Structure And Function Of Microbial Communities Processing Dissolved Organic Matter In Marine Environments

The current study added to the growing information regarding the composition of bacterial community in aquatic environments and the role of specific bacterial groups in DOM assimilation. In particular, this study was the first to unfold the relation between structure and function of the bacterial community in the Arctic Ocean, the only cold environment studied in that aspect to date. The molecular study of GH5 revealed the potential of the community for polysaccharides degradation, however, more need to be done to broaden our understanding of the mineralization of these compounds in the marine environment.

Marine dissolved organic matter (DOM) is a complex mixture of molecules found throughout the world's oceans. It plays a key role in the export, distribution, and sequestration of carbon in the oceanic water column, posited to be a source of atmospheric climate regulation. Biogeochemistry of Marine Dissolved Organic Matter, Second Edition, focuses on the chemical constituents of DOM and its biogeochemical, biological, and ecological significance in the global ocean, and provides a single, unique source for the references, information, and informed judgments of the community of marine biogeochemists. Presented by some of the world's leading scientists, this revised edition reports on the major advances in this area and includes new chapters covering the role of DOM in ancient ocean carbon cycles, the long term stability of marine DOM, the biophysical dynamics of DOM, fluvial DOM qualities and fate, and the Mediterranean Sea. Biogeochemistry of Marine Dissolved Organic Matter, Second Edition, is an extremely useful resource that helps people interested in the largest pool of active carbon on the planet (DOC) get a firm grounding on the general paradigms and many of the relevant references on this topic. Features up-to-date knowledge of DOM, including five new chapters The only published work to synthesize recent research on dissolved organic carbon in the Mediterranean Sea Includes chapters that address inputs from freshwater terrestrial DOM

Overviews of the source, supply and variability of DOM, surveys of the processes that mediate inputs to microbial food webs, and syntheses consolidating research findings provide a comprehensive review of what is known of DOM in freshwater. This book will be important to anyone interested in understanding the fundamental factors associated with DOM that control aquatic ecosystems."--BOOK JACKET.

Natural organic matter is important to the quality of drinking water. It constitutes precursors for disinfectant by-product formation and supports regrowth of bacteria. The drinking water industry is involved in work designed to improve biological treatment of water, control bacterial regrowth in distribution systems, and measure biodegradable NOM concentrations. These efforts would benefit from a knowledge of NOM composition and structure and the composition of microbial communities that colonize biological filters and distribution systems. In this project the researchers addressed four major goals: (1) to determine the structure and composition of natural organic matter (NOM), (2) to describe the structure of heterotrophic bacterial communities supported by raw and treated source water, (3) to measure the responses of heterotrophic bacterial communities to seasonally driven variations in NOM and temperature, and (4) to determine whether bioreactor systems can serve as small-scale models for the development and refinement of drinking water treatment processes. The five source waters selected for this project included a broad range of physiographic provinces, vegetation zones, and NOM concentrations. The research team analyzed NOM and microbial communities from an analytical hierarchy involving assessment of concentration, composition, and structure. Concentrations of NOM and BOM were estimated from dissolved organic carbon (DOC) and biodegradable DOC concentrations. NOM composition was assessed from analyses of carbohydrates with ion chromatography with pulsed amperometric detection, humic substances with XAD-8 resin, and functional groups with NMR. Molecular structure was determined from tetramethylammonium hydroxide thermochemolysis (TMAH) GC/MS. Microbial community composition was assessed from comparative ribosomal ribonucleic acid (RNA) sequencing, specifically, terminal restriction fragment length polymorphisms (t-RFLP), to provide an overview of microbial population structure and detect population shifts at the level of species. NOM Composition NOM and BOM concentrations showed extensive temporal variation in all of the source waters, but a general pattern of concentration ranges was discernable, indicating that each watershed has a particular concentration signal. Compositional studies revealed that humic substances and complex carbohydrates are components of both NOM and BOM. Structural and compositional studies identified unique NOM signatures for the different source waters, with some classes of molecules observed only in specific source waters. The BOM pool included humic substances and lignin, sources generally presumed to be relatively resistant to biodegradation. Additional novel insights included the quantitative contribution of aromatic molecules to the BOM pool and the potential for bacterial demethylation of lignin. Bacterial Communities The communities of microorganisms that developed in bioreactors that were fed water from different watersheds were unique. NOM influenced the genetic composition of resulting microbial communities, and seasonal shifts were observed for watersheds possessing strong seasonal temperature signals. Thus, temperature and organic matter quantity and quality probably influenced parameters important to the biological treatment of drinking water. A comparison of bioreactor metabolism with rapid sand filters showed some overlap, suggesting the bioreactors may indicate the ultimate potential of rapid sand filters for BOM processing. The researchers recommend the following: Bioreactors designed to monitor a BOM source should ideally be inoculated, colonized, and maintained by that source; at a minimum, acclimation to the source over several months is needed. Seasonal changes in the microbial community colonizing a biologically active filter may diminish filter performance and require an acclimation period to restore performance. Molecular-based methods for both microbial and chemical analyses of drinking water and treatment processes should be targeted for continued development and implementation within the drinking water industry. Originally published by AwwaRF for its subscribers in 2004.

Heterotrophic bacteria are responsible for degrading dissolved organic matter (DOM), and process 50% or more of Earth’s net primary production. Although integral to global nutrient cycling, the complexity of bacterial communities makes it difficult to resolve the mechanisms by which they degrade DOM. Adding to the complexity of this interaction is the compositional diversity of DOM. The St. Lawrence Estuary (SLE) is an important repository for DOM, produced both internally by phytoplankton and externally by terrestrial plants. I aim to identify the bacterial taxa that respond to differential DOM inputs using 16S rRNA abundance as a proxy for metabolic activity. A microcosm experiment was conducted in the SLE in which marine DOM and terrestrial DOM were extracted by ultrafiltration and solid-phase extraction. DOM extracts were amended to microcosms of raw SLE water and incubated at 7°C and 25°C for 32 hours. The Gammaproteobacterial lineage Pseudoalteromonas experienced a 70% increase in metabolic activity in response to HMW marine DOM at both 7°C and 25°C, which was not observed in any other DOM treatment. Terrestrial DOM treatments resulted in a significant increase in alpha-diversity within the bacterial community at 25ºC, indicating a relative increase in the activity of rare bacteria in response to freshwater DOM. Microcosm experiments such as this aim to provide a better understanding of how DOM composition can influence bacterial community structure and metabolism. Considerations for future experiments include transcriptomics analysis to describe the metabolic pathways involved in DOM degradation.

Dissolved organic carbon (DOC) is the dominant form of organic matter in aquatic ecosystems and bacteria play a key role in its mobilization to higher trophic levels. The DOC pool is often divided into broad classes such as labile or recalcitrant, based on its ease of uptake by bacteria; or as autochthonous and allochthonous, based on its production within or outside the ecosystem. In this dissertation, I examined the relationship between the composition of the DOC pool and bacterial community structure and function. The three research chapters address this relationship in different freshwater ecosystems. In the first research chapter, the effect of presence or absence of Microcystis, a dominant primary producer in the western basin of Lake Erie as well as an autochthonous DOC source, on bacterial community structure and heterotrophic productivity was studied. This study revealed that bacterial responses were independent of the presence of the dominant primary producer. In second research chapter, the effect of compositional diversity of DOC within labile and recalcitrant categories, on stream bacterial community structure and denitrification rates was investigated. Use of different compounds within each category, administered individually and in mixtures, contributed to the heterogeneity. Results of this study suggest molecular heterogeneity of DOC can lead to differences in bacterial structure and denitrification potential. In my final research chapter, bacterial responses to differences in proportion of autochthonous and allochthonous DOC between a river and reservoir ecosystem were compared. The findings of this study demonstrated that, rather than the proportion of the two DOC sources, each source, considered individually, played a more important role in determining bacterial response. Regardless of the study, in all cases bacterial community structure was not linked to function, emphasizing the requirement to study both. The results indicate that differences in DOC quality, rather than the quantity, may play a greater role in determining bacterial responses and that structure and function can be decoupled.

The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

The ocean contains one of the largest reservoirs of reduced carbon on Earth in the form of dissolved organic matter (DOM). Heterotrophic bacteria serve as the primary force regulating the degradation of this material, recycling the majority of dissolved organic carbon (DOC) produced in the surface ocean by phytoplankton back to carbon dioxide. While it is known that microbial community structure plays a role in determining the rate and magnitude of DOM turnover, the quantitative contribution of individuals to this process remains unknown. The objective of this dissertation was to investigate the constraints on DOM turnover by bacterial communities by focusing on how a single bacterial strain makes a living in the sea. I found that a single bacterial strain, Alteromonas sp. AltSIO, has the capacity to consume an equivalent magnitude of DOC as diverse bacterial communities, suggesting that bacterial diversity may not be required for the complete removal of labile DOC in the surface ocean. In long-term microcosms, however, bacterial diversity was required for continued degradation of semi-labile DOC. To test the generality of this capacity among individual bacteria, a culture-based study was conducted where >100 phylogenetically diverse bacterial strains were isolated to screen for growth in unamended seawater. No other bacterial strain tested exhibited the capacity to consume a measureable quantity of DOC when grown in isolation, suggesting that this phenomenon may not be common among readily culturable marine bacteria. Physiological investigations of this isolate reveal a broad capacity for processing carbohydrates, yet an apparent preference for disaccharides and inability to metabolize glucose. Genomic analysis confirmed that this strain lacks a glucose-specific permease required for the exogenous uptake of glucose, but is endowed with additional carbohydrate-specific transporters not found in genomes of closely related bacterial strains. Genomic insights also show the potential to reduce nitrate, a high capacity to scavenge iron, and a complete chemotaxis apparatus potentially used for disaccharide acquisition. DOM characterization by ultrahigh resolution mass spectrometry revealed that AltSIO and diverse seawater communities significantly alter the composition of ambient DOM.