Marine microbiology ecology and applications pdf

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marine microbiology ecology and applications pdf

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German Rosas-Acosta ed. Ibrahim Hashim,

The Simons Foundation invites applications for postdoctoral fellowships to support basic research on fundamental problems in marine microbial ecology, with an emphasis on understanding the role of microorganisms in shaping ocean processes, and vice versa. The foundation is particularly interested in applicants with training in different fields, as well as applicants with experience in modeling or theory development. While these cross-disciplinary applicants will receive particular attention, applicants already involved in ocean research are also encouraged to apply. The foundation anticipates awarding five fellowships in

Marine microbiology: ecology and applications (2nd Edn)

The unique physical processes associated with sea ice growth and development shape the associated biological diversity and ecosystem function. Microbes make up the base of all marine food webs and the overwhelming majority of biomass in the sea ice ecosystem. Despite their biomass, microbial processes are not fully integrated into marine ecosystem models.

Recent applications of novel molecular biology technologies to studies of marine ecology have elucidated numerous microbial-mediated processes interfaced by previously unknown organisms and processes. These discoveries are yielding more in-depth studies on the relevance of mixotrophy, the ecology of fungi, and the interplay between major microbial clades.

In ecosystem studies, the basis of the food web is frequently neglected even though the accessibility of energy, recycling of nutrients, and parasitism are crucial factors shaping the environment for grazers and higher trophic levels.

In this review, we focus on the species composition, abundance, and functions of microalgae, bacteria, archaea, fungi, and viruses in the sea ice-covered seas throughout the year. A strong emphasis will be put on advances in molecular methods that empower scientists to further investigate microorganisms in more detail. Since microbes make up the majority of all oceanic biomass, we believe that it is impossible to accurately forecast the biological fate of polar marine ecosystems without placing a proportional emphasis on microbes relative to their biomass.

Within the polar marine ecosystems, sea ice formation and subsequent coverage influence light transmittance that seasonally governs under-ice primary production and the associated heterotrophic biological community.

It provides microhabitats for microalgae, chemoautotrophic and heterotrophic bacteria, archaea, viruses, fungi, and multicellular organisms Bluhm et al. The sea ice habitat is characterized by strong gradients in temperature, salinity, nutrients, and light.

The small-scale spatial distribution of sea ice-associated sympagic biota is determined to a large extent by these physical properties Krembs et al. The two major ice types found in polar environments provide different habitat characteristics e. Multiyear ice MYI persists at least one melting season, whereas first-year ice FYI follows a seasonal pattern of ice formation and melt.

FYI is often structurally less complex, characterized by greater light penetration through the ice that is prone to an earlier onset of seasonal melt Moline et al. Changes within the ice biological system might have cascading effects on the ice-associated ecosystem Secretariat of Arctic Council The open water in sea ice-covered seas is a special system in itself. At the marginal ice zone or in open leads, a system with high levels of light and nutrients may support ice edge phytoplankton blooms dominated by different species compared to sea ice Assmy et al.

With climate change, these areas are expected to increase, changing the microbial community structure in sea-ice covered seas Oziel et al.

The consequences for higher trophic levels and carbon export are a topic of recent studies. In the Arctic and Antarctic, a large part of the ocean is ice-free during the polar night. The absence of light challenges the pelagic microbial food web due to a lack of photosynthetic primary production.

Nevertheless, microbes have been found to be active throughout the polar night and different biogeochemical cycles may be dominant Zhang et al. The polar marine environment is in a state of rapid transition with tremendous changes in the abiotic environment. In the Arctic Ocean, air and surface-layer temperatures are increasing faster than the global average Serreze and Francis ; Holding et al.

This replacement has contributed to an earlier onset of seasonal ice melt, an increased duration of ice melt Stroeve et al. A strong reduction in overall Arctic sea ice extent occurred over the last two decades, with the lowest summer minimum ice extent in 3. Specifically during autumn, the surface of the ocean surrounding the Antarctic continent begins to freeze, forming sea ice of about 0.

Overall, the ice extent in the Antarctic has been much less impacted compared to the Arctic. In the Antarctic Peninsula and Bellinghausen Sea region, the ice-free summer season is extended by three months, whereas in the western Ross Sea region, the ice-free season is shortened by two months Lange et al.

Due to strong wind events, large quantities of heat are extracted from the surface ocean, facilitating rapid formation of frazil ice Eicken Surface salinities vary from 9 in the southern part to below 1 in the innermost parts Voipio Even though the seasonal ice of the Baltic Sea has many similarities with the seasonal ice in the polar areas, fresher water results in sea ice with lower bulk salinities and smaller brine channels, despite the comparably high temperatures Meiners et al.

Low brine volumes reduce the rate of seawater exchange across the ice-water interface that affects rates of nutrient replenishment, convective heat transport, and desalination processes Lytle and Ackley The high dissolved organic matter DOM content in Baltic Sea water and ice leads to different chemical characteristics and causes increased absorption of solar radiation at shorter wavelengths than are utilized for photosynthesis Granskog et al.

During early winter most of the Baltic Sea is ice free and below the Arctic Circle, where daylight is available for photosynthesis throughout the year in contrast to the polar night in polar regions.

As a result, the microbial community differs considerably from polar sea ice environments. Advances in marine microbial ecology are driven by methodological advances in understanding both, the environment, as well as the biological taxa that inhabit the environment.

With advancing resolution in microscopy, it was possible to get a better understanding of microbial diversity and abundances that has now ushered in the -omics era. These microbial methodologies have evolved in parallel with in situ technologies. Early approaches measured primary production in slices of an ice core incubated in surrounding ice Mock and Gradinger Since these early studies, technological advancements have allowed for in situ measurements of primary production; oxygen microsensors have been used successfully in artificial sea ice experiments to measure in situ ecosystem production Mock et al.

Stable- and radioisotope incubations allowed estimates of microbial activities and associated organic matter utilization. The future of methods for studying biogeochemistry in sea ice may be in situ technologies reviewed by Miller et al. Methods for water sampling and biogeochemical studies have been similar to traditional work in other pelagic systems. The application of molecular fingerprinting methods e. Amplicon-based sequencing of the taxonomically informative small ribosomal subunit became a standard genetic barcode, which allowed the identification of microbial taxa down to the level of ecotypes.

Advancing sequencing technologies are generating more sequence reads at a lower cost, affording high spatial and temporal resolution of microbial primarily bacterial communities and subsequent investigation of their connectivity, seasonal successions, and biogeography e.

Novel sequencing tools, such as the Nanopore MinION have the potential to be used for in-field sequencing, and have been used in remote polar regions e. Novel sequencing technologies are evolving in parallel with bioinformatic tools that can identify small, yet significant community differences.

Recent studies are focusing more on full genome, metagenomic shotgun sequencing approaches. Approaches, which simultaneously generate taxonomic and functional gene information. So far, only several studies have applied metagenomic shotgun sequencing to sea ice samples e.

Metagenomic sequencing efforts have demonstrated bacterial-mediated chemical cycling in frost flowers Bowman et al. With increasing throughput of sequence generation and decreasing costs, deep sequencing i.

Other -omics studies that target byproducts of protein synthesis and secondary metabolism are rare in sea ice. While metagenomics can demonstrate the genetic potential of microbes, RNA-based studies, such as metatranscriptomics, can show whether the genes are expressed. For example, Koh et al. Interdisciplinary research with biochemists identified the functions of translated proteins and ascribed a functional purpose for gene products used in survival and metabolism in sea ice reviewed by Feller and Gerday ; Feng et al.

Metaproteomics is not only possible for cultured bacteria, but can be used for understanding the biochemical functions of the in situ community Junge et al. Ultimately, combined -omics studies are important for a thorough understanding of microbial ecology and biogeochemistry Junge et al. In cultures, the potential to combine proteomics and genomics has already been shown to help understanding key genes for a life in subzero temperatures Feng et al.

To date, metaproteomics and metabolomics studies of the whole community have yet to be applied to studies of sea ice. Ribosomal gene sequencing data have been used to develop fluorescently labeled nucleotide probes that target taxonomically informative genetic loci, namely, fluorescence in situ hybridization FISH Pernthaler et al.

The application of FISH has informed analyses of spatial interactions and abundances of specific taxa, without the known biases associated with DNA sequencing De Corte et al. Only a few of the metabolic capacities mentioned in this chapter have been measured and a common limitation is still the separation of biogeochemical rate measurements and investigations of the genetic potential of communities, or organisms. Studies coupling the function, activity, and diversity of bacteria are lacking in sea ice systems, but their potential has been shown in other marine systems.

RNA stable isotope probing is one recent method, which could be used to overcome these limitations. For example, Fortunato and Huber coupled stable isotope probing with metatranscriptomics to identify taxa and pathways involved in chemolithotrophic processes at hydrothermal vents.

Methods for visualization of radioisotope Microautoradiography, Nierychlo et al. One of the major applications of novel ecological data is the incorporation into ecosystem models. Despite the increasing computational power, the representation of microbial interactions in ecosystem models is still rudimentary. For example, bacterial activities are often hidden in functions for organic matter remineralization and respiration e.

A recent ecosystem model in the Baltic Sea started realizing for the first time the importance of bacteria beyond nutrient remineralization. Specifically, aerobic and anaerobic bacterial taxa were separately considered, both as crucial for remineralization processes and for generating anaerobic conditions linked to algal production Tedesco et al. Linking metabolic pathway models, bacterial functions such as denitrification and nitrogen fixation , and viral lysis may further improve the accuracy of models with increasing data availability and computational power.

In most ecosystem models and discussions, the role of sea ice bacteria and archaea is seen in the heterotrophic aerobic remineralization of DOM e. The base of polar food webs is comprised of microbial organisms allied to multiple clades of life. Additional challenges arise for ice-associated biota, with extreme cold temperatures, highly variable salinities and only temporary existence of their habitat Meier et al. The balance between producers and consumers seasonally shifts with light availability which drives taxa-specific abundances.

Diatoms and other microalgae haptophytes, prasinophytes, dinoflagellates are some of the most common eukaryotic producers that support a diverse heterotrophic community of prokaryotes, fungi, and fungal-like organisms, ciliates, and larger multicellular organisms.

These organisms are all presumably susceptible to viral infection, which can rapidly shunt organic material into the available dissolved organic material pool.

Together, these organisms cycle carbon and exchange genes that maintain ecosystem function and support the feeding needs of higher trophic levels. The microalgae community in polar sea ice is dominated by diatoms that comprise the most biomass and greatest species richness, including up to species predominated by Nitzschia sp.

Arrigo Pennate diatoms dominate the spring ice algal bloom in Arctic FYI, as well as in Antarctic sea ice due to the nutrient-rich Southern Ocean Arrigo et al. Sea ice associated phytoplankton blooms are often dominated by aggregates of Phaeocystis sp. Other algae groups in the pico- and nanoplankton-size fraction contribute substantially to the pelagic and sympagic winter community.

Micromonas sp. Still, reliable identification and quantification of pico- and nanosized eukaryotes are lacking Piwosz et al. As a consequence of the lower water salinity and corresponding small-sized brine ice channels, the Baltic Sea ice is dominated by smaller protists Kaartokallio et al. In early spring, centric diatoms dominate under-ice biomass. These centric diatoms are supplemented by large contributions of Melosira arctica and the cyanobacterium Aphanizomenon sp. In contrast to Arctic and Antarctic sea ice communities, dinoflagellates and green algae contribute to a large fraction of the biomass in Baltic Sea ice and open water Kaartokallio et al.

Furthermore, the surface-layer algal biomass can significantly contribute to the overall sea ice algal biomass Meiners et al. So far, the knowledge of species composition and distribution is limited, and there is only little known on the overwintering of cyanobacteria, which are typical for the Baltic Sea Laamanen The most common orders found in sea ice are Alteromonadales Gammaproteobacteria and Flavobacteriales Bacteroidetes with the most common genera Pseudoalteromonas , Colwellia , Shewanella , Flavobacterium , and Polaribacter Bowman et al.

Rarer phyla are the Alphaproteobacteria , Betaproteobacteria , Actinobacteria , and Firmicutes Bowman et al.

Progress in Microbial Ecology in Ice-Covered Seas

PeerJ Preprints. Limnology and Oceanography Letters doi: Environmental Microbiology. Biology Letters. Philosophical Transactions of the Royal Society B.

Request PDF | On Jan 1, , Tom Fenchel published Marine microbiology: ecology and applications Colin Munn (with foreword by Farooq.

Marine Microbiology - E-bog

The unique physical processes associated with sea ice growth and development shape the associated biological diversity and ecosystem function. Microbes make up the base of all marine food webs and the overwhelming majority of biomass in the sea ice ecosystem. Despite their biomass, microbial processes are not fully integrated into marine ecosystem models. Recent applications of novel molecular biology technologies to studies of marine ecology have elucidated numerous microbial-mediated processes interfaced by previously unknown organisms and processes.

Slideshare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our User Agreement and Privacy Policy. See our Privacy Policy and User Agreement for details. Published on Aug 1,

Progress in Microbial Ecology in Ice-Covered Seas

Slideshare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our User Agreement and Privacy Policy. See our Privacy Policy and User Agreement for details. Published on Aug 28, The Second Edition takes into account many new discoveries in the field including the role of microbes in ocean processes and nutrient cycles, the importance of viruses, the beneficial role of marine microbes in biotechnology, biofuels, metagenomics and synthetic biology, and new research on the impact of climate change and ocean acidification. The first three sections review the main features of the marine environment and key aspects of marine microbial life; the second section examines the role of marine microorganisms in ecology; and the final section considers some of the applications of this knowledge in areas such as disease and biodegradation.

The third edition of this bestselling text has been rigorously updated to reflect major new discoveries and concepts since , especially progress due to extensive application of high-throughput sequencing, single cell genomics and analysis of large datasets. Significant advances in understanding the diversity and evolution of bacteria, archaea, fungi, protists, and viruses are discussed and their importance in marine processes is explored in detail. Now in full colour throughout, all chapters have been significantly expanded, with many new diagrams, illustrations and boxes to aid students' interest and understanding.

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Marine microbiology: ecology and applications Colin Munn (with foreword by Farooq Azam). Tom Fenchel. This article may be used for research, teaching, and​.

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