Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition (original) (raw)
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Journal of Marine Systems, 2013
Coastal upwelling systems play an essential role in bringing cold and nutrient-rich water into the euphotic zone, hence enhancing the biological productivity of the world's oceans. We describe a "cryptic" upwelling occurring in South Australian waters, in which cold upwelled waters do not reach surface waters and do not exhibit a sea surface temperature (SST) signature. Due to the wide continental shelf (ca. 100 km), upwelled waters form a sub-surface cold water pool and are forced north-west after a secondary event. Using flow cytometry we investigated the abundance and composition of viruses, heterotrophic bacteria and pico-phytoplankton within upwelling affected and unaffected waters. Our results identified the presence of upwelled waters at and below the Deep-Chlorophyll Maximum (DCM), where water temperature was at least 4°C colder than surface waters. In contrast to previous studies, no significant differences were observed between upwelled and non-upwelled waters for most individual viral, bacterial and pico-phytoplankton sub-groups. However, one viral, one bacterial and two pico-phytoplankton sub-groups were significantly more abundant at the DCM. This indicates the presence of depth-and population-specific shifts in abundance and potential niche partitioning of these cytometrically-defined sub-groups that may be related to their host organisms and/or resource availability.
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Upwelling, a common oceanographic event, can make great contributions, directly or indirectly, to deep ocean carbon sequestration. However, the extent of its contribution indirectly depends on the composition of microbial communities and the interactions between bacterioplankton and other microorganisms. This study provides insights into the influence of upwelling on bacterioplankton at the whole community level and predicts their potential functional profiles. The α diversity of the bacterial community exhibited no significant differences between the upwelling area and non-upwelling area, while the community composition varied clearly in different habitats. Proteobacteria, Cyanobacteria, Bacteroidota, Firmicutes, and Actinobacteria were the five dominant phyla in all of the habitats. The proportions of members of Firmicutes were increased whereas Cyanobacteria were reduced in upwelling water. However, the percentage of Cyanobacteria was enhanced in the upwelling deep water. Functio...
Variability in bacterial community structure during upwelling in the coastal ocean
Hydrobiologia, 1999
Over the last 30 years, investigations at the community level of marine bacteria and phytoplankton populations suggest they are tightly coupled. However, traditional oceanographic approaches cannot assess whether associations between specific bacteria and phytoplankton exist. Recently, molecular based approaches have been implemented to characterize specific members of different marine bacterial communities. Yet, few molecular-based studies have examined coastal upwelling situations.
The ISME Journal, 2012
and 5 Informatics, J Craig Venter Institute, Rockville, MD, USA Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrientrich water into surface ocean microbial communities. The data set consists of B5.8 million predicted proteins across seven sites, from three different size classes: 0.1-0.8, 0.8-3.0 and 3.0-200.0 lm. Taxonomic and metabolic analyses suggest that sequences from the 0.1-0.8 lm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8-200 lm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.
Marine Microbial Community Composition During the Upwelling Season in the Southern Benguela
Frontiers in Marine Science, 2020
The microbial communities of the southern Benguela upwelling region were sampled quarterly through 1 year, with sampling for prokaryotes taking place in May, September, November and February, spanning the 2015-2016 upwelling season. Picoeukaryote samples were taken in November and February only. Community dynamics were assessed at stations both inside and outside a typical upwelling site. 16S and 18S rRNA amplicon results, respectively, revealed differences in both bacterioplankton and picoeukaryote communities in both space and time (season). There was a significant difference between sites in picoeukaryote community structure and diversity during the upwelling season in February, but not in November. Prokaryote community structure showed significant changes by water type as well as by sampling time or site. The parasitic dinoflagellate, Syndiniales, dominated February samples, and diatoms (Mediophyceae) mostly occurred in November samples, with nitrate driving community structure. Prokaryote results revealed presence of Nitrosopumillus, an ammonium oxidizer, offshore in February. Nitrospina sp., a nitrite oxidizer, was also present in September in hypoxic and deep water samples. This study reveals significant changes in community variability, leading to shifts within interspecies interactions in this region in response to upwelling events. This has far reaching implications with regard to biogeochemical cycling and ecosystem functioning at the microbial level.
Viruses as regulators of nutrient cycles in aquatic environments
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Viruses are abundant and dynamic members of marine environments. The persistence of viral communities in aquatic systems requires the daily destruction of a significant proportion of the bacterial and phytoplankton populations. While the destruction of host cells by viruses has several implications, one of the most important effects may be the role viruses play as regulators of nutrient cycles. Over the last several years we have obtained estimates of viral turnover rates and viral production for a variety of environments. We have used these estimates to infer the remobilization of nutrients in marine systems attributable to viral lysis. For example, viral lysis of bacterioplankton in the western Gulf of Mexico was estimated to liberate 0.12 to 0.55 µg C L -1 d -1 in offshore waters and 0.72 to 5.2 µg C L -1 d -1 in coastal waters. Similarly, virally mediated carbon release in the Strait of Georgia, British Columbia, ranged from 1.0 to 8.3 µg C L -1 d -1 , with the highest estimates associated with strong tidal mixing. Viruses also play an important role in the remobilization of organic nutrients and trace elements. For example, in the Strait of Georgia viral lysis was estimated to result in the remobilization of 0.3 to 1.7 ug L -1 d -1 of organic nitrogen, 0.03 to 0.14 ug L -1 d -1 of organic phosphorus and 0.06 to 0.33 ng L -1 d -1 of organically complexed iron. The information presented demonstrates the importance of including viral processes in models of marine carbon and nutrient fluxes.
Nature Communications
The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong...