosis due to the sea lion lungworm, Parafilaroides decorus, in a Guadalupe fur seal (Arctocephalus philippii townsendi). Submitted, J. Wildlife Diseases.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Choudhury, A. and S. A. Nadler. Phylogenetic relationships of spiruromorph nematodes (Spirurina: Spiruromorpha) in North American freshwater fishes. Submitted, J. Parasitology.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Society of Nematologists 56th Annual Meeting, Williamsburg, VA (August 13-16, 2017), Symposium: Nematode Systematics  Challenges and Advances in Nematode Taxonomy, Systematics and Phylogeny, "Lessons Learned During Thirty Years Of Inferring Nematode Phylogenies"


Progress 10/29/15 to 09/30/16

Outputs
Target Audience:This research is designed to be of value to a large community of scientists (ecologists, nematologists, parasitologists, soil scientists) in the form of DNA sequences useful for nematode identification. These sequences are published in open public databases (GenBank) where they form the reference basis (along with type specimens) for species diagnostics and comparisons of species, providing evolutionary context for understanding nematodes, including pathogens of plants and animals. In addition, the field research done at Deep Canyon Reserve provides a systematic foundation for more detailed studies of trophic and other ecological relationships between nematodes and other soil organisms that inhabit the rhizosphere of plants. Changes/Problems:During this project period, methods for metagenetics changed substantially to overcome unanticipated problems in methods base solely on PCR. This was coupled with changes in next-generation sequencing technology. Therefore, during the course of the project we changed the way that we did metagenetics to reflect these improvements. These changes include dual-indexing of experimental amplicons, preparation of libraries, and use of Illumina sequencing. These methods were used in experiments on soil nematodes conducted at Deep Canyon Reserve. What opportunities for training and professional development has the project provided?During the project period, training has been provided for four graduate students, twenty undergraduates, and seven visiting scientists. Four of the undergraduates completed research training required for their undergraduate practicum project for the degree in Animal Biology (ABI). One visiting postdoctoral scholar (Dr. Limin Zhang) learned PCR based techniques, and applied these in a project to use metagenetics to characterize prey of predatory nematodes. How have the results been disseminated to communities of interest?Through publication of scientific papers in peer-reviewed journals (citations provided in this report), presentations at scientific meetings, invited seminars at universities, and through deposits of sequence data in the GenBank nucleotide database. What do you plan to do during the next reporting period to accomplish the goals?Our lab is focused on completing metagenetic work for comparison to the curated individual sequences. This requires completion of sequences and bioinformatics; this work will take much of the remainder of the project year.

Impacts
What was accomplished under these goals? During the project period, this research has focused mainly on biodiversity, phylogenetics, and molecular diagnostic research for a diverse group of nematodes, including plant and animal parasites, soil microbivores, and predators. Accomplishments included growth in systematic and taxonomic knowledge resulting from the generation and analysis of new sequence data. Journal publications during the project reflect new detailed hypotheses for relationships of these nematode groups. Hatch funds have been used to leverage federal funding in the form of a three-year NSF grant that permits investigations of nematode biodiversity through support for equipment and supplies, and undergraduate and graduate student funding. Identifying new species of nematodes, understanding how many species are found in particular hosts or soil environments, and characterizing the evolutionary relationships among known species are important activities for advancing research in agricultural and environmental nematology. Most recently the lab has focused considerable effort on biodiversity research involving soil nematodes from a University of California reserve site, Boyd Deep Canyon Reserve. This desert soil environment was selected to serve as a model system for investigating new higher-throughput methodologies. These soil nematodes are dominated by microbe-feeding nematodes, but also include plant parasites and predatory species that feed on other nematodes. The main research activities have involved documenting morphological diversity by through-focus microscopy and image capture, with correlated molecular sequence identifiers for these individual nematodes. Molecular investigations of these nematodes were conducted using large-scale sampling of individual nematodes with sequencing of 28S identifiers, and metagenetic tools. These approaches permit accurate identifications of species and more rapid diagnostics of the species present in samples. Moreover, the methods under development have the potential to be used for any environment within which nematodes are found. Research still in progress involves comparing assessments of nematode species abundance based on sequencing of individual nematodes versus estimates based on metagenetic next-generation sequencing. Molecular identification tools for these organisms and disease agents benefit efforts to minimize their impact and more generally, to understand their ecology.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu, G.-H, S. A. Nadler, S.-S. Liu, M. Podolska, S. DAmelio, R. Shao, R. B. Gasser, X.-Q. Zhu. 2016. Mitochondrial phylogenomics yields strongly supported hypotheses for ascaridomorph nematodes. Scientific Reports, 6:39248; doi: 10.1038/srep39248.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kim, J., E. Kern, T. Kim, M. Sim, J. Kim, Y. Kim, C. Park, S. A. Nadler, J.-K. Park. 2017. Phylogenetic analysis of two Plectus mitochondrial genomes (Nematoda: Plectida) supports a sister group relationship between Plectida and Rhabditida within Chromadorea. Molecular Phylogenetics and Evolution, 107:90-102.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Holovachov, O., L. Camp, and S. A. Nadler. 2015. Sensitivity of ribosomal RNA character sampling in the phylogeny of Rhabditida. Journal of Nematology, 47:337-355
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2016 Citation: Choudhury, A., and S. A. Nadler. 2016. Phylogenetic relationships of Cucullanidae (Nematoda), with observations on Seuratoidea, and the monophyly of Cucullanus, Dichelyne and Truttaedacnitis. Journal of Parasitology, 102:87-93.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cid del Prado Vera, I., H. Ferris, and S. A. Nadler. 2016. Five new species of the family Trischistomatidae (Nematoda: Enoplida) from North and Central America, with keys to the species of Trischistoma and Tripylina. Zootaxa, 4109:173-197.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cid del Prado Vera, I., H. Ferris, and S. A. Nadler. 2016. Five new species of the genus Tripylella (Nematoda: Enoplida: Tripylidae). Zootaxa, 4109:198-217.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Sol�rzano-Garc�a, B., S. A. Nadler, and G. P�rez Ponce de Le�n. 2016. Pinworm diversity in free-ranging howler monkeys (Alouatta spp.) in Mexico: Morphological and molecular evidence for two new Trypanoxyuris species (Nematoda: Oxyuridae). Parasitology International, 65:401-411.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: P�rez-Ponce de Le�n, G., and S. A. Nadler. 2016. The importance of recognising parasite cryptic diversity for research programmes on foodborne trematodiases. Transactions of The Royal Society of Tropical Medicine and Hygiene, 110:4-5.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kim, T., J. Kim, S. A. Nadler, and J. K. Park. 2015. The complete mitochondrial genome of Koerneria sudhausi (Diplogasteromorpha: Nematoda) supports monophyly of Diplogasteromorpha within Rhabditomorpha. Current Genetics, DOI 10.1007/s00294-015-0536-4.