ORCID Profile
0000-0003-4048-5316
Current Organisation
Hakai Institute
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Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24621
Abstract: Our growing awareness of the microbial world’s importance and ersity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community s les collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of ersity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial ersity.
Publisher: Elsevier BV
Date: 12-2011
Publisher: Wiley
Date: 22-05-2023
DOI: 10.1002/EDN3.422
Abstract: During the outmigration of Pacific Salmon, the early marine phase is a critical period when high mortality can occur. Traditional s ling and monitoring of juvenile salmon migration can be limited by logistically intensive gear requirements, accessibility, and cost. Improved understanding of the early marine phase, for ex le, migration duration and habitat use, requires innovative techniques that can improve the spatial and temporal coverage of monitoring. Environmental DNA (eDNA) is genetic fragments present in the environment that can be used as a proxy for organism presence and can be effectively and efficiently collected through water s les. Estimating fish abundance or biomass from eDNA concentration data would provide a valuable fisheries tool but remains challenging to calibrate. To quantify the relationship between eDNA abundance and fish biomass, we used a controlled mesocosm experiment, in which eDNA s les were collected from 15 aquaria (340 L) with varying densities of juvenile Chinook salmon per tank (0, 5, 10, 20, and 30). The concentration of eDNA was obtained by qPCR scaled with fish biomass (ANOVA, p 0.05). However, we also observed that variability of eDNA concentrations among replicates of the same treatment positively scaled biomass (ANOVA, p 0.05). Therefore, higher biomasses of fish can yield more challenging data to interpret. This study lays important groundwork for the application of eDNA for monitoring juvenile salmonids yet highlights caveats for the applicability of eDNA as a stand‐alone method to assess biomass in a field setting.
Publisher: Wiley
Date: 06-2021
DOI: 10.1002/HYP.14198
Abstract: The Kwakshua Watersheds Observatory (KWO) is an integrative watersheds observatory on the coastal margin of a rain‐dominated bog‐forest landscape in British Columbia (BC), Canada. Established in 2013, the goal of the KWO is to understand and model the flux of terrestrial materials from land to sea – the origins, pathways, processes and ecosystem consequences – in the context of long‐term environmental change. The KWO consists of seven gauged watersheds and a network of observation sites spanning from land to sea and along drainage gradients within catchments. Time‐series datasets include year‐round measurements of weather, soil hydrology, streamflow, aquatic biogeochemistry, microbial ecology and nearshore oceanographic conditions. Sensor measurements are recorded every 5 min and water s les are collected approximately monthly. Additional observations are made during high‐flow conditions. We used remote sensing to map watershed terrain, drainage networks, soils and terrestrial ecosystems. The watersheds range in size from 3.2 to 12.8 km 2 , with varying catchment characteristics that influence hydrological and biogeochemical responses. Despite local variation, the overall study area is a global hotspot for yields of dissolved organic carbon, dissolved organic nitrogen and dissolved iron at the coastal margin. This observatory helps fill an important gap in the global network of observatories, in terms of spatial location (central coast of BC), climate (temperate oceanic), hydrology (very high runoff, pluvial regime), geology (igneous intrusive, glacially scoured), vegetation (bog rainforest) and soils (large stores of organic carbon).
Publisher: Oxford University Press (OUP)
Date: 02-02-2023
Abstract: Protists (eukaryotic microorganisms) commonly form symbiotic associations with crustacean zooplankton, but their ersity, prevalence and ecological roles are underestimated due to the limited scope of previous investigations. Using metabarcoding of the V4 region of the 18S rRNA gene, we characterized the eukaryotic microbiomes of the dominant crustacean zooplankton, specifically copepods, euphausiids, hipods and ostracods, from the Strait of Georgia, Canada. Sequence reads from the alveolates dominated all zooplankton examined, which mostly comprised ciliates and dinoflagellates of known symbiont lineages. These lineages included not only those of parasitoids but also those of uncharacterized species. Apostome ciliate reads were the most abundant in all hosts except for cyclopoid copepods, which were dominated by the parasitic Syndiniales. Most symbiont lineages showed some degree of host preference, particularly Pseudocolliniidae ciliate parasites with ostracods, but were often detected in all hosts indicating broad host specificity. Reads from free-living protists, including diatoms and surprisingly hydrozoans, were inferred to be part of their diet. Hydrozoans may have been ingested from free organic matter, such as detritus or marine snow, suggesting a likely underestimated pathway of carbon cycling. This investigation contributes to resolving the interactions between zooplankton and protists and the potential ecological significance of symbioses on zooplankton productivity.
Location: United States of America
No related grants have been discovered for Colleen Kellogg.