Download or read book Investigating Bacterial Community Structure Over Temporal and Spatial Scales in the Northwest Atlantic Ocean written by Jackie Zorz and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Temporal Bacterial Community Dynamics in the Coastal Northwest Atlantic Ocean written by Heba El-Swais and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Spatial and Temporal Variation in the Population Structures Carbon Use and Climate Responses of Heterotrophic Microbial Communities in Coastal and Offshore Northwest Atlantic Sites written by Ryan Matthew John Murphy and published by . This book was released on 2010 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book INFERENCE AND INVESTIGATION OF MARINE MICROBIAL COMMUNITY STRUCTURES IN THE GLOBAL OCEANS written by Rana Omer Bashwih and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Molecular Ecological Characterisation of High latitude Bacterioplankton written by Taylor Priest and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Interactions in the Marine Benthos written by Stephen J. Hawkins and published by Cambridge University Press. This book was released on 2019-08-29 with total page 535 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive account of how abiotic and biotic interactions shape patterns of coastal marine biodiversity and ecosystem processes globally.
Download or read book Microbial Community Structure in the Northwest Atlantic Ocean as Determined by Fluorescence in Situ Hybridization written by Kimberley F. Keats and published by . This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Temporal and Spatial Dynamics of Marine Microorganisms in Ice covered Seas written by Magda Guadalupe Cardozo-Mino and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Diversity and Community Composition of Active Microbial Communities in Southern High Latitude Ecosystems written by Claudia Maturana Martínez and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Bacterial Community Heterogeneity Across Surface Waters of the Pacific Ocean written by Mark S. Demarest and published by . This book was released on 2000 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This study provides a survey of marine bacterial community structure over large spatial distances.
Download or read book Temporal Analysis of Bacterial Community Structure in the North Eastern Gulf of Mexico written by Katelyn T. Knight and published by . This book was released on 2018 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Bacteria are found in all oceans around the globe and dominate marine processes because of their abundance and contribution to biogeochemical cycles. Resource availability and environmental parameters are both key factors in determining bacterioplankton growth and community structure. Understanding temporal changes in the microbial community structure in the Gulf of Mexico has the potential to shed new light on the dynamics of energy transfer and organic processing. A two-year seasonal study was conducted at a station 40 km south of Choctawhatchee Bay on the Florida Shelf in the Northeast Gulf of Mexico. A total of 31 water column samples were collected from surface and bottom waters (~90 m) and mid-water deep chlorophyll maxima, when present, at 12 different time points. In addition to microbial diversity, chemical, physical, and biological environmental parameters such as bacterial production, nutrients, temperature, salinity, chlorophyll a, and bacterial counts were also taken. 16S rRNA clone libraries generated 2,160 high quality clones that were used for community analysis. 535 OTUs were obtained at 97% similarity. Samples were analyzed in three different categorical groupings: all OTUs, all OTUs grouped together at order level, and OTUs without dominant taxa. Environmental patterns were seen to correlate directly with seasonal changes; however, community structure was independent of seasonal trends. Depth, nutrients, and salinity were seen to have a slight influence on the community structure. This shows that no single parameter is driving the community structure, but rather the community structure is the result of complex interactions between many factors.
Download or read book Spatial and Temporal Analysis of Dark Microbial Community Metabolism in the Atlantic Ocean written by Jessica Zehnpfennig and published by . This book was released on 2020 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Norwegian Coastal Current written by and published by Fagbokforlaget. This book was released on 2007 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Norwegian coastal current originates primarily from the freshwater outflow from the Baltic and the freshwater runoff from Norway. It flows northwards along the coast of Norway as a low-salinity current. This coastal region is the spawning ground for a number of important oceanic fish stocks, and the physical environment has an impact on the recruitment, growth, and geographical distribution of these stocks. In the late 1920s and early 1930s, the Institute of Marine Research in Norway established a coastal oceanographic observation system. This continued to evolve, and its core elements are still in operation. Drawing on the results generated by this observation system, as well as by other coastal studies, this book reviews the current understanding of the physical/chemical conditions in the Norwegian coastal current in such a way as to make the material more easily accessible to non-specialists. A series of chapters introduces readers to the geography, currents, water masses, and the temporal and spatial variability of the Norwegian coastal current. Interannual fluctuations in physical conditions are most likely to be the prime cause of ecosystem variability. The editor hopes that this book will act as a point of departure for a future summary of the ecology of Norwegian coastal waters.
Download or read book Temporal and Spatial Decorrelation Scales in the North Atlantic Ocean written by Rebecca Hummels and published by . This book was released on 2007 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fjord Oceanography written by Howard Freeland and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 691 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fjords are deep, glacia11y carved estuaries that are pecu1iar to certain coast1ines, and have severa1 characteristics that dist inguish them from sha110wer embayments. At higher latitudes they indent the western coast1ines of Scandinavia, North and South America, and New Zea1and. They are a1so a common feature of much of the arctic coast1ine. The papers contained in this vo1ume were presented at a workshop funded by the NATO Advanced Studies Institute in Victoria, British Co1umbia. It may seem curious to the reader that this specia1 c1ass of estuaries shou1d have attracted an international gathering of oceanographers from severa1 different discip1ines. The reas on for this interest stems from both practica1 and scientific considerations. On the one hand, fjords are a feature common to the coast1ines of severa1 countries that depend heavi1y on the oceans for communication, fisheries and other resources. The impact of man's activities on these coasts has created a demand for new know1edge of the physica1, bio10gica1 and chemica1 aspects of fjords. Sometimes man's inf1uence on the ocean is intentiona1 as, for examp1e, in the artificia1 contro1 of ice cover; often it is the more insidious bui1d-up of toxic wastes that is of concern. These prob1ems are particu1ar1y acute where the conf1icting demands of fisheries, industria1 deve10pment and re creation meet in a sing1e fjord; and indeed, this is a common occurence a10ng severa1 of the fjords in Scandinavia and Canada.
Download or read book The Spatial Distribution of Microbes in the Environment written by Rima Franklin and published by Springer Science & Business Media. This book was released on 2007-09-04 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume highlights recent advances that have contributed to our understanding of spatial patterns and scale issues in microbial ecology. The book brings together research conducted at a range of spatial scales (from μm to km) and in a variety of different types of environments. These topics are addressed in a quantitative manner, and a primer on statistical methods is included. In soil ecosystems, both bacteria and fungi are discussed.
Download or read book State of Lake Michigan written by T. Edsall and published by Aquatic Ecosystem Health & Mgmt Soc. This book was released on 2005 with total page 668 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, cataloging and analyzing the current science on the state of Lake Michigan, is an important part of Great Lakes recovering science. It carries forward the singular contribution that the binational Great Lakes scientific community has made not only to restoring the Great Lakes but also to the world's body of knowledge about large lake ecology, the long-range transport of pollutants, and the importance of habitat in ensuring ecosystem health.
