Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is ...limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.
Nitrification, the microbial oxidation of ammonium to nitrate, is a central part of the nitrogen cycle. In the ocean's surface layer, the process alters the distribution of inorganic nitrogen species ...available to phytoplankton and produces nitrous oxide. A widely held idea among oceanographers is that nitrification is inhibited by light in the ocean. However, recent evidence that the primary organisms involved in nitrification, the ammonia-oxidizing archaea (AOA), are present and active throughout the surface ocean has challenged this idea. Here we show, through field experiments coupling molecular genetic and biogeochemical approaches, that competition for ammonium with phytoplankton is the strongest regulator of nitrification in the photic zone. During multiday experiments at high irradiance a single ecotype of AOA remained active in the presence of rapidly growing phytoplankton. Over the course of this three day experiment, variability in the intensity of competition with phytoplankton caused nitrification rates to decline from those typical of the lower photic zone (60 nmol L-1 d-1) to those in well-lit layers (<1 nmol L-1 d-1). During another set of experiments, nitrification rates exhibited a diel periodicity throughout much of the photic zone, with the highest rates occurring at night when competition with phytoplankton is lowest. Together, the results of our experiments indicate that nitrification rates in the photic zone are more strongly regulated by competition with phytoplankton for ammonium than they are by light itself. This finding advances our ability to model the impact of nitrification on estimates of new primary production, and emphasizes the need to more strongly consider the effects of organismal interactions on nutrient standing stocks and biogeochemical cycling in the surface of the ocean.
Declining oxygen in the global ocean and coastal waters Breitburg, Denise; Levin, Lisa A; Oschlies, Andreas ...
Science (American Association for the Advancement of Science),
01/2018, Letnik:
359, Številka:
6371
Journal Article, Web Resource
Recenzirano
Odprti dostop
Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and ...coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.
Marine photosynthetic plankton are responsible for approximately 50 petagrams (10(15)) of carbon per year of net primary production, an amount equivalent to that on land. This primary production ...supports essentially all life in the oceans and profoundly affects global biogeochemical cycles and climate. This review discusses the general distribution of primary production in the sea, the processes that regulate this distribution, and how marine primary production is sensitive to climate variability and change. Statistical modes of ocean variability and their characteristic interannual to multi-decadal timescales over the last century are described. Recent in situ and satellite time-series of primary production can be clearly linked to interannual ocean variability. Global marine primary production appears to have increased over the past several decades in association with multi-decadal variations. A paleoclimate record extends discussion to the centennial scale, providing contrasting insights into how marine primary production might vary in the future.
Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic ...interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015-2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies.
•Seasonal regulation of primary production (PP) in upwelling systems is investigated.•Examined drivers are nitrate and iron supply, light, physical export, and temperature.•The ratio of nitrate ...supply to PP is an indicator of nitrate vs. other regulations.•PP seasonal regulation is highly variable in space and time and across systems.
The regulation of seasonal satellite-derived primary production (PP) was investigated within a 150km coastal box in four eastern boundary upwelling systems (EBUS): California, Peru, Northwest Africa and Benguela. The following regulating factors were considered: (1) wind-driven nitrate supply; (2) iron supply inferred from proxies (shelf mud belt width, modeled atmospheric iron deposition, river discharge); (3) temperature; (4) light and (5) physical export consisting of offshore export, eddy-driven and wind-driven subduction. The ratio of potential new production (carbon-equivalent of nitrate supply) to primary production, termed the N-ratio, is shown to be an indicator of PP limitation by nitrate supply (low N-ratios) vs. inhibition by other factors (high N-ratios). The factors regulating PP were assessed by analyzing the N-ratios and computing spatial correlations between PP and each factor each month. The regulation of primary production was found to vary spatially, seasonally and from one EBUS to another. Macronutrient supply is shown to be the dominant regulating factor off Northwest Africa and during some seasons and locations in other systems. Light regulation within the mixed layer occurs in all EBUS in winter but may only inhibit PP (high N-ratios) off Peru and Benguela. Evidence for iron limitation was found in each EBUS (except Northwest Africa) at varying levels and was greatest off Peru during austral winter when iron demand by phytoplankton increases due to low light levels. Rapid offshore advection combined with wind-driven and/or eddy-driven subduction may inhibit PP off California. A simple generalization regarding the regulation of primary production in EBUS is not forthcoming.
A simple combination of wind‐driven nutrient upwelling, surface currents, and plankton growth/grazing equations generates zooplankton patchiness and hotspots in coastal upwelling regions. Starting ...with an initial input of nitrate from coastal upwelling, growth and grazing equations evolve phytoplankton and zooplankton over time and space following surface currents. The model simulates the transition from coastal (large phytoplankton, e.g., diatoms) to offshore (picophytoplankton and microzooplankton) communities, and in between generates a large zooplankton maximum. The method was applied to four major upwelling systems (California, Peru, Northwest Africa, and Benguela) using latitudinal estimates of wind‐driven nitrate supply and satellite‐based surface currents. The resulting zooplankton simulations are patchy in nature; areas of high concentrations coincide with previously documented copepod and krill hotspots. The exercise highlights the importance of the upwelling process and surface currents in shaping plankton communities.
Key Points
Plankton growth and grazing equations initialized by coastal nitrate supply represent offshore plankton succession in upwelling systems
When coupled with surface currents, the model simulates a patchy zooplankton distribution and known zooplankton hotspots
Surface currents are a key driver of zooplankton hotspots
Plain Language Summary
Copepods and krill are important prey species for a diverse array of predators and a key link in oceanic food webs. These zooplankton concentrate in “hotspots” that draw fish, marine mammals, and other predators. Here we present results from a simple ecosystem model that is coupled to winds and surface currents estimated from satellite. When applied to coastal upwelling systems (California, Peru, Northwest Africa, and Benguela), the model predicts locations of zooplankton hotspots that are very similar to those identified from ship‐based surveys. The results indicate that surface currents are a key driver of zooplankton spatial distribution.
In the southeastern tropical Pacific anchovy (Engraulis ringens) and sardine (Sardinops sagax) abundance have recently fluctuated on multidecadal scales and food and temperature have been proposed as ...the key parameters explaining these changes. However, ecological and paleoecological studies, and the fact that anchovies and sardines are favored differently in other regions, raise questions about the role of temperature. Here we investigate the role of oxygen in structuring fish populations in the Peruvian upwelling ecosystem that has evolved over anoxic conditions and is one of the world's most productive ecosystems in terms of forage fish. This study is particularly relevant given that the distribution of oxygen in the ocean is changing with uncertain consequences.
A comprehensive data set is used to show how oxygen concentration and oxycline depth affect the abundance and distribution of pelagic fish. We show that the effects of oxygen on anchovy and sardine are opposite. Anchovy flourishes under relatively low oxygen conditions while sardine avoid periods/areas with low oxygen concentration and restricted habitat. Oxygen consumption, trophic structure and habitat compression play a fundamental role in fish dynamics in this important ecosystem.
For the ocean off Peru we suggest that a key process, the need to breathe, has been neglected previously. Inclusion of this missing piece allows the development of a comprehensive conceptual model of pelagic fish populations and change in an ocean ecosystem impacted by low oxygen. Should current trends in oxygen in the ocean continue similar effects may be evident in other coastal upwelling ecosystems.
Significance Microbes drive biogeochemical cycles across the globe, collectively playing a central role in shaping the biosphere. Despite their immense importance, the in situ activities of ...communities of microbes, in particular uncultivated lineages of “microbial dark matter,” remain poorly elucidated. In this study, we report that common temporal and ecological dynamics underpin disparate marine microbial communities, providing the first evidence that trans-Pacific diurnal transcriptional patterns in these communities may regulate ecological and biogeochemical processes across the ocean. In total, our findings indicate a remarkable regularity in the timing of community-wide activity in the ocean, and suggest that global patterns of a variety of biogeochemical transformations may be temporally predictable and governed by structured ecological determinants.
Planktonic microbial communities in the ocean are typically dominated by several cosmopolitan clades of Bacteria , Archaea , and Eukarya characterized by their ribosomal RNA gene phylogenies and genomic features. Although the environments these communities inhabit range from coastal to open ocean waters, how the biological dynamics vary between such disparate habitats is not well known. To gain insight into the differential activities of microbial populations inhabiting different oceanic provinces we compared the daily metatranscriptome profiles of related microbial populations inhabiting surface waters of both a coastal California upwelling region (CC) as well as the oligotrophic North Pacific Subtropical Gyre (NPSG). Transcriptional networks revealed that the dominant photoautotrophic microbes in each environment ( Ostreococcus in CC, Prochlorococcus in NPSG) were central determinants of overall community transcriptome dynamics. Furthermore, heterotrophic bacterial clades common to both ecosystems (SAR11, SAR116, SAR86, SAR406, and Roseobacter ) displayed conserved, genome-wide inter- and intrataxon transcriptional patterns and diel cycles. Populations of SAR11 and SAR86 clades in particular exhibited tightly coordinated transcriptional patterns in both coastal and pelagic ecosystems, suggesting that specific biological interactions between these groups are widespread in nature. Our results identify common diurnally oscillating behaviors among diverse planktonic microbial species regardless of habitat, suggesting that highly conserved temporally phased biotic interactions are ubiquitous among planktonic microbial communities worldwide.
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