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Author: Jackie Zorz Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Bacteria are important members of every marine ecosystem and the composition of their communities has implications for global biogeochemical cycling. The Northwest Atlantic Ocean is an ecologically and economically significant region that exhibits wide ranges in physiochemical parameters that vary seasonally. In this thesis the bacterial community structure of two areas within the Northwest Atlantic Ocean, the Scotian Shelf and the Bedford Basin, were analyzed using 16S rRNA gene sequencing. The Scotian Shelf was analyzed spatially over two time points. Environmental parameters of the region, seasonality, and depth were found to heavily influence community structure. In the Bedford Basin, a weekly bacterial time series was established and the first year of data from the deepest samples were analyzed. The deep basin exhibited seasonal patterns with respect to community similarity, diversity, and composition. Overall, these datasets provide novel information regarding community composition and drivers of community shifts in this region.
Author: Jackie Zorz Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Bacteria are important members of every marine ecosystem and the composition of their communities has implications for global biogeochemical cycling. The Northwest Atlantic Ocean is an ecologically and economically significant region that exhibits wide ranges in physiochemical parameters that vary seasonally. In this thesis the bacterial community structure of two areas within the Northwest Atlantic Ocean, the Scotian Shelf and the Bedford Basin, were analyzed using 16S rRNA gene sequencing. The Scotian Shelf was analyzed spatially over two time points. Environmental parameters of the region, seasonality, and depth were found to heavily influence community structure. In the Bedford Basin, a weekly bacterial time series was established and the first year of data from the deepest samples were analyzed. The deep basin exhibited seasonal patterns with respect to community similarity, diversity, and composition. Overall, these datasets provide novel information regarding community composition and drivers of community shifts in this region.
Author: Taylor Priest Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
The Arctic Ocean is undergoing irreversible perturbations as a result of accelerated climate warming. Of major significance is the expanding influence of Atlantic water that expedites sea-ice decline, alters stratification and vertical mixing of the water column and facilitates northward expansion of temperate biota. Our understanding on how these processes will impact biological communities is severely limited. The Fram Strait is the primary entry route for Atlantic water into the Arctic Ocean and exit point for polar water and sea-ice. With the presence of two major current systems combined with horizontal mixing processes, the Fram Strait is characterised by a longitudinal gradient of hydrographic regimes reflective of Arctic, mixed and Atlantic conditions. This provides an invaluable opportunity to study the ecology of microbes over an environmental gradient and under changing conditions. Furthermore, given its high-latitude position, it also facilitates investigations on how dramatic seasonal transformations in conditions, such as sea-ice cover and light availability, influence microbes in the context of water mass history. This thesis provides an ecological characterisation of microbial communities over temporal and spatial scales in the Fram Strait in an effort to address these topics. In Chapter II, we employed metagenomics from short- and long-read sequencing platforms to gain insights into microbial community composition across water masses in the Fram Strait. As that study incorporated the first PacBio HiFi (long-read) metagenomes from the marine environment, it was necessary to perform a methodological comparison. We show that using PacBio HiFi metagenomes, we are able to recover more metagenome-assembled genomes (MAGs) that, on average, are more complete, less fragmented and more frequently contain complete rRNA gene operons compared to using short-read metagenomes. This not only influenced our investigative toolkit throughout the remainder of this thesis but provides valuable data for future considerations on using long-read metagenomics in the study of marine microbial ecology. From the analysis conducted in Chapter II, we observed a flavobacterial clade that is commonly associated with coastal temperate ecosystems, the NS5 Marine Group, to be prominent in high-latitude waters. This motivated us to delve deeper into this group and understand their diversity and function. By combining cultivation, metagenomics, epifluorescence and transmission electron microscopy, we were able to delineate this group into four novel candidate genera and evidence distinctions in function and spatiotemporal dynamics at the species and genus level (Chapter III). In that study, we also presented the first pure isolate and complete genome for a member of the NS5 Marine Group. In Chapter IV, we performed the first high-resolution temporal analysis on microbial taxonomy and function in Arctic polar waters. Using a four-year 16S amplicon dataset and one annual cycle of PacBio HiFi metagenomes, we evidenced that Atlantic water influx and sea-ice cover had a profound impact on the composition and function of microbial communities. Based on their omnipresence irrespective of conditions, we also identified a small fraction of the community that likely represents the resident microbiome of the Fram Strait. Furthermore, we showed that a transition to low-ice and high Atlantic water influx shifted the community to one dominated by heterotrophic clades that are functionally linked to phytoplankton-derived organic matter. Our findings suggest that the continued expansion of Atlantic water into the Arctic Ocean will be reflected in a Biological Atlantification of the microbial community, with populations adapted to Arctic conditions exhibiting reduced ecological niche space. These changes will have implications for the future ecosystem functioning and the carbon cycle. In Chapter V of this thesis, we combined metagenomics and metatranscriptomics with analytical techniques to characterise the carbohydrate fraction of particulate organic matter and carbohydrate utilisation by microbes in the Atlantic waters of the Fram Strait during late summer. A high spatial heterogeneity was observed in both carbohydrates and their utilisation, which indicated patchiness in local productivity and a responsive microbial community. Carbohydrate utilisation was dominated by distinct microbial assemblages across sampling sites and consisted of populations making use of labile (communal) and more complex (specialist) substrates. We therein proposed that local biological and physical processes are important for continuing to shape the availability and utilisation of carbohydrates into the late summer. In an effort to clearly and concisely convey the main findings from this thesis in the context of its original aims, a detailed description on the current and future state of the Fram Strait and Arctic Ocean microbiome is provided in the discussion. In addition, insights and recommendations on how to apply long-read metagenomes to answer questions on microbial ecology is provided, given its fundamental importance for this thesis and its relative infancy in environmental research applications. Lastly, owing to it representing an underlying theme throughout much of the research conducted, a discussion on the ecological niche concept is provided along with a proposal for its redefinition in marine microbial ecology.
Author: Rana Omer Bashwih Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Marine microbial communities are complex, and represent a serious analytical challenge. The Bayesian model for inference of microbial community structure (BioMiCo) was used to characterize microbial populations using 16S rRNA within polar, tropical, and temperate environmental zones. Global-scale and local analyses were performed on 356 microbial samples and 72853 OTUs within the ICOMM database. Global analysis showed that polar and tropical zones had distinct community structures with high predictive value and little seasonal variation, although seasonal variation was noticeable in the temperate zone. Local analysis on polar communities demonstrated that there were distinct community structures for the Arctic and Antarctic zones. Within the North Atlantic, temporal heterogeneity differed locally, and this impeded the predictive value of models for the entire North Atlantic. Training a model on a single, well-sampled, North Atlantic site, L4 in the English Channel, substantially improved the predictive value of the model. Finally, the model for the L4 site had predictive value for other English Channel sites, but not for more distant sites within the western and eastern North Atlantic. This result appears to be due to differences among North Atlantic sites in the timing of their seasonal community transitions, and because most other sites have not been nearly as well sampled as the L4 site. The only other well-sampled site in the North Atlantic (Bedford Basin) also exhibits regular seasonal transitiona from year to year. Taken together, these results suggest that environmental changes are the primary drivers of marine biogeographic patterns within the North Atlantic. Four methodological investigations were applied to Arctic and Antarctic samples, and to the samples from L4 station in the English Channel, for the purpose of exploring the impact of how users might choose to make inferences using BioMiCo. The first was an exploration of different ways of defining the predominant OTUs within an assemblage. The size of the assemblage was very sensitive to the method. I recommend defining predominant OTUs as those having >0.01 posterior probability, as this was the most conservative. The second was an exploration of the impact of "burn-in". As expected, increasing burin-in yielded more stable assemblages; however, the burn-in did not need to exceed 1000 iterations. The third was an exploration the effect of training and testing design on prediction of Arctic and Antarctic samples. The results showed that better predictions were obtained from larger training sets of data. However, training on more than 2/3 of the data did not generate significant improvement. Thus, designs such as leave-one-out cross validation can be reserved for cases where the total sample size is very small. Otherwise, uses should run several replicates on data randomly divided into 2/3 training sets and 1/3 test sets. The fourth explored the effect of pre-specifying different numbers of assemblages (the value of L within the model). The results showed that running 25 communities was sufficient. In conclusion, the choices that users make when running the MCMC can impact their results, but, the approach is robust and good results can be obtained with just L=25 if the training data is of a sufficient size, and if a sufficient amount of burn-in is discarded.
Author: Stephen J. Hawkins Publisher: Cambridge University Press ISBN: 110841608X Category : Nature Languages : en Pages : 535
Book Description
A comprehensive account of how abiotic and biotic interactions shape patterns of coastal marine biodiversity and ecosystem processes globally.
Author: Magda Guadalupe Cardozo-Mino Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
The anthropogenic emissions of CO2 and other climate-active gases lead to a steep increase of global temperatures. Global climate change is particularly amplified in the Arctic (e.g., Serreze et al., 2009; Serreze and Barry, 2011). Increasing temperatures and the rapid sea ice decline have shown profound effects on life in the Arctic ecosystem (Wassmann et al., 2011). Climate model predictions suggest a seasonally sea ice-free Arctic well before the first half of this century (Overland and Wang, 2013; Docquier and Koenigk, 2021). The composition, structure and function of the Arctic microbiome will be altered with distinct effects on the marine system, on primary productivity, carbon fluxes and food web structures. Changes in the composition and structure of primary producers were already observed in Fram Strait (Nöthig et al., 2015), the boundary and highly dynamic zone between the Atlantic and the Arctic Ocean. These changes were reflected in the export flux of particulate organic matter (Lalande et al., 2013), also observable in the benthic communities (Jacob, 2014). Thus, understanding how the microbial communities changed over time under different environmental conditions is a scientific task needed to assess future changes in the Arctic ecosystem. This thesis aimed to understand the composition, distribution and function of bacteria, archaea and eukaryotic communities in Fram Strait across different spatial and temporal scales and their relationship with environmental variables. The overall objective was to identify signature groups and key factors of change, to provide a baseline to the effects of climate change and sea ice retreat. It provides a comprehensive overview of the Arctic microbiome by the incorporation of seawater, sinking particles and sea ice samples to identify key microbial indicators of change and environmental drivers in these communities. Samples were obtained in the frame work of the Long-Term Ecological Research (LTER) site HAUSGARTEN and the FRontiers in Marine Monitoring (FRAM) program. 8 The results of Chapter I and Chapter II highlight the usage of methods free of compositional- bias and meta'omics approaches necessary to understand the role of microbial communities. The observations in Chapter I revealed that different water masses characterized by different physicochemical conditions harboured different active microbial communities. A late phytoplankton bloom dominated by diatoms in the surface waters of the eastern Fram Strait was identified, where members of the Bacteroidetes, Alteromonadales, Oceanospirillales and Rhodobacterales were significantly active. Abundant transcripts of transporters and fundamental cellular functions supported the degradation of organic matter. The deeper waters of Atlantic origin were marked by strong chemolithotrophic activities by members of Thaumarchaeota. In Chapter II I analysed bacterial and archaeal groups in deep-sea waters that benefitted from a phytoplankton bloom at the surface. Chapter III studied the development of microbial composition of sinking particles using a 12-year time-series study. The presence of sea ice and the passing warm anomaly were the drivers of change in these communities. In Chapter IV, microcosm experiments revealed bacterial taxa that responded to eukaryotes and substrates sourced from the sea ice during sea ice melt in seawater. Altogether, the results of this thesis provide baseline knowledge to better assess the effects of climate change on the Arctic microbiome and the consequences for ecosystem functioning and carbon cycling.
Author: Claudia Maturana Martínez Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Southern high latitudes marine ecosystems (HLME) are highly sensitive to climate change, impacting physical, chemical, and biological processes, however, their prominent role in climate modulation and water masses circulation, contrast with the relatively low number of studies on their functioning. Relatively few studies on bacterioplankton community structure have been reported for southern Chilean Patagonia and for the Southern Ocean (SO) on a large scale, and none have targeted the active fraction of the bacterioplankton community. We used 16S rRNA sequencing to analyze and describe the community structure of the active bacterioplankton communities in southern HLME. The main objective of this thesis was to characterize de diversity and abundance of bacterioplankton communities along environmental and geographical gradients in southern HLME. First, we investigated whether nearby fjords of the southern Chilean Patagonia, with similar climate and location but different freshwater inflows, had different communities. Second, we investigated interannual changes experienced by the bacterioplankton community of the Yendegaia fjord. Third, we examined the large-scale spatial structure of the bacterioplankton community along a transect across the Pacific sector of the SO. Ours results show that southern polar bacterioplanktonic communities are structured according to physical, chemical, and biological parameters characteristic of the area. In addition, we also demonstrated that changes in environmental, spatial, and temporal parameters affect the structure of bacterioplanktonic communities. Thus, highlighting the importance of microbial ecology studies in areas sensitive to global climate change such as southern HLME.
Author: Jackie Zorz
Author: Jackie Zorz
Author: Heba El-Swais
Author: Ryan Matthew John Murphy
Author: Taylor Priest
Author: Rana Omer Bashwih
Author: Stephen J. Hawkins
Author: Kimberley F. Keats
Author: Magda Guadalupe Cardozo-Mino
Author: Claudia Maturana Martínez
Author: Mark S. Demarest