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Thomson-Laing G, Howarth JD, Atalah J, Vandergoes MJ, Li X, Pearman JK, Fitzsimons S, Moy C, Moody A, Shepherd C, McKay N, Wood SA. Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake. Sci Total Environ 2024; 922:171266. [PMID: 38417515 DOI: 10.1016/j.scitotenv.2024.171266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes.
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Affiliation(s)
- Georgia Thomson-Laing
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand; School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand.
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Javier Atalah
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand
| | | | - Xun Li
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand
| | - John K Pearman
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Sean Fitzsimons
- School of Geography, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand
| | - Chris Moy
- Department of Geology, University of Otago, 360 Leith Street, North Dunedin, Dunedin 9054, New Zealand
| | - Adelaine Moody
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Claire Shepherd
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand
| | - Nicholas McKay
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson 7010, New Zealand
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2
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Kihika JK, Pearman JK, Wood SA, Rhodes LL, Smith KF, Miller MR, Butler J, Ryan KG. Fatty acid production and associated gene pathways are altered by increased salinity and dimethyl sulfoxide treatments during cryopreservation of Symbiodinium pilosum (Symbiodiniaceae). Cryobiology 2024; 114:104855. [PMID: 38301952 DOI: 10.1016/j.cryobiol.2024.104855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
The Symbiodinium genus is ancestral among other Symbiodiniaceae lineages with species that are both symbiotic and free living. Changes in marine ecosystems threaten their existence and crucial ecological roles. Cryopreservation offers an avenue for their long-term storage for future habitat restoration after coral bleaching. In our previous study we demonstrated that high salinity treatments of Symbiodiniaceae isolates led to changes in their fatty acid (FA) profiles and higher cell viabilities after cryopreservation. In this study, we investigated the role of increased salinity on FA production and the genes involved in FA biosynthesis and degradation pathways during the cryopreservation of Symbiodinium pilosum. Overall, there was a twofold increase in mass of FAs produced by S. pilosum after being cultured in medium with increased salinity (54 parts per thousand; ppt). Dimethyl sulfoxide (Me2SO) led to a ninefold increase of FAs in standard salinity (SS) treatment, compared to a fivefold increase in increased salinity (IS) treatments. The mass of the FA classes returned to baseline during recovery. Transcriptomic analyses showed an acyl carrier protein gene was significantly upregulated after Me2SO treatment in the SS cultures. Cytochrome P450 reductase genes were significantly down regulated after Me2SO addition in SS treatment preventing FA degradation. These changes in the expression of FA biosynthesis and degradation genes contributed to more FAs in SS treated isolates. Understanding how increased salinity changes FA production and the roles of specific genes in regulating FA pathways will help improve current freezing protocols for Symbiodiniaceae and other marine microalgae.
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Affiliation(s)
- Joseph K Kihika
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand.
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Lesley L Rhodes
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | | | - Juliette Butler
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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3
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Thomson-Laing G, Schallenberg L, Kelly D, Howarth JD, Wood SA. An integrative approach to assess the impact of disturbance on native fish in lakes. Biol Rev Camb Philos Soc 2024; 99:85-109. [PMID: 37621123 DOI: 10.1111/brv.13013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Freshwater fish are in a perilous state with more than 30% of species considered critically endangered. Yet significant ecological and methodological complexities constrain our ability to determine how disturbances are impacting native fish communities. We review current methods used to assess the responses of fish communities, especially native fish, to disturbances, with a focus on lakes. These methods include contemporary population surveys, manipulative experimental approaches, paleolimnological approaches and Indigenous Knowledge and social histories. We identify knowledge gaps, such as a lack of baseline data for native fish, an inability to assess the impact of historical disturbances, stressor response dynamics in contemporary multi-stressor environments, and natural disturbance regimes. Our assessment of the current methods highlights challenges to filling these knowledge gaps using the reviewed methods. We advocate strongly for the implementation of an integrative approach that combines emerging technologies (i.e. molecular-based techniques in contemporary surveys and paleolimnology) and underutilised knowledge streams (i.e. Indigenous Knowledge and social histories) which should be used in concert with conventional methods. This integrative approach will allow researchers to determine the key drivers of decline and the degree of change, which will enable more informed and successful management actions.
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Affiliation(s)
- Georgia Thomson-Laing
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson, 7010, New Zealand
- Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | | | - David Kelly
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson, 7010, New Zealand
| | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax Street, The Wood, Nelson, 7010, New Zealand
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4
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Wheeler C, Pearman JK, Howarth JD, Vandergoes MJ, Holt K, Trewick SA, Li X, Thompson L, Thomson-Laing G, Picard M, Moy C, Mckay NP, Moody A, Shepherd C, van den Bos V, Steiner K, Wood SA. A paleoecological investigation of recent cyanobacterial blooms and their drivers in two contrasting lakes. Harmful Algae 2024; 131:102563. [PMID: 38212085 DOI: 10.1016/j.hal.2023.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Cyanobacterial blooms are one of the most significant threats to global water security and freshwater biodiversity. Interactions among multiple stressors, including habitat degradation, species invasions, increased nutrient runoff, and climate change, are key drivers. However, assessing the role of anthropogenic activity on the onset of cyanobacterial blooms and exploring response variation amongst lakes of varying size and depth is usually limited by lack of historical records. In the present study we applied molecular, paleolimnological (trace metal, Itrax-µ-XRF and hyperspectral scanning, chronology), paleobotanical (pollen) and historical data to reconstruct cyanobacterial abundance and community composition and anthropogenic impacts in two dune lakes over a period of up to 1200 years. Metabarcoding and droplet digital PCR results showed very low levels of picocyanobacteria present in the lakes prior to about CE 1854 (1839-1870 CE) in the smaller shallow Lake Alice and CE 1970 (1963-1875 CE) in the larger deeper Lake Wiritoa. Hereafter bloom-forming cyanobacteria were detected and increased notably in abundance post CE 1984 (1982-1985 CE) in Lake Alice and CE 1997 (1990-2007 CE) in Lake Wiritoa. Currently, the magnitude of blooms is more pronounced in Lake Wiritoa, potentially attributable to hypoxia-induced release of phosphorus from sediment, introducing an additional source of nutrients. Generalized linear modelling was used to investigate the contribution of nutrients (proxy = bacterial functions), temperature, redox conditions (Mn:Fe), and erosion (Ti:Inc) in driving the abundance of cyanobacteria (ddPCR). In Lake Alice nutrients and erosion had a statistically significant effect, while in Lake Wiritoa nutrients and redox conditions were significant.
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Affiliation(s)
- Caitlin Wheeler
- Massey University, Tennent Drive, Palmerston North 4410, Aotearoa, New Zealand
| | - John K Pearman
- Cawthron Institute, Private Bag 2 Aotearoa, Nelson 7042, New Zealand
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600 Aotearoa, Wellington 6012, New Zealand
| | | | - Katherine Holt
- Massey University, Tennent Drive, Palmerston North 4410, Aotearoa, New Zealand
| | - Steven A Trewick
- Massey University, Tennent Drive, Palmerston North 4410, Aotearoa, New Zealand
| | - Xun Li
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600 Aotearoa, Wellington 6012, New Zealand
| | - Lucy Thompson
- Cawthron Institute, Private Bag 2 Aotearoa, Nelson 7042, New Zealand
| | | | - Mailys Picard
- Cawthron Institute, Private Bag 2 Aotearoa, Nelson 7042, New Zealand; Department of Ecology and Environmental Science, Umeå Universitet, Linnaeus väg 4-6, Umeå 907 36, Sweden
| | - Chris Moy
- Department of Geology, University of Otago, 360 Leith Street Aotearoa, North Dunedin, Dunedin 9054, New Zealand
| | - Nicholas P Mckay
- School of Earth and Sustainability, Northern Arizona University, Flagstaf, AZ, United States
| | - Adelaine Moody
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600 Aotearoa, Wellington 6012, New Zealand
| | - Claire Shepherd
- GNS Science, 1 Fairway Drive Aotearoa, Avalon, Lower Hutt 5011, New Zealand
| | | | - Konstanze Steiner
- Cawthron Institute, Private Bag 2 Aotearoa, Nelson 7042, New Zealand
| | - Susanna A Wood
- Massey University, Tennent Drive, Palmerston North 4410, Aotearoa, New Zealand.
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5
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Dengg M, Stirling CH, Safi K, Lehto NJ, Wood SA, Seyitmuhammedov K, Reid MR, Verburg P. Bioavailable iron concentrations regulate phytoplankton growth and bloom formation in low-nutrient lakes. Sci Total Environ 2023; 902:166399. [PMID: 37611704 DOI: 10.1016/j.scitotenv.2023.166399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
The growth of phytoplankton in lakes is thought to be primarily controlled by macronutrient concentrations, but the availability of trace metal micronutrients, such as iron (Fe), are increasingly recognised as important regulators of lake primary production. This study evaluates the role of Fe in regulating phytoplankton growth in lakes of different nutrient status in New Zealand. The results of this unique year-long study, combining highly sensitive trace metal concentration analysis of waters and particulates with advanced trace metal bioavailability and speciation modelling, constrains thresholds for bioavailable Fe and colloidal Fe of 0.8 nmol·L-1 and 30 nmol·L-1, respectively, below which phytoplankton growth-limitation occurs. These thresholds specifically control diatom bloom formation and termination in lakes, thereby exerting a strong influence on freshwater carbon sequestration, given the dominance of diatoms in lake bloom assemblages. Importantly, potentially toxic cyanobacteria thrived only after events of bottom water anoxia, when additional dissolved Fe in concentrations ≥4 nmol·L-1 was released into the water column. These new thresholds for bioavailable and colloidal Fe offer the potential to manage micronutrient levels in lakes for the purpose of regulating algal bloom formation and carbon sequestration, while at the same time, suppressing the formation of harmful cyanobacterial blooms.
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Affiliation(s)
- Markus Dengg
- Department of Geology, University of Otago, PO Box 56, 9016 Dunedin, New Zealand; Centre for Trace Element Analysis, University of Otago, PO Box 56, 9016 Dunedin, New Zealand.
| | - Claudine H Stirling
- Department of Geology, University of Otago, PO Box 56, 9016 Dunedin, New Zealand; Centre for Trace Element Analysis, University of Otago, PO Box 56, 9016 Dunedin, New Zealand.
| | - Karl Safi
- National Institute of Water and Atmospheric Research (NIWA), 3251 Hamilton, New Zealand
| | - Niklas J Lehto
- Faculty of Agriculture and Life Sciences, Lincoln University, 7647 Lincoln, New Zealand
| | | | - Kyyas Seyitmuhammedov
- Department of Geology, University of Otago, PO Box 56, 9016 Dunedin, New Zealand; Centre for Trace Element Analysis, University of Otago, PO Box 56, 9016 Dunedin, New Zealand
| | - Malcolm R Reid
- Department of Geology, University of Otago, PO Box 56, 9016 Dunedin, New Zealand; Centre for Trace Element Analysis, University of Otago, PO Box 56, 9016 Dunedin, New Zealand
| | - Piet Verburg
- National Institute of Water and Atmospheric Research (NIWA), 3251 Hamilton, New Zealand
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6
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Gregersen R, Pearman JK, Atalah J, Waters S, Vandergoes MJ, Howarth JD, Thomson-Laing G, Thompson L, Wood SA. A taxonomy-free diatom eDNA-based technique for assessing lake trophic level using lake sediments. J Environ Manage 2023; 345:118885. [PMID: 37659373 DOI: 10.1016/j.jenvman.2023.118885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Anthropogenic eutrophication is one of the most pressing issues facing lakes globally. Our ability to manage lake eutrophication is hampered by the limited spatial and temporal extents of monitoring records, stemming from the time-consuming and expensive nature of physiochemical and biological monitoring. Diatom-based biomonitoring presents an alternative to traditional eutrophication monitoring, yet it is restricted by the high degree of taxonomic expertise required. Environmental DNA metabarcoding, while providing a promising substitute for diatom community enumeration, is plagued by inadequate taxonomic coverage of reference databases and methodological bias, limiting its use for biomonitoring. Here we show that taxonomy-free diatom-biomonitoring, in which environmental DNA metabarcoding data is utilised but not assigned to specific taxonomic classes, presents an accurate, fast, and relatively automated alternative to taxonomically assigned eutrophication biomonitoring. Our taxonomy-free index accounted for 85% of trophic level variability across 89 lakes and had the lowest average prediction error of the three approaches tested. By not relying on taxonomic identification or metabarcoding reference databases, taxonomy-free biomonitoring maintains diatom diversity that is lost in taxonomic assignment using molecular approaches. Furthermore, by utilising lake sediments, the approach outlined here presents a time-integrated estimation of lake trophic level and thus does not require time-consuming seasonal sampling. Taxonomy-free biomonitoring addresses the limitations of traditional physicochemical eutrophication monitoring and taxonomic biomonitoring alternatives and can be used to extend the spatial and temporal extents of eutrophication monitoring.
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Affiliation(s)
- Rose Gregersen
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand.
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Javier Atalah
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Sean Waters
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | | | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
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7
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Puddick J, Naeher S, Pearman JK, Page CD, Romanazzi D, Schallenberg LA, Howarth JD, Vandergoes MJ, Wood SA. Characterizing carotenoids in cyanobacterial cultures - Opportunities and implications for paleolimnological studies. Harmful Algae 2023; 127:102481. [PMID: 37544666 DOI: 10.1016/j.hal.2023.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Cyanobacterial blooms are increasing in frequency and intensity globally, impacting lake ecosystem health and posing a risk to human and animal health due to the toxins they can produce. Cyanobacterial pigments preserved in lake sediments provide a useful means of understanding the changes that have led to cyanobacterial blooms in lakes. However, there is some uncertainty as to whether specific carotenoids are unique to certain genera or types of cyanobacteria. To fill this knowledge gap, we analyzed pigments in 34 cyanobacteria cultures and applied the findings to sediments from three New Zealand lakes. The cyanobacterial carotenoids canthaxanthin, echinenone and zeaxanthin were detected in all cultures, whereas myxoxanthophyll was only detected in ten cultures (Microcoleus, Planktothrix and the picocyanobacteria cultures; Synechococcaceae). The sum of the individual carotenoid concentrations provided the strongest relationship with cyanobacterial biomass (R2 = 0.58) and could be used in paleolimnology studies to evaluate general cyanobacterial abundance. Ratios of canthaxanthin, zeaxanthin and myxoxanthophyll relative to echinenone indicated that carotenoid ratios could be used to differentiate picocyanobacteria and bloom-forming cyanobacteria, to some degree. High zeaxanthin/echinenone ratios were measured in picocyanobacteria and low zeaxanthin/echinenone ratios were measured in bloom-forming cyanobacteria. The zeaxanthin/echinenone ratio was applied to sediment core samples where the cyanobacterial community was also evaluated by 16S rRNA gene metabarcoding, with the zeaxanthin/echinenone ratios showing similar patterns to those observed in the cultures. The preliminary assessment described here suggests that zeaxanthin/echinenone ratios could provide a valuable paleoecological proxy for evaluating historical shifts in cyanobacterial communities and warrants further exploration.
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Affiliation(s)
- Jonathan Puddick
- Cawthron Institute, 98 Halifax Street-East, Nelson 7010, New Zealand.
| | | | - John K Pearman
- Cawthron Institute, 98 Halifax Street-East, Nelson 7010, New Zealand
| | - Carrie D Page
- Cawthron Institute, 98 Halifax Street-East, Nelson 7010, New Zealand
| | - Donato Romanazzi
- Cawthron Institute, 98 Halifax Street-East, Nelson 7010, New Zealand
| | | | - Jamie D Howarth
- Victoria University of Wellington, Kelburn, Wellington 6012, New Zealand
| | | | - Susanna A Wood
- Cawthron Institute, 98 Halifax Street-East, Nelson 7010, New Zealand
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8
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Durán-Vinet B, Araya-Castro K, Zaiko A, Pochon X, Wood SA, Stanton JAL, Jeunen GJ, Scriver M, Kardailsky A, Chao TC, Ban DK, Moarefian M, Aran K, Gemmell NJ. CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning. CRISPR J 2023; 6:316-324. [PMID: 37439822 PMCID: PMC10494903 DOI: 10.1089/crispr.2023.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023] Open
Abstract
Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.
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Affiliation(s)
- Benjamín Durán-Vinet
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile; Berkeley, Berkeley, California, USA
| | - Karla Araya-Castro
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile; Berkeley, Berkeley, California, USA
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
- Sequench Ltd, Nelson, New Zealand; Berkeley, Berkeley, California, USA
| | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
| | - Susanna A. Wood
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
| | - Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Gert-Jan Jeunen
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Michelle Scriver
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
| | - Anya Kardailsky
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Department of Zoology, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Tzu-Chiao Chao
- Institute of Environmental Change and Society, Department of Biology, University of Regina, Regina, Canada; Berkeley, Berkeley, California, USA
| | - Deependra K. Ban
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
| | - Maryam Moarefian
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
- Cardea Bio Inc., San Diego, California, USA; and Berkeley, Berkeley, California, USA
- University of California, Berkeley, Berkeley, California, USA
| | - Neil J. Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
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9
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Kelly LT, Reed L, Puddick J, Hawes I, Hicks BJ, Allan MG, Lehmann MK, Wood SA. Growth conditions impact particulate absorption and pigment concentrations in two common bloom forming cyanobacterial species. Harmful Algae 2023; 125:102432. [PMID: 37220985 DOI: 10.1016/j.hal.2023.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 05/25/2023]
Abstract
Remote sensing using satellite imagery has been promoted as a method to broaden the scale and frequency of cyanobacterial monitoring. This relies on the ability to establish relationships between the reflectance spectra of water bodies and the abundance of cyanobacteria. A challenge to achieving this comes from a limited understanding of the extent to which the optical properties of cyanobacteria vary according to their physiological state and growth environment. The aim of the present study was to determine how growth stage, nutrient status and irradiance affect pigment concentrations and absorption spectra in two common bloom forming cyanobacterial taxa: Dolichospermum lemmermannii and Microcystis aeruginosa. Each species was grown in laboratory batch culture under a full factorial design of low or high light intensity and low, medium, or high nitrate concentrations. Absorption spectra, pigment concentrations and cell density were measured throughout the growth phases. The absorption spectra were all highly distinguishable from each other, with greater interspecific than intraspecific differences, indicating that both D. lemmermannii and M. aeruginosa can be readily differentiated using hyperspectral absorption spectra. Despite this, each species exhibited different responses in the per-cell pigment concentrations with varying light intensity and nitrate exposure. Variability among treatments was considerably higher in D. lemmermannii than in M. aeruginosa, which exhibited smaller changes in pigment concentrations among the treatments. These results highlight the need to understand the physiology of the cyanobacteria and to take caution when estimating biovolumes from reflectance spectra when species composition and growth stage are unknown.
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Affiliation(s)
| | - Lisa Reed
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | | | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Brendan J Hicks
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | | | - Moritz K Lehmann
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand; Xerra Earth Observation Institute, Alexandra, New Zealand
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10
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Gregersen R, Howarth JD, Atalah J, Pearman JK, Waters S, Li X, Vandergoes MJ, Wood SA. Paleo-diatom records reveal ecological change not detected using traditional measures of lake eutrophication. Sci Total Environ 2023; 867:161414. [PMID: 36621498 DOI: 10.1016/j.scitotenv.2023.161414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/12/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Lakes provide crucial ecosystem services and harbour unique and rich biodiversity, yet despite decades of research and management focus, cultural eutrophication remains a predominant threat to their health. Our ability to manage lake eutrophication is restricted by the lack of long-term monitoring records. To circumvent this, we developed a bio-indicator approach for inferring trophic level from lake diatom communities and applied this to sediment cores from two lakes experiencing eutrophication stress. Diatom indicators strongly predicted observed trophic levels, and when applied to sediment cores, diatom predicted trophic level reconstructions were consistent with monitoring data and land-use histories. However, there were significant recent shifts in diatom communities not captured by the diatom-based index or monitoring data, suggesting that conventional trophic level indices obscure important ecological change. New approaches, such as the one in this study, are critical to detect early changes in water quality and prevent the decline of lake ecosystems worldwide.
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Affiliation(s)
- Rose Gregersen
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand.
| | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Javier Atalah
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Sean Waters
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xun Li
- GNS Science, PO Box 30-368, Lower Hutt 5040, New Zealand
| | | | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
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11
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Picard MH, Zaiko A, Tidy AM, Kelly DJ, Thomson-Laing G, Wilkinson SP, Pochon X, Vandergoes MJ, Hawes I, Wood SA. Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA. PeerJ 2023; 11:e15210. [PMID: 37151294 PMCID: PMC10162041 DOI: 10.7717/peerj.15210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
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Affiliation(s)
- Maïlys H.V. Picard
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - David J. Kelly
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - Ian Hawes
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
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12
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Kihika JK, Wood SA, Rhodes L, Smith KF, Butler J, Ryan KG. Assessment of the recovery and photosynthetic efficiency of Breviolum psygmophilum and Effrenium voratum (Symbiodiniaceae) following cryopreservation. PeerJ 2023; 11:e14885. [PMID: 36874975 PMCID: PMC9983422 DOI: 10.7717/peerj.14885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/22/2023] [Indexed: 03/06/2023] Open
Abstract
Many strains of Symbiodiniaceae have been isolated and their genetics, taxonomy, and metabolite production studied. Maintaining these cultures requires careful and regular sub-culturing that is costly with a high risk of species contamination or loss. Cryopreservation is a viable alternative for their long-term storage; however, there is uncertainty as to whether cryopreservation impacts the photosynthetic performance of Symbiodiniaceae. We investigated the growth rates and photosynthetic efficiency of two species, Breviolum psygmophilum and Effrenium voratum before and after cryopreservation. Rapid light curves (RLCs) produced using Pulse Amplitude Modulated (PAM) fluorometry were used to generate detailed information on the characteristics of photosystem II (PSII). The maximum electron transport rate (ETRmax) and the quantum yield (Fv/Fm) of the control (non-cryopreserved) and cryopreserved culture isolates were assessed across the growth cycle. The non-cryopreserved isolate of B. psygmophilum had a higher quantum yield than the cryopreserved isolate from day 12 to day 24, whereas there were no differences from day 28 to the late stationary phase. There were no significant differences in ETRmax. No significant differences were observed in quantum yield or ETRmax between the control and cryopreserved E. voratum isolates. The ability of cryopreserved strains to recover and regain their photosynthetic efficiency after freezing demonstrates the utility of this method for the long-term storage of these and other Symbiodiniaceae species.
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Affiliation(s)
- Joseph K Kihika
- Department of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.,Cawthron Institute, Nelson, New Zealand
| | | | | | - Kirsty F Smith
- Cawthron Institute, Nelson, New Zealand.,Department of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Ken G Ryan
- Department of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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13
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Audrézet F, Zaiko A, Cahill P, Champeau O, Tremblay LA, Smith D, Wood SA, Lear G, Pochon X. Does plastic type matter? Insights into non-indigenous marine larvae recruitment under controlled conditions. PeerJ 2022; 10:e14549. [PMID: 36570004 PMCID: PMC9774007 DOI: 10.7717/peerj.14549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/20/2022] [Indexed: 12/23/2022] Open
Abstract
Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine 'hitchhikers' by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversity, ecosystem services/functions and hence, important economic consequences. Over the past decade, increasing research interest has been directed towards the characterization of biological communities colonizing plastic debris, the so called Plastisphere. Despite remarkable advances in this field, little is known regarding the recruitment patterns of NIS larvae and propagules on MPD, and the factors influencing these patterns. To address this knowledge gap, we used custom-made bioassay chambers and ran four consecutive bioassays to compare the settlement patterns of four distinct model biofouling organisms' larvae, including the three notorious invaders Crassostrea gigas, Ciona savignyi and Mytilus galloprovincialis, along with one sessile macro-invertebrate Spirobranchus cariniferus, on three different types of polymers, namely Low-Linear Density Polyethylene (LLDPE), Polylactic Acid (PLA), Nylon-6, and a glass control. Control bioassay chambers were included to investigate the microbial community composition colonizing the different substrates using 16S rRNA metabarcoding. We observed species-specific settlement patterns, with larvae aggregating on different locations on the substrates. Furthermore, our results revealed that C. savignyi and S. cariniferus generally favoured Nylon and PLA, whereas no specific preferences were observed for C. gigas and M. galloprovincialis. We did not detect significant differences in bacterial community composition between the tested substrates. Taken together, our results highlight the complexity of interactions between NIS larvae and plastic polymers. We conclude that several factors and their potential interactions influenced the results of this investigation, including: (i) species-specific larval biological traits and ecology; (ii) physical and chemical composition of the substrates; and (iii) biological cues emitted by bacterial biofilm and the level of chemosensitivity of the different NIS larvae. To mitigate the biosecurity risks associated with drifting plastic debris, additional research effort is critical to effectively decipher the mechanisms involved in the recruitment of NIS on MPD.
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Affiliation(s)
- François Audrézet
- Cawthron Institute, Nelson, New Zealand,University of Auckland, Institute of Marine Science, Auckland, New Zealand
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand,University of Auckland, Institute of Marine Science, Auckland, New Zealand
| | | | | | - Louis A. Tremblay
- Cawthron Institute, Nelson, New Zealand,University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | | | | | - Gavin Lear
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand,University of Auckland, Institute of Marine Science, Auckland, New Zealand
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14
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Gregersen R, Howarth JD, Wood SA, Vandergoes MJ, Puddick J, Moy C, Li X, Pearman JK, Moody A, Simon KS. Resolving 500 Years of Anthropogenic Impacts in a Mesotrophic Lake: Nutrients Outweigh Other Drivers of Lake Change. Environ Sci Technol 2022; 56:16940-16951. [PMID: 36379054 DOI: 10.1021/acs.est.2c06835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Interactions among multiple stressors, legacies of past perturbations, and the lack of historical information make it difficult to determine the influence of individual anthropogenic impacts on lakes and separate them from natural ecosystem variability. In the present study, we coupled paleolimnological approaches, historical data, and ecological experiments to disentangle the impacts of multiple long-term stressors on lake ecosystem structure and function. We found that the lake structure and function remained resistant to the impacts of catchment deforestation and erosion, and the introduction of several exotic fish species. Changes in ecosystem structure and function were consistent, with nutrient enrichment being the primary driver of change. Significant and sustained changes in the lake diatom community structure (and their nutrient requirements), bacterial community function, and paleolimnological proxies of ecosystem function coincided with nitrogen and phosphorus fertilizers in the catchment. The results highlight that the effects of increased nutrient inputs are much stronger than the influence of other, potentially significant, drivers of ecosystem change, and that the degree of nutrient impact can be underestimated by environmental monitoring due to its diffuse and accumulative nature. Delineating the effects of multiple anthropogenic drivers requires long-term records of both impacts and lake ecosystem change across multiple trophic levels.
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Affiliation(s)
| | | | | | | | | | - Chris Moy
- University of Otago, Dunedin 9016, New Zealand
| | - Xun Li
- GNS Science, Lower Hutt 5040, New Zealand
| | | | | | - Kevin S Simon
- The University of Auckland, Auckland 1010, New Zealand
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15
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Kihika JK, Wood SA, Rhodes L, Smith KF, Pochon X, Thompson L, Butler J, Schattschneider J, Oakley C, Ryan KG. Cryopreservation of diverse Symbiodiniaceae dinoflagellates: Assessment of their fatty acid profiles in response to increased salinity treatments. Cryobiology 2022. [DOI: 10.1016/j.cryobiol.2022.11.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Pearman JK, Thomson-Laing G, Thompson L, Waters S, Vandergoes MJ, Howarth JD, Duggan IC, Hogg ID, Wood SA. Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes. PeerJ 2022; 10:e14378. [PMID: 36389411 PMCID: PMC9661969 DOI: 10.7717/peerj.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.
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Affiliation(s)
| | | | | | | | | | | | | | - Ian D. Hogg
- University of Waikato, Hamilton, New Zealand,Canadian High Arctic Research Station, Nunavut, Canada
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17
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Picard M, Pochon X, Atalah J, Pearman JK, Rees A, Howarth JD, Moy CM, Vandergoes MJ, Hawes I, Khan S, Wood SA. Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes. Sci Rep 2022; 12:12810. [PMID: 35896561 PMCID: PMC9329365 DOI: 10.1038/s41598-022-14216-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.
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Affiliation(s)
- Maïlys Picard
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand. .,Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand.
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand.,Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Andrew Rees
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Christopher M Moy
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | | | - Ian Hawes
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand
| | - Samiullah Khan
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
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18
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Kihika JK, Wood SA, Rhodes L, Smith KF, Miller MR, Pochon X, Thompson L, Butler J, Schattschneider J, Oakley C, Ryan KG. Cryopreservation of six Symbiodiniaceae genera and assessment of fatty acid profiles in response to increased salinity treatments. Sci Rep 2022; 12:12408. [PMID: 35859115 PMCID: PMC9300622 DOI: 10.1038/s41598-022-16735-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Symbiodiniaceae are a diverse group of dinoflagellates, the majority of which are free-living and/or associated with a variety of protists and other invertebrate hosts. Maintenance of isolated cultures is labour-intensive and expensive, and cryopreservation provides an excellent avenue for their long-term storage. We aimed to cryopreserve 15 cultured isolates from six Symbiodiniaceae genera using dimethyl sulfoxide (DMSO) as the cryoprotectant agent (CPA). Under 15% DMSO, 10 isolates were successfully cryopreserved using either rapid freezing or controlled-rate freezing. Cultures that failed or had low survival, were subjected to (1) a reduction of CPA to 10%, or (2) increased salinity treatment before freezing. At 10% DMSO, three further isolates were successfully cryopreserved. At 15% DMSO there were high cell viabilities in Symbiodinium pilosum treated with 44 parts per thousand (ppt) and 54 ppt culture medium. An isolate of Fugacium sp. successfully cryopreserved after salinity treatments of 54 ppt and 64 ppt. Fatty acid (FA) analyses of S. pilosum after 54 ppt salinity treatment showed increased saturated FA levels, whereas Fugacium sp. had low poly-unsaturated FAs compared to normal salinity (34 ppt). Understanding the effects of salinity and roles of FAs in cryopreservation will help in developing protocols for these ecologically important taxa.
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Affiliation(s)
- Joseph Kanyi Kihika
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand. .,School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand.
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Lesley Rhodes
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | | | - Xavier Pochon
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand.,Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Juliette Butler
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Clint Oakley
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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19
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Xiao M, Burford MA, Wood SA, Aubriot L, Ibelings BW, Prentice MJ, Galvanese EF, Harris TD, Hamilton DP. Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria. FEMS Microbiol Rev 2022; 46:6617595. [PMID: 35749580 PMCID: PMC9629505 DOI: 10.1093/femsre/fuac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
David Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.
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Affiliation(s)
- Man Xiao
- Corresponding author: Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, Jiangsu, China. E-mail:
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, 7010, New Zealand
| | - Luis Aubriot
- Phytoplankton Physiology and Ecology Group, Sección Limnología, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias; Universidad de la República, Montevideo, 11400, Uruguay
| | - Bas W Ibelings
- Department F.-A. Forel for Aquatic and Environmental Sciences and Institute for Environmental Sciences, University of Geneva, Geneva, 1290, Switzerland
| | - Matthew J Prentice
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Elena F Galvanese
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba-PR, 81531-998, Brazil,Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba-PR, 80060-140, Brazil
| | - Ted D Harris
- Kansas Biological Survey and Center for Ecological Research, Lawrence, KS, 66047, United States
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
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20
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Androić D, Armstrong DS, Bartlett K, Beminiwattha RS, Benesch J, Benmokhtar F, Birchall J, Carlini RD, Cornejo JC, Covrig Dusa S, Dalton MM, Davis CA, Deconinck W, Dowd JF, Dunne JA, Dutta D, Duvall WS, Elaasar M, Falk WR, Finn JM, Forest T, Gal C, Gaskell D, Gericke MTW, Gray VM, Grimm K, Guo F, Hoskins JR, Jones DC, Jones MK, Kargiantoulakis M, King PM, Korkmaz E, Kowalski S, Leacock J, Leckey J, Lee AR, Lee JH, Lee L, MacEwan S, Mack D, Magee JA, Mahurin R, Mammei J, Martin JW, McHugh MJ, Meekins D, Mesick KE, Michaels R, Micherdzinska A, Mkrtchyan A, Mkrtchyan H, Narayan A, Ndukum LZ, Nelyubin V, van Oers WTH, Owen VF, Page SA, Pan J, Paschke KD, Phillips SK, Pitt ML, Radloff RW, Rajotte JF, Ramsay WD, Roche J, Sawatzky B, Seva T, Shabestari MH, Silwal R, Simicevic N, Smith GR, Solvignon P, Spayde DT, Subedi A, Suleiman R, Tadevosyan V, Tobias WA, Tvaskis V, Waidyawansa B, Wang P, Wells SP, Wood SA, Yang S, Zang P, Zhamkochyan S, Christy ME, Horowitz CJ, Fattoyev FJ, Lin Z. Determination of the ^{27}Al Neutron Distribution Radius from a Parity-Violating Electron Scattering Measurement. Phys Rev Lett 2022; 128:132501. [PMID: 35426696 DOI: 10.1103/physrevlett.128.132501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
We report the first measurement of the parity-violating elastic electron scattering asymmetry on ^{27}Al. The ^{27}Al elastic asymmetry is A_{PV}=2.16±0.11(stat)±0.16(syst) ppm, and was measured at ⟨Q^{2}⟩=0.02357±0.00010 GeV^{2}, ⟨θ_{lab}⟩=7.61°±0.02°, and ⟨E_{lab}⟩=1.157 GeV with the Q_{weak} apparatus at Jefferson Lab. Predictions using a simple Born approximation as well as more sophisticated distorted-wave calculations are in good agreement with this result. From this asymmetry the ^{27}Al neutron radius R_{n}=2.89±0.12 fm was determined using a many-models correlation technique. The corresponding neutron skin thickness R_{n}-R_{p}=-0.04±0.12 fm is small, as expected for a light nucleus with a neutron excess of only 1. This result thus serves as a successful benchmark for electroweak determinations of neutron radii on heavier nuclei. A tree-level approach was used to extract the ^{27}Al weak radius R_{w}=3.00±0.15 fm, and the weak skin thickness R_{wk}-R_{ch}=-0.04±0.15 fm. The weak form factor at this Q^{2} is F_{wk}=0.39±0.04.
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Affiliation(s)
- D Androić
- University of Zagreb, Zagreb, HR 10002, Croatia
| | | | - K Bartlett
- William & Mary, Williamsburg, Virginia 23185, USA
| | | | - J Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Benmokhtar
- Christopher Newport University, Newport News, Virginia 23606, USA
| | - J Birchall
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - R D Carlini
- William & Mary, Williamsburg, Virginia 23185, USA
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J C Cornejo
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Dalton
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - C A Davis
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - W Deconinck
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J F Dowd
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J A Dunne
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - W S Duvall
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - M Elaasar
- Southern University at New Orleans, New Orleans, Louisiana 70126, USA
| | - W R Falk
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J M Finn
- William & Mary, Williamsburg, Virginia 23185, USA
| | - T Forest
- Idaho State University, Pocatello, Idaho 83209, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - C Gal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M T W Gericke
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - V M Gray
- William & Mary, Williamsburg, Virginia 23185, USA
| | - K Grimm
- William & Mary, Williamsburg, Virginia 23185, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - F Guo
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J R Hoskins
- William & Mary, Williamsburg, Virginia 23185, USA
| | - D C Jones
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M K Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | | | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - E Korkmaz
- University of Northern British Columbia, Prince George, British Columbia V2N4Z9, Canada
| | - S Kowalski
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J Leacock
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J Leckey
- William & Mary, Williamsburg, Virginia 23185, USA
| | - A R Lee
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J H Lee
- William & Mary, Williamsburg, Virginia 23185, USA
- Ohio University, Athens, Ohio 45701, USA
| | - L Lee
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - S MacEwan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - D Mack
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J A Magee
- William & Mary, Williamsburg, Virginia 23185, USA
| | - R Mahurin
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Mammei
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J W Martin
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - M J McHugh
- George Washington University, Washington, DC 20052, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - K E Mesick
- George Washington University, Washington, DC 20052, USA
- Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | | | - A Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - H Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - A Narayan
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - L Z Ndukum
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - V Nelyubin
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - W T H van Oers
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - V F Owen
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S A Page
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Pan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - K D Paschke
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - S K Phillips
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - M L Pitt
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | | | - J F Rajotte
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - W D Ramsay
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - J Roche
- Ohio University, Athens, Ohio 45701, USA
| | - B Sawatzky
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Seva
- University of Zagreb, Zagreb, HR 10002, Croatia
| | - M H Shabestari
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Silwal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - N Simicevic
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - G R Smith
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Solvignon
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D T Spayde
- Hendrix College, Conway, Arkansas 72032, USA
| | - A Subedi
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Suleiman
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Tadevosyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - W A Tobias
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - V Tvaskis
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | | | - P Wang
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - S P Wells
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - S A Wood
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Yang
- William & Mary, Williamsburg, Virginia 23185, USA
| | - P Zang
- Syracuse University, Syracuse, New York 13244, USA
| | - S Zhamkochyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - M E Christy
- Hampton University, Hampton, Virginia 23668, USA
| | - C J Horowitz
- Indiana University, Bloomington, Indiana 47405, USA
| | - F J Fattoyev
- Indiana University, Bloomington, Indiana 47405, USA
| | - Z Lin
- Indiana University, Bloomington, Indiana 47405, USA
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21
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Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA. Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. MBMG 2022. [DOI: 10.3897/mbmg.6.79265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved in many geochemical cycling processes in lakes and a greater understanding of their functions could assist in guiding more targeted remedial actions. Recent advances in metagenomics now make it possible to determine the functional potential of entire microbial communities. The present study investigated microbial communities and their functional potential in surface sediments collected from three lakes with differing trophic states and characteristics. Surface sediments were analysed for their nutrient and elemental contents and metagenomics and metabarcoding analysis undertaken. The nutrients content of the surface sediments did not show as distinct a gradient as water chemistry monitoring data, likely reflecting effects of other lake characteristics, in particular, depth. Metabarcoding and metagenomics revealed differing bacterial community composition and functional potential amongst lakes. Amongst the differentially abundant metabolic pathways, the most prominent were clusters in the energy and xenobiotics pathways. Differences in the energy metabolism paths of photosynthesis and oxidative phosphorylation were observed. These were most likely related to changes in the community composition and especially the presence of cyanobacteria in two of the three lakes. Xenobiotic pathways, such as those involving polycyclic aromatic hydrocarbons, were highest in the lakes with the greatest agricultural land-use in their catchment. These results highlight how microbial metagenomics can be used to gain insights into the causes of differences in trophic status amongst lakes.
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22
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Pearman JK, Wood SA, Vandergoes MJ, Atalah J, Waters S, Adamson J, Thomson-Laing G, Thompson L, Howarth JD, Hamilton DP, Pochon X, Biessy L, Brasell KA, Dahl J, Ellison R, Fitzsimons SJ, Gard H, Gerrard T, Gregersen R, Holloway M, Li X, Kelly DJ, Martin R, McFarlane K, McKay NP, Moody A, Moy CM, Naeher S, Newnham R, Parai R, Picard M, Puddick J, Rees ABH, Reyes L, Schallenberg M, Shepherd C, Short J, Simon KS, Steiner K, Šunde C, Terezow M, Tibby J. A bacterial index to estimate lake trophic level: National scale validation. Sci Total Environ 2022; 812:152385. [PMID: 34942258 DOI: 10.1016/j.scitotenv.2021.152385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Lakes and their catchments have been subjected to centuries to millennia of exploitation by humans. Efficient monitoring methods are required to promote proactive protection and management. Traditional monitoring is time consuming and expensive, which limits the number of lakes monitored. Lake surface sediments provide a temporally integrated representation of environmental conditions and contain high microbial biomass. Based on these attributes, we hypothesized that bacteria associated with lake trophic states could be identified and used to develop an index that would not be confounded by non-nutrient stressor gradients. Metabarcoding (16S rRNA gene) was used to assess bacterial communities present in surface sediments from 259 non-saline lakes in New Zealand encompassing a range of trophic states from alpine microtrophic lakes to lowland hypertrophic lakes. A subset of lakes (n = 96) with monitoring data was used to identify indicator amplicon sequence variants (ASVs) associated with different trophic states. A total of 10,888 indicator taxa were identified and used to develop a Sediment Bacterial Trophic Index (SBTI), which signficantly correlated (r2 = 0.842, P < 0.001) with the Trophic Lake Index. The SBTI was then derived for the remaining 163 lakes, providing new knowledge of the trophic state of these unmonitored lakes. This new, robust DNA-based tool provides a rapid and cost-effective method that will allow a greater number of lakes to be monitored and more effectively managed in New Zealand and globally. The SBTI could also be applied in a paleolimnological context to investigate changes in trophic status over centuries to millennia.
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Affiliation(s)
- John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand.
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Javier Atalah
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Sean Waters
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Janet Adamson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, Qld 4111, Australia
| | - Xavier Pochon
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Laura Biessy
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Jenny Dahl
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Riki Ellison
- Waka Taurua Consulting, Lower Hutt 5040, New Zealand
| | | | - Henry Gard
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Tania Gerrard
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Rose Gregersen
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | | | - Xun Li
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - David J Kelly
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | | | - Nicholas P McKay
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ 86011, United States
| | - Adelaine Moody
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Chris M Moy
- University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | | | - Rewi Newnham
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Russleigh Parai
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Maïlys Picard
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Andrew B H Rees
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Lizette Reyes
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | | | | | - Julia Short
- Adelaide University, Adelaide, South Australia 5005, Australia
| | - Kevin S Simon
- Auckland University, Private Bag 92019, Auckland 1142, New Zealand
| | | | | | | | - John Tibby
- Adelaide University, Adelaide, South Australia 5005, Australia
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23
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Pearman JK, Thomson-Laing G, Thomson-Laing J, Thompson L, Waters S, Reyes L, Howarth JD, Vandergoes MJ, Wood SA. The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes. Front Microbiol 2022; 12:793441. [PMID: 35250905 PMCID: PMC8888906 DOI: 10.3389/fmicb.2021.793441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Sean Waters
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, University of Victoria, Wellington, New Zealand
| | | | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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24
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Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA. Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. MBMG 2022. [DOI: 10.3897/mbmg.6.78128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
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25
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Picard M, Wood SA, Pochon X, Vandergoes MJ, Reyes L, Howarth JD, Hawes I, Puddick J. Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores. Microorganisms 2022; 10:microorganisms10020279. [PMID: 35208733 PMCID: PMC8876145 DOI: 10.3390/microorganisms10020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding the historical onset of cyanobacterial blooms in freshwater bodies can help identify their potential drivers. Lake sediments are historical archives, containing information on what has occurred in and around lakes over time. Paleolimnology explores these records using a variety of techniques, but choosing the most appropriate method can be challenging. We compared results obtained from a droplet digital PCR assay targeting a cyanobacterial-specific region of the 16S rRNA gene in sedimentary DNA and cyanobacterial pigments (canthaxanthin, echinenone, myxoxanthophyll and zeaxanthin) analysed using high-performance liquid chromatography in four sediment cores. There were strong positive relationships between the 16S rRNA gene copy concentrations and individual pigment concentrations, but relationships differed among lakes and sediment core depths within lakes. The relationships were more consistent when all pigments were summed, which we attribute to different cyanobacteria species, in different lakes, at different times producing different suites of pigments. Each method had benefits and limitations, which should be taken into consideration during method selection and when interpreting paleolimnological data. We recommend this biphasic approach when making inferences about changes in the entire cyanobacterial community because they yielded complementary information. Our results support the view that molecular methods can yield results similar to traditional paleolimnological proxies when caveats are adequately addressed.
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Affiliation(s)
- Maïlys Picard
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; (S.A.W.); (X.P.); (J.P.)
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand;
- Correspondence:
| | - Susanna A. Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; (S.A.W.); (X.P.); (J.P.)
| | - Xavier Pochon
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; (S.A.W.); (X.P.); (J.P.)
- Institute of Marine Science, University of Auckland, Private Bag 349, Auckland 0941, New Zealand
| | - Marcus J. Vandergoes
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand; (M.J.V.); (L.R.)
| | - Lizette Reyes
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5011, New Zealand; (M.J.V.); (L.R.)
| | - Jamie D. Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6012, New Zealand;
| | - Ian Hawes
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand;
| | - Jonathan Puddick
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; (S.A.W.); (X.P.); (J.P.)
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26
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Dengg M, Stirling CH, Reid MR, Verburg P, Armstrong E, Kelly LT, Wood SA. Growth at the limits: comparing trace metal limitation of a freshwater cyanobacterium (Dolichospermum lemmermannii) and a freshwater diatom (Fragilaria crotonensis). Sci Rep 2022; 12:467. [PMID: 35013511 PMCID: PMC8748459 DOI: 10.1038/s41598-021-04533-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/16/2021] [Indexed: 12/04/2022] Open
Abstract
Freshwater phytoplankton blooms are increasing in prevalence and there are conflicting views on whether trace metals limit growth of key species and thus bloom formation. The Taupō Volcanic Zone (TVZ), New Zealand, was formed by multiple eruptions of a super-volcano which emitted rhyolitic tephra leaving lakes depleted in trace metals. This provides an opportunity to test the potential of trace metal limitation on freshwater phytoplankton growth under nanomolar concentrations. Growth responses of two algal species isolated from Lake Taupō, Dolichospermum lemmermannii (cyanobacteria) and Fragilaria crotonensis (diatom), to six biologically important trace metals (manganese, iron, zinc, cobalt, copper and molybdenum) were examined in culture experiments. These were conducted at three trace metal concentrations: (1) ambient, (2) two-times ambient, and (3) ten-times ambient concentrations in Lake Taupō. Elevated concentrations of iron significantly increased growth rates and maximum cell densities in D. lemmermannii, whereas no significant concentration dependence was observed for other trace metals. Fragilaria crotonensis showed no significant growth response to elevated concentrations of trace metals. These results highlight the importance of iron as a growth limiting nutrient for cyanobacteria and indicate that even small (twofold) increases in Fe concentrations could enhance cyanobacteria growth rates in Lake Taupō, potentially causing cyanobacterial blooms.
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Affiliation(s)
- Markus Dengg
- Department of Geology and Centre for Trace Element Analysis, University of Otago, Dunedin, 9016, New Zealand.
| | - Claudine H Stirling
- Department of Geology and Centre for Trace Element Analysis, University of Otago, Dunedin, 9016, New Zealand
| | - Malcolm R Reid
- Department of Geology and Centre for Trace Element Analysis, University of Otago, Dunedin, 9016, New Zealand
| | - Piet Verburg
- National Institute of Water and Atmospheric Research (NIWA), Hamilton, 3251, New Zealand
| | - Evelyn Armstrong
- Department of Marine Science, NIWA/University of Otago Research Centre for Oceanography, University of Otago, Dunedin, 9010, New Zealand
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27
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Milner AM, Wood SA, Docherty C, Biessy L, Takenaka M, Tojo K. Winter diet of Japanese macaques from Chubu Sangaku National Park, Japan incorporates freshwater biota. Sci Rep 2021; 11:23091. [PMID: 34845236 PMCID: PMC8629975 DOI: 10.1038/s41598-021-01972-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023] Open
Abstract
The Japanese macaque (Macaca fuscata) is native to the main islands of Japan, except Hokkaido, and is the most northerly living non-human primate. In the Chubu Sangaku National Park of the Japanese Alps, macaques live in one of the coldest areas of the world, with snow cover limiting the availability of preferred food sources. Winter is typically a bottleneck for food availability potentially resulting in marked energy deficits, and mortality may result from famine. However, streams with groundwater upwelling flow during the winter with a constant water temperature of about 5 °C are easily accessible for Japanese macaques to search for riverine biota. We used metabarcoding (Cytochrome c oxidase I) of fecal samples from Japanese macaques to determine their wintertime diet. Here we provide the first robust evidence that Japanese macaques feed on freshwater biota, including brown trout, riverine insects and molluscs, in Chubu Sangaku National Park. These additional food sources likely aid their winter survival.
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Affiliation(s)
- Alexander M Milner
- School of Geography, Earth and Environmental Science, University of Birmingham, Birmingham, UK.
- Institute of Mountain Science, Shinshu University, Matsumoto, Japan.
| | | | - Catherine Docherty
- School of Geography, Earth and Environmental Science, University of Birmingham, Birmingham, UK
- Institute of Mountain Science, Shinshu University, Matsumoto, Japan
| | | | - Masaki Takenaka
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Ueda, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Japan
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28
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Schallenberg LA, Pearman JK, Burns CW, Wood SA. Metabarcoding Reveals Lacustrine Picocyanobacteria Respond to Environmental Change Through Adaptive Community Structuring. Front Microbiol 2021; 12:757929. [PMID: 34867882 PMCID: PMC8633389 DOI: 10.3389/fmicb.2021.757929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Picocyanobacteria (Pcy) are important yet understudied components of lake foodwebs. While phylogenetic studies of isolated strains reveal a high diversity of freshwater genotypes, little is known about abiotic drivers associated with Pcy in different lakes. Due to methodological limitations, most previous studies assess potential drivers using total cell abundances as a response, with often conflicting and inconsistent results. In the present study, we explored how picocyanobacterial communities respond to environmental change using a combination of epifluorescence microscopy and community data determined using 16S rRNA gene metabarcoding. Temporal shifts in picocyanobacterial abundance, diversity and community dynamics were assessed in relation to potential environmental drivers in five contrasting lakes over 1year. Cell abundances alone were not consistently related to environmental variables across lakes. However, the addition of metabarcoding data revealed diverse picocyanobacterial communities that differed significantly between lakes, driven by environmental variables related to trophic state. Within each lake, communities were temporally dynamic and certain amplicon sequence variants (ASVs) were strongly associated with specific environmental drivers. Rapid shifts in community structure and composition were often related to environmental changes, indicating that lacustrine Pcy can persist at high abundances through collective community adaptation. These results demonstrate that a combination of microscopy and metabarcoding enables an in-depth characterisation of picocyanobacterial communities and reveals strain-specific drivers. We recommend that future studies cease referring to picocyanobacterial as one functional group and take strain specific variability into consideration.
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Affiliation(s)
| | - John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Carolyn W. Burns
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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Tee HS, Wood SA, Bouma-Gregson K, Lear G, Handley KM. Genome Streamlining, Plasticity, and Metabolic Versatility Distinguish Co-occurring Toxic and Nontoxic Cyanobacterial Strains of Microcoleus. mBio 2021; 12:e0223521. [PMID: 34700377 PMCID: PMC8546630 DOI: 10.1128/mbio.02235-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Harmful cyanobacterial bloom occurrences have increased worldwide due to climate change and eutrophication, causing nuisance and animal deaths. Species from the benthic cyanobacterial genus Microcoleus are ubiquitous and form thick mats in freshwater systems, such as rivers, that are sometimes toxic due to the production of potent neurotoxins (anatoxins). Anatoxin-producing (toxic) strains typically coexist with non-anatoxin-producing (nontoxic) strains in mats, although the reason for this is unclear. To determine the genetic mechanisms differentiating toxic and nontoxic Microcoleus, we sequenced and assembled genomes from 11 cultures and compared these to another 31 Microcoleus genomes. Average nucleotide identities (ANI) indicate that toxic and nontoxic strains are distinct species (ANI, <95%), and only 6% of genes are shared across all 42 genomes, suggesting a high level of genetic divergence among Microcoleus strains. Comparative genomics showed substantial genome streamlining in toxic strains and a potential dependency on external sources for thiamine and sucrose. Toxic and nontoxic strains are further differentiated by an additional set of putative nitrate transporter (nitrogen uptake) and cyanophycin (carbon and nitrogen storage) genes, respectively. These genes likely confer distinct competitive advantages based on nutrient availability and suggest nontoxic strains are more robust to nutrient fluctuations. Nontoxic strains also possess twice as many transposable elements, potentially facilitating greater genetic adaptation to environmental changes. Our results offer insights into the divergent evolution of Microcoleus strains and the potential for cooperative and competitive interactions that contribute to the co-occurrence of toxic and nontoxic species within mats. IMPORTANCE Microcoleus autumnalis, and closely related Microcoleus species, compose a geographically widespread group of freshwater benthic cyanobacteria. Canine deaths due to anatoxin-a poisoning, following exposure to toxic proliferations, have been reported globally. While Microcoleus proliferations are on the rise, the mechanisms underpinning competition between, or coexistence of, toxic and nontoxic strains are unknown. This study identifies substantial genetic differences between anatoxin-producing and non-anatoxin-producing strains, pointing to reduced metabolic flexibility in toxic strains, and potential dependence on cohabiting nontoxic strains. Results provide insights into the metabolic and evolutionary differences between toxic and nontoxic Microcoleus, which may assist in predicting and managing aquatic proliferations.
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Affiliation(s)
- Hwee Sze Tee
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Keith Bouma-Gregson
- U.S. Geological Survey, California Water Science Center, Sacramento, California, USA
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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30
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Vadeboncoeur Y, Moore MV, Stewart SD, Chandra S, Atkins KS, Baron JS, Bouma-Gregson K, Brothers S, Francoeur SN, Genzoli L, Higgins SN, Hilt S, Katona LR, Kelly D, Oleksy IA, Ozersky T, Power ME, Roberts D, Smits AP, Timoshkin O, Tromboni F, Zanden MJV, Volkova EA, Waters S, Wood SA, Yamamuro M. Blue Waters, Green Bottoms: Benthic Filamentous Algal Blooms Are an Emerging Threat to Clear Lakes Worldwide. Bioscience 2021; 71:1011-1027. [PMID: 34616235 PMCID: PMC8490932 DOI: 10.1093/biosci/biab049] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nearshore (littoral) habitats of clear lakes with high water quality are increasingly experiencing unexplained proliferations of filamentous algae that grow on submerged surfaces. These filamentous algal blooms (FABs) are sometimes associated with nutrient pollution in groundwater, but complex changes in climate, nutrient transport, lake hydrodynamics, and food web structure may also facilitate this emerging threat to clear lakes. A coordinated effort among members of the public, managers, and scientists is needed to document the occurrence of FABs, to standardize methods for measuring their severity, to adapt existing data collection networks to include nearshore habitats, and to mitigate and reverse this profound structural change in lake ecosystems. Current models of lake eutrophication do not explain this littoral greening. However, a cohesive response to it is essential for protecting some of the world's most valued lakes and the flora, fauna, and ecosystem services they sustain.
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Affiliation(s)
| | | | | | - Sudeep Chandra
- Biology Department and the Global Water Center, University of Nevada, Reno, Nevada, United States
| | - Karen S Atkins
- University of California, Davis, Davis, California, United States
| | - Jill S Baron
- US Geological Survey, Fort Collins, Colorado, United States
| | - Keith Bouma-Gregson
- California State Water Resources Control Board, Sacramento, California, United States
| | | | | | - Laurel Genzoli
- Flathead Lake Biological Station and the University of Montana, Missoula, Montana, United States
| | - Scott N Higgins
- International Institute for Sustainable Development, Experimental Lakes Area, with its head office in Winnipeg, Manitoba, Canada
| | - Sabine Hilt
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | | | | | | | - Ted Ozersky
- Large Lakes Observatory, University of Minnesota, Duluth, Minnesota, United States
| | - Mary E Power
- University of California, Berkeley, Berkeley, California, United States
| | - Derek Roberts
- San Francisco Estuary Institute, Richmond, California, United States
| | - Adrianne P Smits
- University of California, Davis, Davis, California, United States
| | - Oleg Timoshkin
- Siberian Branch of the Russian Academy of Sciences’ Limnological Institute, Irkutsk, Russian Federation
| | - Flavia Tromboni
- Biology Department and the Global Water Center, University of Nevada, Reno, Nevada, United States
| | - M Jake Vander Zanden
- Center for Limnology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Ekaterina A Volkova
- Siberian Branch of the Russian Academy of Sciences’ Limnological Institute, Irkutsk, Russian Federation
| | | | | | - Masumi Yamamuro
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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31
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Thomson-Laing G, Parai R, Kelly LT, Pochon X, Newnham R, Vandergoes MJ, Howarth JD, Wood SA. Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned ( Anguilla dieffenbachii) and short-finned ( Anguilla australis) eels in environmental samples. PeerJ 2021; 9:e12157. [PMID: 34692247 PMCID: PMC8483004 DOI: 10.7717/peerj.12157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
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Affiliation(s)
| | | | | | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Rewi Newnham
- Victoria University of Wellington, Wellington, New Zealand
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32
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Pearman JK, Biessy L, Howarth JD, Vandergoes MJ, Rees A, Wood SA. Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives. Mol Ecol Resour 2021; 22:877-890. [PMID: 34562066 DOI: 10.1111/1755-0998.13515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 01/04/2023]
Abstract
Lake sediments accumulate information on biological communities thus acting as natural archives. Traditionally paleolimnology has focussed on fossilized remains of organisms, however, many organisms do not leave fossil evidence, meaning major ecosystem components are missing from environmental reconstructions. Many paleolimnology studies now incorporate molecular methods, including investigating microbial communities using environmental DNA (eDNA), but there is uncertainty about the contribution of living organisms to molecular inventories. In the present study, we obtained DNA and RNA inventories from sediment spanning 700 years to investigate the contribution of past and active communities to the molecular signal from sedimentary archives. Additionally, a droplet digital PCR (ddPCR) targeting the 16S ribosomal RNA (16S rRNA) gene of the photosynthetic cyanobacterial genera Microcystis was used to explore if RNA signals were from legacy RNA. We posit that the RNA signal is a mixture of legacy RNA, dormant cells, living bacteria and modern-day trace level contaminants that were introduced during sampling and preferentially amplified. The presence of legacy RNA was confirmed by the detection of Microcystis in sediments aged to ~200 years ago. Recent comparisons between 16S rRNA gene metabarcoding and traditional paleo proxies showed that past changes in bacterial communities can be reconstructed from sedimentary archives. The recovery of RNA in the present study has provided new insights into the origin of these signals. However, caution is required during analysis and interpretation of 16S rRNA gene metabarcoding data especially in recent sediments were there are potentially active bacteria.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Andrew Rees
- University of Victoria, Wellington, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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33
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Zaiko A, Greenfield P, Abbott C, von Ammon U, Bilewitch J, Bunce M, Cristescu ME, Chariton A, Dowle E, Geller J, Ardura Gutierrez A, Hajibabaei M, Haggard E, Inglis GJ, Lavery SD, Samuiloviene A, Simpson T, Stat M, Stephenson S, Sutherland J, Thakur V, Westfall K, Wood SA, Wright M, Zhang G, Pochon X. Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Mol Ecol Resour 2021; 22:519-538. [PMID: 34398515 DOI: 10.1111/1755-0998.13485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/21/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia.,Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Cathryn Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Jaret Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Michael Bunce
- Environmental Protection Authority, Wellington, New Zealand
| | | | - Anthony Chariton
- Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Eddy Dowle
- School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jonathan Geller
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | | | | | - Emmet Haggard
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Graeme J Inglis
- National Institute of Water & Atmospheric Research Ltd (NIWA), Christchurch, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Tiffany Simpson
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Michael Stat
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Judy Sutherland
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Vibha Thakur
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristen Westfall
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Brasell KA, Howarth J, Pearman JK, Fitzsimons SJ, Zaiko A, Pochon X, Vandergoes MJ, Simon K, Wood SA. Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances. Mol Ecol 2021; 30:5137-5150. [PMID: 34379827 DOI: 10.1111/mec.16110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1,100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, c. 50 yrs) phases directly after the earthquakes and more stable (interseismic, c. 250 yr) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrates communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase likely represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.
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Affiliation(s)
- Katie A Brasell
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - Kevin Simon
- University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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Wood SA, Puddick J, Hawes I, Steiner K, Dietrich DR, Hamilton DP. Variability in microcystin quotas during a Microcystis bloom in a eutrophic lake. PLoS One 2021; 16:e0254967. [PMID: 34288957 PMCID: PMC8294494 DOI: 10.1371/journal.pone.0254967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/08/2021] [Indexed: 11/18/2022] Open
Abstract
Microcystis is a bloom-forming genus of cyanobacteria with some genotypes that produce highly toxic microcystin hepatotoxins. In waterbodies where biological and physical factors are relatively homogenous, toxin quotas (the average amount of toxin per cell), at a single point in time, are expected to be relatively constant. In this study we challenged this assumption by investigating the spatial distribution of microcystin quotas at a single point in time on two separate occasions in a lake with a major Microcystis bloom. Microcystis cell concentrations varied widely across the lake on both sampling occasions (730- and 137-fold) together with microcystin quotas (148- and 362-fold). Cell concentrations and microcystin quotas were strongly positively correlated (R2 = 0.89, P < 0.001, n = 28; R2 = 0.67, P < 0.001, n = 25). Analysis of Microcystis strains using high-throughput sequencing of the 16S-23S rRNA intergenic spacer region showed no relationship between microcystin quota and the relative abundance of specific sequences. Collectively, the results of this study indicate an association between microcystin production and cell density that magnifies the potential for bloom toxicity at elevated cell concentrations.
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Affiliation(s)
| | | | - Ian Hawes
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | | | | | - David P. Hamilton
- Australian Rivers Institute, Griffith University, Brisbane, Australia
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36
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Schallenberg LA, Pearman JK, Burns CW, Wood SA. Spatial abundance and distribution of picocyanobacterial communities in two contrasting lakes revealed using environmental DNA metabarcoding. FEMS Microbiol Ecol 2021; 97:fiab075. [PMID: 34100943 DOI: 10.1093/femsec/fiab075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater picocyanobacteria (Pcy) are important yet understudied components of lake ecosystems. Most previous studies have relied on cell abundances to assess Pcy dynamics in largely oligotrophic lakes, while little is known about spatial diversity and dynamics across different lake types. In the present study we assessed the horizontal-spatial abundance and community structure of Pcy in two contrasting (oligotrophic and hypertrophic) New Zealand lakes using epifluorescence microscopy and 16S rRNA metabarcoding. Pcy abundance and community composition differed significantly both between and within the oligotrophic and hypertrophic lakes. While spatial variability was observed in both study lakes, these differences were particularly pronounced in the oligotrophic, morphometrically complex Lake Wanaka where cell abundances were typically higher in bays than open-water sites and community structure differed significantly between sites. Community structuring appeared to be driven by localised environmental conditions, with different factors influencing each lake. These results suggest that single spot-samples are insufficient to gain an understanding of Pcy dynamics and consequently, phytoplankton dynamics in lakes.
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Affiliation(s)
- Lena A Schallenberg
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - John K Pearman
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
| | - Carolyn W Burns
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
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37
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Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR. Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data. J Microbiol Methods 2021; 188:106271. [PMID: 34146605 DOI: 10.1016/j.mimet.2021.106271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023]
Abstract
Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.
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Affiliation(s)
- Natascha Lewe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Syrie Hermans
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura T Kelly
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Barbara Weisbrod
- Human and Environmental Toxicology, Department of Biology, Universität Konstanz, 78457 Konstanz, Germany
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Robert A Keyzers
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand.
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Laroche O, Pochon X, Wood SA, Keeley N. Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments. Mol Ecol Resour 2021; 21:2264-2277. [PMID: 33971078 DOI: 10.1111/1755-0998.13426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have recently been developed which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alternative to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥1,200 m from Norwegian salmon farms, and three metabolic inference approaches (Paprica, Picrust2 and Tax4Fun2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed between approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomic data ranged from 0.52 and 0.60 to 0.76 and 0.79, respectively. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for Paprica and Tax4Fun2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.
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Affiliation(s)
- Olivier Laroche
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Nigel Keeley
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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Pearman JK, Thomson-Laing G, Howarth JD, Vandergoes MJ, Thompson L, Rees A, Wood SA. Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores. PLoS One 2021; 16:e0250783. [PMID: 33939728 PMCID: PMC8092796 DOI: 10.1371/journal.pone.0250783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- * E-mail:
| | | | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Andrew Rees
- Victoria University of Wellington, Wellington, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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Durán-Vinet B, Araya-Castro K, Chao TC, Wood SA, Gallardo V, Godoy K, Abanto M. Potential applications of CRISPR/Cas for next-generation biomonitoring of harmful algae blooms: A review. Harmful Algae 2021; 103:102027. [PMID: 33980455 DOI: 10.1016/j.hal.2021.102027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/01/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Research on harmful algal and cyanobacterial blooms (HABs and CHABs) has risen dramatically due to their increasing global distribution, frequency, and intensity. These blooms jeopardize public health, ecosystem function, sustainability and can have negative economic impacts. Numerous monitoring programs have been established using light microscopy, liquid chromatography coupled to mass spectrometry (LC-MS), ELISA, and spectrophotometry to monitor HABs/CHABs outbreaks. Recently, DNA/RNA-based molecular methods have been integrated into these programs to replace or complement traditional methods through analyzing environmental DNA and RNA (eDNA/eRNA) with techniques such as quantitative polymerase chain reaction (qPCR), fluorescent in situ hybridization (FISH), sandwich hybridization assay (SHA), isothermal amplification methods, and microarrays. These have enabled the detection of rare or cryptic species, enhanced sample throughput, and reduced costs and the need for visual taxonomic expertise. However, these methods have limitations, such as the need for high capital investment in equipment or detection uncertainties, including determining whether organisms are viable. In this review, we discuss the potential of newly developed molecular diagnosis technology based on Clustered Regularly Interspaced Short Palindromic Repeats/Cas proteins (CRISPR/Cas), which utilizes the prokaryotic adaptative immune systems of bacteria and archaea. Cas12 and Cas13-based platforms can detect both DNA and RNA with attomolar sensitivity within an hour. CRISPR/Cas diagnostic is a rapid, inexpensive, specific, and ultrasensitive technology that, with some further development, will provide many new platforms that can be used for HABs/CHABs biomonitoring and research.
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Affiliation(s)
- B Durán-Vinet
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile.
| | - K Araya-Castro
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - T C Chao
- Institute of Environmental Change & Society, Department of Biology, University of Regina, Wascana Parkway, 3737 Regina, Canada
| | - S A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | - V Gallardo
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - K Godoy
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Microscopy and Flow Cytometry Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - M Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
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Bhetuwal D, Matter J, Szumila-Vance H, Kabir ML, Dutta D, Ent R, Abrams D, Ahmed Z, Aljawrneh B, Alsalmi S, Ambrose R, Androic D, Armstrong W, Asaturyan A, Assumin-Gyimah K, Ayerbe Gayoso C, Bandari A, Basnet S, Berdnikov V, Bhatt H, Biswas D, Boeglin WU, Bosted P, Brash E, Bukhari MHS, Chen H, Chen JP, Chen M, Christy EM, Covrig S, Craycraft K, Danagoulian S, Day D, Diefenthaler M, Dlamini M, Dunne J, Duran B, Evans R, Fenker H, Fomin N, Fuchey E, Gaskell D, Gautam TN, Gonzalez FA, Hansen JO, Hauenstein F, Hernandez AV, Horn T, Huber GM, Jones MK, Joosten S, Karki A, Keppel C, Khanal A, King PM, Kinney E, Ko HS, Kohl M, Lashley-Colthirst N, Li S, Li WB, Liyanage AH, Mack D, Malace S, Markowitz P, Meekins D, Michaels R, Mkrtchyan A, Mkrtchyan H, Nazeer SJ, Nanda S, Niculescu G, Niculescu I, Nguyen D, Pandey B, Park S, Pooser E, Puckett A, Rehfuss M, Reinhold J, Santiesteban N, Sawatzky B, Smith GR, Sun A, Tadevosyan V, Trotta R, Wood SA, Yero C, Zhang J. Ruling out Color Transparency in Quasielastic ^{12}C(e,e^{'}p) up to Q^{2} of 14.2 (GeV/c)^{2}. Phys Rev Lett 2021; 126:082301. [PMID: 33709760 DOI: 10.1103/physrevlett.126.082301] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/15/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Quasielastic ^{12}C(e,e^{'}p) scattering was measured at spacelike 4-momentum transfer squared Q^{2}=8, 9.4, 11.4, and 14.2 (GeV/c)^{2}, the highest ever achieved to date. Nuclear transparency for this reaction was extracted by comparing the measured yield to that expected from a plane-wave impulse approximation calculation without any final state interactions. The measured transparency was consistent with no Q^{2} dependence, up to proton momenta of 8.5 GeV/c, ruling out the quantum chromodynamics effect of color transparency at the measured Q^{2} scales in exclusive (e,e^{'}p) reactions. These results impose strict constraints on models of color transparency for protons.
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Affiliation(s)
- D Bhetuwal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - J Matter
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - H Szumila-Vance
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M L Kabir
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Ent
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D Abrams
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - Z Ahmed
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - B Aljawrneh
- North Carolina A & T State University, Greensboro, North Carolina 27411, USA
| | - S Alsalmi
- Kent State University, Kent, Ohio 44240, USA
| | - R Ambrose
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - D Androic
- University of Zagreb, Zagreb, Croatia
| | - W Armstrong
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - A Asaturyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - K Assumin-Gyimah
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C Ayerbe Gayoso
- Mississippi State University, Mississippi State, Mississippi 39762, USA
- The College of William & Mary, Williamsburg, Virginia 23185, USA
| | - A Bandari
- The College of William & Mary, Williamsburg, Virginia 23185, USA
| | - S Basnet
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - V Berdnikov
- Catholic University of America, Washington, DC 20064, USA
| | - H Bhatt
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Biswas
- Hampton University, Hampton, Virginia 23669, USA
| | - W U Boeglin
- Florida International University, University Park, Florida 33199, USA
| | - P Bosted
- The College of William & Mary, Williamsburg, Virginia 23185, USA
| | - E Brash
- Christopher Newport University, Newport News, Virginia 23606, USA
| | | | - H Chen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - J P Chen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Chen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - E M Christy
- Hampton University, Hampton, Virginia 23669, USA
| | - S Covrig
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - K Craycraft
- University of Tennessee, Knoxville, Tennessee 37996, USA
| | - S Danagoulian
- North Carolina A & T State University, Greensboro, North Carolina 27411, USA
| | - D Day
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M Diefenthaler
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Dlamini
- Ohio University, Athens, Ohio 45701, USA
| | - J Dunne
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - B Duran
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - R Evans
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - H Fenker
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - N Fomin
- University of Tennessee, Knoxville, Tennessee 37996, USA
| | - E Fuchey
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T N Gautam
- Hampton University, Hampton, Virginia 23669, USA
| | - F A Gonzalez
- Stony Brook University, Stony Brook, New York 11794, USA
| | - J O Hansen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Hauenstein
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - A V Hernandez
- Catholic University of America, Washington, DC 20064, USA
| | - T Horn
- Catholic University of America, Washington, DC 20064, USA
| | - G M Huber
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - M K Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Joosten
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - A Karki
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C Keppel
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Khanal
- Florida International University, University Park, Florida 33199, USA
| | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - E Kinney
- University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - H S Ko
- Institut de Physique Nucleaire, Orsay, France
| | - M Kohl
- Hampton University, Hampton, Virginia 23669, USA
| | | | - S Li
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - W B Li
- The College of William & Mary, Williamsburg, Virginia 23185, USA
| | - A H Liyanage
- Hampton University, Hampton, Virginia 23669, USA
| | - D Mack
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Malace
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Markowitz
- Florida International University, University Park, Florida 33199, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Mkrtchyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - H Mkrtchyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - S J Nazeer
- Hampton University, Hampton, Virginia 23669, USA
| | - S Nanda
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - G Niculescu
- James Madison University, Harrisonburg, Virginia 22807, USA
| | - I Niculescu
- James Madison University, Harrisonburg, Virginia 22807, USA
| | - D Nguyen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - B Pandey
- Hampton University, Hampton, Virginia 23669, USA
| | - S Park
- Stony Brook University, Stony Brook, New York 11794, USA
| | - E Pooser
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Puckett
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - M Rehfuss
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - J Reinhold
- Florida International University, University Park, Florida 33199, USA
| | - N Santiesteban
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - B Sawatzky
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - G R Smith
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Sun
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - V Tadevosyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - R Trotta
- Catholic University of America, Washington, DC 20064, USA
| | - S A Wood
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - C Yero
- Florida International University, University Park, Florida 33199, USA
| | - J Zhang
- Stony Brook University, Stony Brook, New York 11794, USA
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Audrézet F, Zaiko A, Lear G, Wood SA, Tremblay LA, Pochon X. Biosecurity implications of drifting marine plastic debris: Current knowledge and future research. Mar Pollut Bull 2021; 162:111835. [PMID: 33220912 DOI: 10.1016/j.marpolbul.2020.111835] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS and pathogens rafting on marine plastic debris (MPD). Despite an increasing research interest and recent progress in characterizing the plastisphere, this manuscript highlights critical knowledge gaps and research priorities towards a better understanding of the biosecurity implications of MPD. We advocate for future research to (i) investigate plastisphere community succession and the factors influencing NIS propagules and pathogens recruitment through robust experimental investigations; (ii) combine microscopy and molecular approaches to effectively assess the presence of specific taxa; (iii) include additional genetic markers to thoroughly characterize the biodiversity associated with MPD and explore the presence of specific marine pests.
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Affiliation(s)
- François Audrézet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; School of Biological Sciences, University of Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Puddick J, van Ginkel R, Page CD, Murray JS, Greenhough HE, Bowater J, Selwood AI, Wood SA, Prinsep MR, Truman P, Munday R, Finch SC. Acute toxicity of dihydroanatoxin-a from Microcoleus autumnalis in comparison to anatoxin-a. Chemosphere 2021; 263:127937. [PMID: 32828056 DOI: 10.1016/j.chemosphere.2020.127937] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
The cyanobacterium Microcoleus autumnalis grows as thick benthic mats in rivers and is becoming increasingly prevalent around the world. M. autumnalis can produce high concentrations of anatoxins and ingestion of benthic mats has led to multiple dog deaths over the past two decades. M. autumnalis produces a suite of different anatoxin congeners including anatoxin-a (ATX), dihydroanatoxin-a, (dhATX), homoanatoxin-a and dihydrohomoanatoxin-a. Benthic mat samples often contain high levels of dhATX, but there is little toxicology information on this congener. In the present study, natural versions of dhATX and ATX were purified from cyanobacteria to determine the acute toxicity by different routes of administration using mice. Nuclear magnetic resonance spectroscopy was used to confirm the putative structure of dhATX. By intraperitoneal (ip) injection, the median lethal dose (LD50) for dhATX was 0.73 mg/kg, indicating a reduced toxicity compared to ATX (LD50 of 0.23 mg/kg). However, by oral administration (both gavage and feeding), dhATX was more toxic than ATX (gavage LD50 of 2.5 mg/kg for dhATX and 10.6 mg/kg for ATX; feeding LD50 of 8 mg/kg for dhATX and 25 mg/kg for ATX). The relative nicotinic acetylcholine receptor-binding affinities of ATX and dhATX were determined using the Torpedo electroplaque assay which showed consistency with the relative toxicity determined by ip injection. This work highlights that toxicity studies based solely on ip injection may not yield LD50 values that are relevant to those derived via oral administration, and hence, do not provide a good estimate of the risk posed to human and animal health in situations where oral ingestion is the likely route of exposure. The high acute oral toxicity of dhATX, and its abundance in M. autumnalis proliferations, demonstrates that it is an important environmental contaminant that warrants further investigation.
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Affiliation(s)
| | - Roel van Ginkel
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Carrie D Page
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - J Sam Murray
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Joel Bowater
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Penelope Truman
- Massey University, PO Box 756, Wellington, 6140, New Zealand
| | - Rex Munday
- AgResearch Limited, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
| | - Sarah C Finch
- AgResearch Limited, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
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Yero C, Abrams D, Ahmed Z, Ahmidouch A, Aljawrneh B, Alsalmi S, Ambrose R, Armstrong W, Asaturyan A, Assumin-Gyimah K, Ayerbe Gayoso C, Bandari A, Bane J, Basnet S, Berdnikov VV, Bericic J, Bhatt H, Bhetuwal D, Biswas D, Boeglin WU, Bosted P, Brash E, Bukhari MHS, Chen H, Chen JP, Chen M, Christy ME, Covrig S, Craycraft K, Danagoulian S, Day D, Diefenthaler M, Dlamini M, Dunne J, Duran B, Dutta D, Ent R, Evans R, Fenker H, Fomin N, Fuchey E, Gaskell D, Gautam TN, Gonzalez FA, Hansen JO, Hauenstein F, Hernandez AV, Horn T, Huber GM, Jones MK, Joosten S, Kabir ML, Karki A, Keppel CE, Khanal A, King P, Kinney E, Lashley-Colthirst N, Li S, Li WB, Liyanage AH, Mack DJ, Malace SP, Matter J, Meekins D, Michaels R, Mkrtchyan A, Mkrtchyan H, Nazeer SJ, Nanda S, Niculescu G, Niculescu M, Nguyen D, Nuruzzaman N, Pandey B, Park S, Perdrisat CF, Pooser E, Rehfuss M, Reinhold J, Sawatzky B, Smith GR, Sun A, Szumila-Vance H, Tadevosyan V, Wood SA, Zhang J. Probing the Deuteron at Very Large Internal Momenta. Phys Rev Lett 2020; 125:262501. [PMID: 33449750 DOI: 10.1103/physrevlett.125.262501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
We measure ^{2}H(e,e^{'}p)n cross sections at 4-momentum transfers of Q^{2}=4.5±0.5 (GeV/c)^{2} over a range of neutron recoil momenta p_{r}, reaching up to ∼1.0 GeV/c. We obtain data at fixed neutron recoil angles θ_{nq}=35°, 45°, and 75° with respect to the 3-momentum transfer q[over →]. The new data agree well with previous data, which reached p_{r}∼500 MeV/c. At θ_{nq}=35° and 45°, final state interactions, meson exchange currents, and isobar currents are suppressed and the plane wave impulse approximation provides the dominant cross section contribution. We compare the new data to recent theoretical calculations, where we observe a significant discrepancy for recoil momenta p_{r}>700 MeV/c.
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Affiliation(s)
- C Yero
- Florida International University, University Park, Florida 33199, USA
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D Abrams
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - Z Ahmed
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - A Ahmidouch
- North Carolina Agricultural and Technical State University, Greensboro, North Carolina 27411, USA
| | - B Aljawrneh
- North Carolina Agricultural and Technical State University, Greensboro, North Carolina 27411, USA
| | - S Alsalmi
- Kent State University, Kent, Ohio 44240, USA
| | - R Ambrose
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - W Armstrong
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - A Asaturyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), 2 Alikhanian Brothers Street, 0036, Yerevan, Armenia
| | - K Assumin-Gyimah
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C Ayerbe Gayoso
- College of William & Mary, Williamsburg, Virginia 23185, USA
| | - A Bandari
- College of William & Mary, Williamsburg, Virginia 23185, USA
| | - J Bane
- University of Tennessee, Knoxville, Tennessee 37996, USA
| | - S Basnet
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - V V Berdnikov
- Catholic University of America, Washington, D.C. 20064, USA
| | - J Bericic
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - H Bhatt
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Bhetuwal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Biswas
- Hampton University, Hampton, Virginia 23669, USA
| | - W U Boeglin
- Florida International University, University Park, Florida 33199, USA
| | - P Bosted
- College of William & Mary, Williamsburg, Virginia 23185, USA
| | - E Brash
- Christopher Newport University, Newport News, Virginia 23606, USA
| | | | - H Chen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - J P Chen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Chen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M E Christy
- Hampton University, Hampton, Virginia 23669, USA
| | - S Covrig
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - K Craycraft
- University of Tennessee, Knoxville, Tennessee 37996, USA
| | - S Danagoulian
- North Carolina Agricultural and Technical State University, Greensboro, North Carolina 27411, USA
| | - D Day
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M Diefenthaler
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Dlamini
- Ohio University, Athens, Ohio 45701, USA
| | - J Dunne
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - B Duran
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Ent
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R Evans
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - H Fenker
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - N Fomin
- University of Tennessee, Knoxville, Tennessee 37996, USA
| | - E Fuchey
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T N Gautam
- Hampton University, Hampton, Virginia 23669, USA
| | - F A Gonzalez
- Stony Brook University, Stony Brook, New York 11794, USA
| | - J O Hansen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Hauenstein
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - A V Hernandez
- Catholic University of America, Washington, D.C. 20064, USA
| | - T Horn
- Catholic University of America, Washington, D.C. 20064, USA
| | - G M Huber
- University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - M K Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Joosten
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M L Kabir
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - A Karki
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C E Keppel
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Khanal
- Florida International University, University Park, Florida 33199, USA
| | - P King
- Ohio University, Athens, Ohio 45701, USA
| | - E Kinney
- University of Colorado Boulder, Boulder, Colorado 80309, USA
| | | | - S Li
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - W B Li
- College of William & Mary, Williamsburg, Virginia 23185, USA
| | - A H Liyanage
- Hampton University, Hampton, Virginia 23669, USA
| | - D J Mack
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S P Malace
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J Matter
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Mkrtchyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), 2 Alikhanian Brothers Street, 0036, Yerevan, Armenia
| | - H Mkrtchyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), 2 Alikhanian Brothers Street, 0036, Yerevan, Armenia
| | - S J Nazeer
- Hampton University, Hampton, Virginia 23669, USA
| | - S Nanda
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - G Niculescu
- James Madison University, Harrisonburg, Virginia 22807, USA
| | - M Niculescu
- James Madison University, Harrisonburg, Virginia 22807, USA
| | - D Nguyen
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - N Nuruzzaman
- Rutgers University, New Brunswick, New Jersey 08854, USA
| | - B Pandey
- Hampton University, Hampton, Virginia 23669, USA
| | - S Park
- Stony Brook University, Stony Brook, New York 11794, USA
| | - C F Perdrisat
- College of William & Mary, Williamsburg, Virginia 23185, USA
| | - E Pooser
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Rehfuss
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - J Reinhold
- Florida International University, University Park, Florida 33199, USA
| | - B Sawatzky
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - G R Smith
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - A Sun
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - H Szumila-Vance
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Tadevosyan
- A.I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), 2 Alikhanian Brothers Street, 0036, Yerevan, Armenia
| | - S A Wood
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J Zhang
- Stony Brook University, Stony Brook, New York 11794, USA
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45
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Pearman JK, Biessy L, Thomson-Laing G, Waters S, Vandergoes MJ, Howarth JD, Rees A, Moy C, Pochon X, Wood SA. Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient. FEMS Microbiol Ecol 2020; 96:5822763. [PMID: 32310266 DOI: 10.1093/femsec/fiaa070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/18/2020] [Indexed: 01/04/2023] Open
Abstract
Lake surface sediments are dominated by microorganisms that play significant roles in biogeochemical cycling within lakes. There is limited knowledge on the relative importance of local environmental factors and altitude on bacterial and microeukaryotic community richness and composition in lake sediments. In the present study, surface sediment samples were collected from 40 lakes along an altitude gradient (2-1215 m). Microbial communities were characterized using 16S (bacteria) and 18S (microeukaryotes) rRNA gene metabarcoding. Bacterial and microeukaryotic richness were not correlated with altitude but instead to environmental variables (e.g. area of water in the catchment (bacteria: R = -0.43). For both bacteria and microeukaryotes, dissimilarity in the community structure had a higher correlation to combined environmental variables (without altitude) (bacteria: R = 0.53; microeukaryotes: R = 0.55) than altitude alone (bacteria: R = 0.34; microeukaryotes: R = 0.47). Sediment sulfur and productive grassland were important variables in determining the relative abundance of sulfate reducing bacteria. Nitrospira, was positively related to altitude but negatively to water column total organic carbon and the proportion of productive grassland in the catchment. Little overlap in amplicon sequence variants was shown amongst lakes. This has important considerations for management decisions, suggesting that to protect biodiversity, conservation of numerous lakes and lake types is required.
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Affiliation(s)
- John K Pearman
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Laura Biessy
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | - Sean Waters
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
| | | | - Jamie D Howarth
- Victoria University of Wellington, School of Geography, Environment and Earth Sciences, PO Box 600, Wellington, New Zealand
| | - Andrew Rees
- Victoria University of Wellington, School of Geography, Environment and Earth Sciences, PO Box 600, Wellington, New Zealand
| | - Chris Moy
- University of Otago, Department of Geology, PO Box 56, Dunedin, 9054, New Zealand
| | - Xavier Pochon
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand.,University of Auckland, Institute of Marine Science, Private Bag 92019, Auckland, 1142, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Coastal and Freshwater Group, 95 Halifax Street East, Nelson, 7010, New Zealand
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46
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Pearman JK, Keeley NB, Wood SA, Laroche O, Zaiko A, Thomson-Laing G, Biessy L, Atalah J, Pochon X. Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture. PeerJ 2020; 8:e10231. [PMID: 33194417 PMCID: PMC7597629 DOI: 10.7717/peerj.10231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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47
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Wood SA, Kelly L, Bouma-Gregson K, Humbert JF, Laughinghouse HD, Lazorchak J, McAllister T, McQueen A, Pokrzywinski K, Puddick J, Quiblier C, Reitz LA, Ryan K, Vadeboncoeur Y, Zastepa A, Davis TW. Toxic benthic freshwater cyanobacterial proliferations: Challenges and solutions for enhancing knowledge and improving monitoring and mitigation. Freshw Biol 2020; 65:1824-1842. [PMID: 34970014 PMCID: PMC8715960 DOI: 10.1111/fwb.13532] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
1. This review summarises knowledge on the ecology, toxin production, and impacts of toxic freshwater benthic cyanobacterial proliferations. It documents monitoring, management, and sampling strategies, and explores mitigation options. 2. Toxic proliferations of freshwater benthic cyanobacteria (taxa that grow attached to substrates) occur in streams, rivers, lakes, and thermal and meltwater ponds, and have been reported in 19 countries. Anatoxin- and microcystin-containing mats are most commonly reported (eight and 10 countries, respectively). 3. Studies exploring factors that promote toxic benthic cyanobacterial proliferations are limited to a few species and habitats. There is a hierarchy of importance in environmental and biological factors that regulate proliferations with variables such as flow (rivers), fine sediment deposition, nutrients, associated microbes, and grazing identified as key drivers. Regulating factors differ among colonisation, expansion, and dispersal phases. 4. New -omics-based approaches are providing novel insights into the physiological attributes of benthic cyanobacteria and the role of associated microorganisms in facilitating their proliferation. 5. Proliferations are commonly comprised of both toxic and non-toxic strains, and the relative proportion of these is the key factor contributing to the overall toxin content of each mat. 6. While these events are becoming more commonly reported globally, we currently lack standardised approaches to detect, monitor, and manage this emerging health issue. To solve these critical gaps, global collaborations are needed to facilitate the rapid transfer of knowledge and promote the development of standardised techniques that can be applied to diverse habitats and species, and ultimately lead to improved management.
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Affiliation(s)
| | | | - Keith Bouma-Gregson
- Office of Information Management and Analysis, California State Water Resources Control Board, Sacramento, California, United States of America
| | | | - H Dail Laughinghouse
- Fort Lauderdale Research and Education Center, University of Florida, Florida, USA
| | - James Lazorchak
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Monitoring and Modeling, Cincinnati, Ohio, United States of America
| | - Tara McAllister
- Te Pūnaha Matatini Centre of Research Excellence for Complex Systems, University of Auckland, Auckland, New Zealand
| | - Andrew McQueen
- Environmental Risk Assessment Branch, US Army Corps of Engineers, Engineering Research & Development Center, Vicksburg, Mississippi, United States of America
| | - Katyee Pokrzywinski
- Environmental Risk Assessment Branch, US Army Corps of Engineers, Engineering Research & Development Center, Vicksburg, Mississippi, United States of America
| | | | | | - Laura A Reitz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Ken Ryan
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Yvonne Vadeboncoeur
- Department of Biological Sciences, Wright State University, Ohio, United States of America
| | - Arthur Zastepa
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Ontario, Canada
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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48
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Androić D, Armstrong DS, Asaturyan A, Bartlett K, Beaufait J, Beminiwattha RS, Benesch J, Benmokhtar F, Birchall J, Carlini RD, Cornejo JC, Dusa SC, Dalton MM, Davis CA, Deconinck W, Dowd JF, Dunne JA, Dutta D, Duvall WS, Elaasar M, Falk WR, Finn JM, Forest T, Gal C, Gaskell D, Gericke MTW, Grames J, Gray VM, Grimm K, Guo F, Hoskins JR, Jones D, Jones MK, Jones RT, Kargiantoulakis M, King PM, Korkmaz E, Kowalski S, Leacock J, Leckey JP, Lee AR, Lee JH, Lee L, MacEwan S, Mack D, Magee JA, Mahurin R, Mammei J, Martin JW, McHugh MJ, Meekins D, Mei J, Mesick KE, Michaels R, Micherdzinska A, Mkrtchyan A, Mkrtchyan H, Morgan N, Narayan A, Ndukum LZ, Nelyubin V, van Oers WTH, Owen VF, Page SA, Pan J, Paschke KD, Phillips SK, Pitt ML, Radloff RW, Rajotte JF, Ramsay WD, Roche J, Sawatzky B, Seva T, Shabestari MH, Silwal R, Simicevic N, Smith GR, Solvignon P, Spayde DT, Subedi A, Subedi R, Suleiman R, Tadevosyan V, Tobias WA, Tvaskis V, Waidyawansa B, Wang P, Wells SP, Wood SA, Yang S, Zang P, Zhamkochyan S. Precision Measurement of the Beam-Normal Single-Spin Asymmetry in Forward-Angle Elastic Electron-Proton Scattering. Phys Rev Lett 2020; 125:112502. [PMID: 32976004 DOI: 10.1103/physrevlett.125.112502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
A beam-normal single-spin asymmetry generated in the scattering of transversely polarized electrons from unpolarized nucleons is an observable related to the imaginary part of the two-photon exchange process. We report a 2% precision measurement of the beam-normal single-spin asymmetry in elastic electron-proton scattering with a mean scattering angle of θ_{lab}=7.9° and a mean energy of 1.149 GeV. The asymmetry result is B_{n}=-5.194±0.067(stat)±0.082 (syst) ppm. This is the most precise measurement of this quantity available to date and therefore provides a stringent test of two-photon exchange models at far-forward scattering angles (θ_{lab}→0) where they should be most reliable.
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Affiliation(s)
- D Androić
- University of Zagreb, Zagreb, HR 10002, Croatia
| | | | - A Asaturyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - K Bartlett
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J Beaufait
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R S Beminiwattha
- Ohio University, Athens, Ohio 45701, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - J Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Benmokhtar
- Duquesne University, Pittburgh, Pennsylvania 15282, USA
| | - J Birchall
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - R D Carlini
- William & Mary, Williamsburg, Virginia 23185, USA
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J C Cornejo
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Dalton
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - C A Davis
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - W Deconinck
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J F Dowd
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J A Dunne
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - W S Duvall
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - M Elaasar
- Southern University at New Orleans, New Orleans, Louisiana 70126, USA
| | - W R Falk
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J M Finn
- William & Mary, Williamsburg, Virginia 23185, USA
| | - T Forest
- Louisiana Tech University, Ruston, Louisiana 71272, USA
- Idaho State University, Pocatello, Idaho 83209, USA
| | - C Gal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M T W Gericke
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Grames
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V M Gray
- William & Mary, Williamsburg, Virginia 23185, USA
| | - K Grimm
- William & Mary, Williamsburg, Virginia 23185, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - F Guo
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J R Hoskins
- William & Mary, Williamsburg, Virginia 23185, USA
| | - D Jones
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M K Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R T Jones
- University of Connecticut, Storrs-Mansfield, Connecticut 06269, USA
| | | | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - E Korkmaz
- University of Northern British Columbia, Prince George, British Columbia V2N4Z9, Canada
| | - S Kowalski
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J Leacock
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - J P Leckey
- William & Mary, Williamsburg, Virginia 23185, USA
| | - A R Lee
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - J H Lee
- William & Mary, Williamsburg, Virginia 23185, USA
- Ohio University, Athens, Ohio 45701, USA
| | - L Lee
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - S MacEwan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - D Mack
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J A Magee
- William & Mary, Williamsburg, Virginia 23185, USA
| | - R Mahurin
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Mammei
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - J W Martin
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - M J McHugh
- George Washington University, Washington, DC 20052, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J Mei
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - K E Mesick
- George Washington University, Washington, DC 20052, USA
- Rutgers, The State University of New Jersey, Piscataway, New Jersey 088754, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | | | - A Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - H Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - N Morgan
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | - A Narayan
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - L Z Ndukum
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - V Nelyubin
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - W T H van Oers
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - V F Owen
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S A Page
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Pan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - K D Paschke
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - S K Phillips
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - M L Pitt
- Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, USA
| | | | - J F Rajotte
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - W D Ramsay
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - J Roche
- Ohio University, Athens, Ohio 45701, USA
| | - B Sawatzky
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Seva
- University of Zagreb, Zagreb, HR 10002, Croatia
| | - M H Shabestari
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Silwal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - N Simicevic
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - G R Smith
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Solvignon
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D T Spayde
- Hendrix College, Conway, Arkansas 72032, USA
| | - A Subedi
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Subedi
- George Washington University, Washington, DC 20052, USA
| | - R Suleiman
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Tadevosyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - W A Tobias
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - V Tvaskis
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - B Waidyawansa
- Ohio University, Athens, Ohio 45701, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - P Wang
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - S P Wells
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - S A Wood
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Yang
- William & Mary, Williamsburg, Virginia 23185, USA
| | - P Zang
- Syracuse University, Syracuse, New York 13244, USA
| | - S Zhamkochyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
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49
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Biessy L, Pearman JK, Smith KF, Hawes I, Wood SA. Seasonal and Spatial Variations in Bacterial Communities From Tetrodotoxin-Bearing and Non-tetrodotoxin-Bearing Clams. Front Microbiol 2020; 11:1860. [PMID: 32849450 PMCID: PMC7419435 DOI: 10.3389/fmicb.2020.01860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/15/2020] [Indexed: 11/13/2022] Open
Abstract
Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, but the source remains uncertain. The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus stutchburyi that lives amongst toxic P. australis populations were also analyzed. Bacterial communities were characterized using 16S ribosomal RNA gene metabarcoding in P. australis sourced monthly from the Hokianga Harbor, a site known to have TTX-bearing clams, for 1 year, from ten sites with varying TTX concentrations around New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was detected in P. australis from sites all around New Zealand and in all P. australis collected monthly from the Hokianga Harbor. The toxin averaged 150 μg kg-1 over the year of sampling in the Hokianga Harbor but no TTX was detected in the A. stutchburyi samples from the same site. Bacterial species diversity differed amongst sites (p < 0.001, F = 5.9) and the diversity in siphon samples was significantly higher than in digestive glands (p < 0.001, F = 65.8). Spirochaetaceae (4-60%) and Mycoplasmataceae (16-78%) were the most abundant families in the siphons and the digestive glands, respectively. The bacterial communities were compared between sites with the lowest TTX concentrations and the Hokianga Harbor (site with the highest TTX concentrations), and the core bacterial communities from TTX-bearing individuals were analyzed. The results from both spatial and temporal studies corroborate with previous hypotheses that Vibrio and Bacillus could be responsible for the source of TTX in bivalves. The results from this study also indicate that marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), should be investigated further as potential TTX producers.
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Affiliation(s)
- Laura Biessy
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand.,Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.,New Zealand Food Safety Science and Research Centre, Palmerston North, New Zealand
| | - John K Pearman
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | - Kirsty F Smith
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | - Ian Hawes
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
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50
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Zaiko A, Wood SA, Pochon X, Biessy L, Laroche O, Croot P, Garcia-Vazquez E. Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses. Environ Sci Technol 2020; 54:8443-8454. [PMID: 32436694 DOI: 10.1021/acs.est.0c01931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21 day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate BW samples were collected every second day and size-fractionated (<2.7, 10, >50 μm). Measurements of adenosine triphosphate (ATP) and metabarcoding of environmental nucleic acid (DNA and RNA) analyses, complemented by microscopy and flow cytometry, were performed on each sample. Measured ATP concentrations exhibited high variance between replicates and a strong negative trend in the large (≥50 μm) fraction over the voyage. In concert with microscopy, the metabarcoding data indicated a die-off of larger metazoans during the first week of study and gradual reductions in dinoflagellates and ochrophytes. The ATP and metabarcoding data signaled persistent or increased cellular activity of heterotrophic bacteria and protists in the BW, which was supported by flow cytometry. The metabarcoding showed the presence of active bacteria in all size fractions, suggesting that the sequential filtration approach does not ensure taxonomical differentiation, which has implications for BW quality assessment. Although our data show that ATP and metabarcoding have potential for indicative BW screening for BW compliance monitoring, further research and technological development is needed to improve representativeness of sampling and deliver the unequivocal response criteria required by the international Ballast Water Management Convention.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
- Marine Research Institute, Klaipeda University, H.Manto 84, 92294 Klaipeda, Lithuania
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Olivier Laroche
- Benthic Resources, The Norwegian Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience (iCRAG), Earth and Ocean Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
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