Biology subjects

Thompson, L. R.

Publications and source records attributed to Thompson, L. R..

8 recordsLinked to original sources

bioRxiv2026

Habitat restoration promotes recolonisation by extirpated species in model meta food webs

Successful ecosystem restoration is intimately linked to the persistence of species in local communities and across landscapes. As such quantitative approaches to ecological restoration require the integration of community and metapopulation ecology. Together these disciplines demonstrate that local colonisation, via habitat connectivity and size, and species interactions, both modulate the process of community assembly. However, thus far restoration ecology still remains disconnected from network ecology this preventing a holistic, community-wide perspective to restoration. We aim to inform ecological restoration using a multi-layer modelling framework integrating ecological interactions and species dispersal dynamics. We explore the drivers that modulate recolonisation dynamics of species across restored landscapes. We further investigate how restoration improves the structural properties of food webs, the number of successful recolonisations and the role of configuration of restored patches in restoration outcomes. We find that recolonisation is the result of a trade-off between dispersal ability and energy requirements. 97% of plant recolonisation and 88% of herbivore recolonisations happened within close proximity to the source patches. Better dispersers - intermediate and top species in the food webs - were able to recolonise habitat by benefitting from the increased biomass influx from restoration. When only a small proportion of the landscape could be restored, the location and connectivity of restored areas strongly influenced the outcome of restoration: more connected patches enabled on average the recolonisation of about 1 additional intermediate species compared to that of isolated patches. However, this difference faded as soon as more patches were restored, and improving larger portions of the landscape always resulted in better outcomes. Restoring 1/3 of the landscape enabled on average the recolonisation of ~4 additional species. Our findings suggest that quantitative models can inform restoration efforts necessary to bring native species back to restored areas. They also suggest that attention should be given to the requirements of the recolonisers, the distance of their introduction from restored areas and their trophic and ecological niche. These aspects are crucial to assess their energy and habitat requirements for successful establishment.

ecology↗

bioRxiv2024

Assessing the effects of warming and carbonate chemistry parameters on marine microbes in the Gulf of Mexico through basin-scale DNA metabarcoding

Ocean acidification and warming threaten marine life, yet the impact of these processes on microbes remains unclear. Here, we performed basin-scale DNA metabarcoding of prokaryotes (16S V4-V5) and protists (18S V9) in the Gulf of Mexico and applied generalized linear models to reveal group-specific environmental correlates of functionally diverse microbes. Models supported prior physiological trends for some groups, like positive temperature effects on SAR11 and SAR86, and a positive effect of pH on Prochlorococcus that implied a negative response to decreasing pH. New insights were revealed for protists, like Syndiniales and Sagenista (e.g., positive pH effects), which offset positive relationships with temperature and reinforced the importance of considering multiple stressors simultaneously. Indicator analysis revealed phytoplankton, like Ostreococcus sp. and Emiliania huxleyi, that were associated with more acidic waters and may reflect candidate indicators of ocean change. Our findings highlight the need for sustained microbial sampling in marine systems, with implications for carbon export, nutrient cycling, and ecosystem health.

microbiology↗

bioRxiv2023

Protected areas enhance avian food webs

Restoring and conserving habitat and the species they shelter has become a primary focus to mitigate the current extinction crisis. Setting aside land designated as protected areas (PAs) is an efficient way of achieving these aims. This strategy has been proven to enhance different aspects of species richness and abundance across ecosystems1-4. However, to truly understand the effects of global environmental change on biodiversity, and the efficiency of our mitigation measures, we must account for one of its fundamental dimensions: species interactions. Here we show that PAs enhance avian food webs across Europe by protecting key network and species traits. Using 376,556 observational records of 509 bird species from citizen science databases distributed across 45 networks of PAs, we found beneficial effects of protection on 10 out of 13 food web properties on an average of 25.9% of sites. PAs enhance food webs by harbouring large top predators, in turn increasing the length of biomass flow paths from basal to top species. Furthermore, we link these beneficial effects to environmental drivers and PA designations. PA benefits were augmented by specific protection goals such as European Directives for conservation. This study provides evidence for the effectiveness of PAs as a strategy to preserve fundamental aspects of biodiversity beyond species richness. We anticipate our study to be a starting point for the development of comprehensive frameworks to assess the critical role of PAs in safeguarding biodiversity worldwide. Improving the mapping of species occurrences and ecological interactions across the globe will is fundamental to develop optimal strategies for establishing networks of PAs aimed at protecting all aspects of ecosystem diversity.

ecology↗

bioRxiv2022

Message in a Bottle: Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages

Marine heatwaves can drive large-scale shifts in marine ecosystems but studying their impacts on whole species assemblages can be difficult. Here, we leverage the taxonomic breadth and resolution of DNA sequences derived from environmental DNA (eDNA) in the ethanol of a set of 23-year longitudinal ichthyoplankton samples, combining these with microscopy-derived ichthyoplankton identification to yield higher-resolution, species-specific quantitative abundance estimates of fish assemblages in the California Current Large Marine Ecosystem during and after the 2014-16 Pacific marine heatwave. This integrated dataset reveals patterns of tropicalization with increases in southern, mesopelagic species and associated declines in important temperate fisheries targets (e.g., North Pacific Hake (Merluccius productus) and Pacific Sardine (Sardinops sagax)). We observed novel assemblages of southern, mesopelagic fishes and temperate species (e.g., Northern Anchovy, Engraulis mordax) even after the return to average water temperatures. Our innovative preservative derived eDNA metabarcoding and quantitative modeling approaches open the door to reconstructing the historical dynamics of assemblages from modern and archived samples worldwide. SummaryNovel quantitative abundance estimates from archived DNA reveals marine heatwave-associated shifts in fish assemblages.

ecology↗

bioRxiv2021

Tourmaline: a workflow for rapid and reproducible amplicon sequence analysis using QIIME 2 and Snakemake

BackgroundAmplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results. FindingsWe developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files--a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences--it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm, assigns taxonomy to the resulting representative sequences, performs analyses of taxonomic, alpha, and beta diversity, and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S rRNA amplicon dataset from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks. ConclusionsAutomated workflows like Tourmaline enable rapid analysis of environmental and biomedical amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.

bioinformatics↗

bioRxiv2021

Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment

As our understanding of the structure and diversity of the microbial world grows, interpreting its function is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of standardization challenges comparisons among studies that could provide insight into the structure and function of microbial communities across multiple habitats on a planetary scale. Technical variation among distinct studies without proper standardization of approaches prevents robust meta-analysis. Here, we present a multi-omics, meta-analysis of a novel, diverse set of microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry), centering our description on relationships and co-occurrences of microbially-related metabolites and microbial taxa across environments. Standardized protocols and analytical methods for characterizing microbial communities, including assessment of molecular diversity using untargeted metabolomics, facilitate identification of shared microbial and metabolite features, permitting us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of a community resource that will become more valuable with time. To provide examples of applying this database, we outline important ecological questions that can be addressed, and test the hypotheses that every microbe and metabolite is everywhere, but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment. The relative abundances of microbially-related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner, and highlight the power of certain chemistry - in particular terpenoids - in distinguishing Earths environments.

ecology↗

bioRxiv2019

Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations upon conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the ocean; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, II) and 5 Prochlorococcus (ecotype HLII) cells from the Red Sea and combined them with globally-sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they could be functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence-absence of OGs.

microbiology↗

bioRxiv2017

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

bioinformatics↗