Biology subjects

Porter, T. M.

Publications and source records attributed to Porter, T. M..

15 recordsLinked to original sources

bioRxiv2024

Soil communities following clearcut and salvage harvest have different early successional dynamics compared with post-wildfire patterns

Understanding the impacts of harvest and subsequent silviculture practices at stand scales on the below-ground biota, and their associated nutrient cycling processes, is needed to more fully evaluate the sustainable management of boreal forest systems. While stand replacing wildfire is the primary natural disturbance mechanism in jack pine-dominated boreal forest systems; clearcut harvest also results in stand renewal so is sometimes used in silvicultural systems to emulate natural disturbance and renewal processes. In this study, we simultaneously assessed the successional trajectories of three major taxa of the below ground soil community, bacteria, fungi, and arthropods using DNA metabarcoding. The objectives of this study were to use a chronosequence framework to: 1) assess whether the soil communities following clearcut harvest and wildfire converge along a successional gradient, 2) assess when the soil community recovers following clearcut harvest to the pre-disturbance, mature, wildfire reference condition, and 3) assess the effects of cumulative disturbance on soil community succession (i.e., wildfire followed by salvage harvesting of fire-killed trees). We found that richness (alpha diversity) did not illustrate any clear patterns of convergence and could, therefore, underestimate recovery times, especially for soil arthropods. Comparisons of the underlying community composition (beta diversity) proved to be more informative. In this case, we found that different soil taxa following clearcut harvest recovered on different timelines compared with succession following stand-replacing wildfire. In general, bacteria appear to be the first to converge to post-wildfire conditions followed by arthropods, however, fungi did not converge within the time frame of the chronosequence. This suggests that more extended periods are required to achieve complete recovery of the soil fungal community to the pre-disturbance condition. The cumulative disturbance associated with salvage harvest appeared to have a greater (compounded) effect on soil communities when compared with wildfire or clearcut harvest. This work showcases the performance of a scalable method for monitoring a diverse arrange of soil biota using DNA metabarcoding. In future work, tracking fungal and arthropod soil communities may provide more insights into the longer-term effects of current forest management practices and provide guidance when comparing alternative approaches. Open Research StatementSequences have been deposited to the NCBI SRA under the GRDI-Ecobiomics project accession PRJNA565010 for the BioSample accessions SAMN26926703 - SAMN26926795 used in this study. The MetaWorks v1.9.3 multi-marker metabarcode bioinformatic pipeline is available from https://github.com/terrimporter/MetaWorks. The ITS classifier based on the ITS UNITE+INSD full dataset v8.2 and trained to work with the RDP Classifier (https://github.com/terrimporter/UNITE_ITSClassifier). The COI classifier v4 is available from https://github.com/terrimporter/CO1Classifier. The code used to produce figures, including infile and metadata files, will be available on https://github.com/terrimporter/Chronosequence_HarvestType.

ecology↗

bioRxiv2022

All boreal forest successional stages needed to maintain the full suite of soil biodiversity following natural wildfire in jack pine-dominated forest ecosites

Wildfire is a natural disturbance in boreal forest systems that has been predicted to increase in frequency, intensity, and extent due to climate change. Most studies tend to assess the recovery of one component of the community at a time but here we use DNA metabarcoding to simultaneously monitor soil bacteria, fungi, and arthropods along an 85-year chronosequence following wildfire in jack pine-dominated ecosites. We describe soil successional and community assembly processes to better inform sustainable forest management practices. Soil taxa showed different recovery trajectories following wildfire. Bacteria shared a large core community across stand development stages (~ 95-97% of their unique sequences) and appeared to recover relatively quickly by crown closure. By comparison fungi and arthropods shared smaller core communities (64-77% and 68-69%, respectively) and each stage appeared to support unique biodiversity. We show the importance of maintaining a mosaic ecosystem that represents each stand development stage to maintain the full suite of biodiversity in soils following wildfire, especially for fungi and arthropods. These results will provide a useful baseline for comparison when assessing the effects of human disturbance such as harvest or for assessing the effects of more frequent wildfire events due to climate change.

ecology↗

bioRxiv2022

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxonomic and functional diversity of macroinvertebrates and their responses to environmental gradients. At the species rank, sites assessed using COI metabarcoding showed more variation than sites assessed using morphological methods. Depending on the assessment method, we detected gradients in magnesium (morphological taxa), ammonia (morphological taxa, COI sequence variants), pH (18S sequence variants) as well as gradients in contaminants such as metals (COI & 18S sequence variants) and organochlorines (COI sequence variants). Observed responses to contaminants such as aromatic hydrocarbons and metals align with known patchy distributions in harbour sediments. We determined that the morphological approach may limit the detection of macroinvertebrate responses to lake environmental conditions due to the effort needed to obtain fine level taxonomic assignments necessary to investigate responses. DNA metabarcoding, however, need not be limited to macroinvertebrates, can be automated, and taxonomic assignments are associated with a certain level of accuracy from sequence variants to named taxonomic groups. The capacity to detect change using a scalable approach such as metabarcoding is critical for addressing challenges associated with biodiversity monitoring and ecological investigations.

genomics↗

bioRxiv2022

Fungal community dynamics and carbon mineralization in coarse woody debris across decay stage, tree species, and stand development stage in northern boreal forests

Fungi are primary agents of coarse woody debris (CWD) decay in forests, playing an essential role in nutrient cycling and carbon storage. Characterizing fungal communities within CWD will promote further understanding of the fungal controls on CWD decomposition. We compared fungal community assemblages using alpha and beta diversity metrics, carbon mineralization, and physical and chemical properties of CWD across 3 tree species (trembling aspen [Populus tremuloides], black spruce [Picea mariana], and jack pine [Pinus banksiana]), 5 decay classes, and 2 stand development stages, differing in time-since-stand replacing disturbance (i.e., young/self-thinning and mature/steady-state) in Ontarios boreal forest region. In total, we sampled 180 individual CWD logs from 6 independent stands, with 3 replicates per each species x decay class combination at each site. We found that fungal community structure significantly differed across tree species, decay stage, and stand age. Higher proportions of white rot fungi were found in trembling aspen CWD, whereas higher proportions of brown rot fungi were found in black spruce and jack pine CWD. Proportions of specialized wood decay fungi increased with decay stage and were higher in CWD located in mature forest stands. Fungal diversity was highest in decay class 4 CWD. We found that Mn and K concentrations, total carbon, C/N ratio, carbon mineralization (mg CO2 g dry CWD-1 d-1), and moisture content were important predictors of fungal composition across CWD species and/or decay stage, though how CWD chemistry influences fungal species composition (and vice versa) is unknown. Carbon mineralization was highest in trembling aspen CWD and increased with decay stage, perhaps facilitated by increased N concentrations. This study suggests that forest management guidelines that consider both deadwood quantity and quality will support a broader range of fungal species and communities through post-disturbance stand development, thereby conserving biodiversity over the longer-term in our managed forest systems.

ecology↗

bioRxiv2021

Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions

Freshwater systems are experiencing rapid biodiversity losses resulting from high rates of habitat degradation. Ecological condition is typically determined through identifying either macroinvertebrate or diatom bioindicator assemblages and comparing them to their known tolerance to stressors. These comparisons are typically conducted at family or genus levels depending on the availability of taxonomic keys and expertise for focal groups. The objective of this study was to test whether a more taxonomically comprehensive assessment of communities in benthic samples can provide a different perspective of ecological conditions. DNA metabarcoding was used to identify macroinvertebrates and diatoms from kick-net samples collected from sites with different habitat status. Sites with good condition were associated with higher beta diversity as well as slightly higher directed connectance and modularity indicating higher resilience compared with fair condition sites. Indicator value and correlation analyses used DNA metabarcoding data to detect 29 site condition indicator species consistent with known bioindicators and expected relative tolerances. DNA metabarcoding and trophic network analysis also recovered 11 keystone taxa. This study demonstrates the importance of taxonomic breadth across trophic levels for generating biotic data to study ecosystem status, with the potential to scale-up ecological assessments of freshwater condition, trophic stability, and resilience.

ecology↗

bioRxiv2021

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

BackgroundPseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for obvious pseudogenes in large COI metabarcode datasets. We do this by: 1) describing gene and pseudogene characteristics from a simulated DNA barcode dataset, 2) show the impact of two different pseudogene removal methods on mock metabarcode datasets with simulated pseudogenes, and 3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile were used to detect pseudogenes. ResultsOur simulations showed that it was more difficult to identify pseudogenes from shorter amplicon sequences such as those typically used in metabarcoding ([~]300 bp) compared with full length DNA barcodes that are used in construction of barcode libraries ([~] 650 bp). It was also more difficult to identify pseudogenes in datasets where there is a high percentage of pseudogene sequences. We show that existing bioinformatic pipelines used to process metabarcode sequences already remove some apparent pseudogenes, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove more. ConclusionsThe combination of open reading frame length and hidden Markov model profile analysis can be used to effectively screen out obvious pseudogenes from large datasets. There is more to learn from COI pseudogenes such as their frequency in DNA barcode and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI pseudogenes to public databases to facilitate future studies.

bioinformatics↗

bioRxiv2020

METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments

Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (animals), rbcL (eukaryotes, land plants, diatoms), 12S (fish), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks is available at https://github.com/terrimporter/MetaWorks along with quick-start instructions using test data, detailed workflow descriptions, and a tutorial for new users.

bioinformatics↗

bioRxiv2020

Deconstructing biodiversity-ecosystem function relationships: Filtering of macroinvertebrate traits in a large river floodplain

The Biodiversity-Ecosystem Function hypothesis postulates that higher biodiversity is correlated with ecosystem function by providing a high number of filled niches through species response types and resource use patterns. Through their high spatio-temporal habitat diversity, floodplains are highly productive ecosystems, supporting communities that are naturally resilient and highly diverse. We examined linkages among floodplain wetland habitats, invertebrate communities and their associated traits, and ecosystem function across 60 sites within the floodplain wetlands of the lower Wolastoq | Saint John River, New Brunswick, using structural equation modelling and Threshold Indicator Taxa ANalysis (TITAN2). We identified key environmental filters of invertebrate communities, namely linking increased niche differentiation through historical change, flood pulse dynamics, and macrophyte bed complexity with increased taxa and functional diversity. Examination of traits linked to ecosystem functions revealed that healthy wetlands with higher primary productivity were associated with greater functional evenness and richness, while habitat patches with increased decomposition rates had low functional richness, reflecting highly disturbed habitat. Our results highlight key differences between wetland and riverine ecosystems, relating to how critical functions support healthy wetland habitats by providing increased resilience to disturbance, here associated with differing levels of conservation protection.

ecology↗

bioRxiv2020

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, periphyton scraping, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional microhabitat periphyton scraping and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton scraping and kick-net methodologies, but there was significant difference between diatom communities depending on site quality (P = 0.029). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms and macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes.

genomics↗

bioRxiv2020

Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

Maintaining the integrity of DNA in bulk environmental samples from source to laboratory is crucial for capturing the true range of taxa present within an ecosystem. Preservation consideration of DNA is particularly important if samples are being collected in remote areas and by non-specialist citizen scientists in nationwide programs. Traditionally, absolute ethanol is used as the preferred preservative for environmental samples collected for downstream DNA metabarcoding analyses. However, transport, shipping and DNA extraction of samples preserved in ethanol is a lengthy procedure due to safety restrictions and the requirement of full ethanol evaporation prior to extraction. We examined the efficacy of an easily accessible, non-toxic propylene glycol-based antifreeze as an alternative to absolute ethanol for preserving macroinvertebrate DNA from bulk-benthos DNA samples. We tested the differences in both cytochrome oxidase I (COI) exact sequence variants (ESVs) and COI taxonomic orders detected in both ethanol and antifreeze samples using two processing methods (no evaporation of preservative versus full evaporation). In addition, we assessed the detection of families and genera within the Arthropoda phylum for preservative type, site and processing method. Our results suggest that antifreeze is a suitable alternative to ethanol, a greater global ESV richness reported for antifreeze samples. Additionally, a higher proportion of arthropod reads in ESVs were detected in antifreeze (average 69%) compared with ethanol (average 53%). Finally, antifreeze samples produced similar results for the different processing methods, whereas ethanol samples failed to produce similar results without prior evaporation. Although ethanol is currently widely used for DNA preservation, our results demonstrate that by using antifreeze, it is possible to achieve similar taxonomic coverage and community assemblages of bulk-benthos DNA samples for macroinvertebrates, with the added simplicity and shorter laboratory processing time achieved using an easily available, unregulated preservative.

genomics↗

bioRxiv2019

Metabarcoding a Metacommunity: detecting change in a wetland wilderness

The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large-scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed, and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification, and DNA metabarcoding. Using multi-species occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification, and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera, and for the first time, quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were near random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales, but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.

ecology↗

bioRxiv2019

Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators based on exact sequence variants

Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for soil arthropod biodiversity assessments. Processing individually collected field samples recovered significantly higher richness (539-596 ESVs) than pooling the same number of field samples (126-154 ESVs), and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Variations in the number of individual or composite samples or DNA extractions resulted in similar sample clustering based on community dissimilarities. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding of local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

ecology↗

bioRxiv2019

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

DNA-based biodiversity analysis has gained major attention due to the use of high throughput sequencing technology in approaches such as mixed community or environmental DNA metabarcoding. Many cytochrome c oxidase subunit I (COI) primer sets are now available for such work. The purpose of this study is to look at how COI primer choice affects the recovery of arthropod richness, beta diversity, and recovery of site indicator taxa in benthos kick-net samples typically used in freshwater biomonitoring. We examine 6 commonly used COI primer sets, on samples collected from 6 freshwater sites. Richness is sensitive to primer choice and the combined use of additional multiple COI amplicons recovers higher richness. Thus, to recover maximum richness, multiple primer sets should be used with COI metabarcoding. Samples consistently cluster by site regardless of amplicon choice or PCR replicate. Thus, for broadscale community analyses, overall beta diversity patterns are robust to COI marker choice. Additionally, the recovery of traditional freshwater bioindicator assemblages such as Ephemeroptera, Trichoptera, Plectoptera, and Diptera may not fully capture the diversity of broadscale arthropod site indicators that can be recovered from COI metabarcoding. Based on these results, studies that use different COI amplicons may not be directly comparable. This work will help future biodiversity and biomonitoring studies develop not just standardized, but optimized workflows that maximize taxon-detection or order taxa along gradients.

genomics↗

bioRxiv2018

Over 2.5 million COI sequences in GenBank and growing

The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. Over 2.5 million COI sequences were found in GenBank, half of which were fully identified to the species rank. From 2003 to 2017, the number of COI Eukaryote records deposited has grown by two orders of magnitude representing a nearly 42-fold increase in unique species. For fully identified records, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing sequences. COI metabarcoders are normally considered consumers of taxonomic data. Here we discuss the potential for taxonomists to reverse this pattern and instead mine metabarcode data to guide species discovery. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.

ecology↗

bioRxiv2017

Automated high throughput animal DNA metabarcode classification

Until now, there has been difficulty assigning names to animal barcode sequences isolated directly from eDNA in a rapid, high-throughput manner, providing a measure of confidence for each assignment. To address this gap, we have compiled nearly 1 million marker gene DNA barcode sequences appropriate for classifying chordates, arthropods, and flag members of other major eukaryote groups. We show that the RDP naive Bayesian classifier can assign the same number of queries 19 times faster than the popular BLAST top hit method and reduce the false positive rate by two-thirds. As reference databases become more representative of current species diversity, confidence in taxonomic assignments should continue to improve. We recommend that investigators can improve the performance of species-level assignments immediately by supplementing existing reference databases with full-length DNA barcode sequences from representatives of local fauna.

bioinformatics↗