The Role Of Organic Matter In Structuring Microbial Communities

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.

Ecological functions and human wellbeing depend on ecosystem services. Among the ecosystem services are provisional (food, feed, fuel, fiber), regulating (carbon sequestration, waste recycling, water cleansing), cultural (aesthetic, recreational, spiritual), and supporting services (soil formation, photosynthesis, nutrient cycling). Many relationships of various degree exist among ecosystem services. Thus, land use and soil management to enhance biospheric carbon sinks for carbon sequestration requires a comprehensive understanding on the effects on ecosystem services. Payments for ecosystem services including carbon pricing must address the relationship between carbon sequestration and ecosystem services to minimize risks of overshoot, and promote sustainable use of land-based carbon sinks for human wellbeing.

Soils into which crop plants root and from which they obtain essential minerals and water contain huge arrays of microbes. Many have highly beneficial effects on crop growth and productivity, others are pathogens causing diseases and losses to yield and quality, a few microbes offer protection from these pathogenic forms and others have little or no effect. These intimate and often complex inter-relationships are being explored with increasing success providing exciting opportunities for increasing crop yields and quality in sustainable harmony with the populations of beneficial soil microbes and to the detriment of pathogens. This book explores current knowledge for each of these aspects of soil microbiology and indicates where future progress is most likely to aid in increasing crop productivity by means which are environmentally benign and beneficial.

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.

The presence - or absence - of soil organic matter (SOM) has important implications for agricultural productivity. It could also have significant implications for global climate due to its role as a source/sink of carbon. Therefore, it is important to understand the issues related to the accumulation or loss of SOM, to use what we have learned from experiments to make sound decisions about soil and crop management, and to test models and future concepts concerning SOM management. A database is included with the book, presenting tabular data for 34 sites in North America. Soil Organic Matter in Temperate Agroecosystems discusses all of these issues and more, answering such questions as:

This book presents a comprehensive collection of articles illustrating the importance of microbial community structure and function for ecosystem sustainability and environmental reclamation. It addresses a diverse range of topics, including microbial diversity, physiology, genomics, ecosystem function, interaction, metabolism, and the fruitful use of microbial communities for crop productivity and environmental remediation. In addition, the book explores issues ranging from general concepts on the diversity of microorganisms in soil, and ecosystem function to the evolution and taxonomy of soil microbiota, with future prospects. It covers cutting-edge methods in soil microbial ecological studies, rhizosphere microflora, the role of organic matter in plant productivity, biological nitrogen fixation and its genetics, microbial transformation of plant nutrients in soil, plant-growth-promoting rhizobacteria, and organic matter transformation. The book also discusses the application of microbes in biodegradation of xenobiotic contaminants. It covers bio-fertilizers and their role in sustainable agriculture and soil health, biological control of insect pests and plant pathogens, and the latest tools of omics in soil microbiology, i.e. genomics, proteomics, transcriptomics and metabolomics, which offer pioneering approaches to the exploration of microbial structure and function.

Dissolved organic matter (DOM) is an important source of nutrients in aquatic systems contributing to the growth of phytoplankton and bacteria. The overall response appears to be driven by the phytoplankton and bacteria species present as well as the composition of DOM provided. This dissertation explores the bioavailability of allochthonous and autochthonous DOM sources to, and its affect on, the growth of marine phytoplankton and bacterial community abundance and composition. This research utilizes advanced chemical (electrospray ionization mass spectrometry (ESI-MS)) and molecular (terminal restriction fragment length polymorphism (TRFLP)) techniques to characterize the DOM and microbial community. To investigate the role of allochthonous DOM in phytoplankton growth, DOM from two different riverine sources from watersheds with different land use practices, was supplied to a natural cyanobacteria population. The bioavailability of autochthonous DOM was investigated by supplying DOM produced by a single culture of cyanobacteria to a natural dinoflagellate bloom community. The potential negative effect of an individual autochthonous DOM compound was investigated through the addition of marine toxin, brevetoxin, to three different natural bacterial communities. This dissertation resulted in the first ESI-MS characterization spectra of the DOM associated with three different natural phytoplankton blooms, a culture of cyanobacteria, and two different South Florida rivers. It was also the first study to identify previously uncharacterized allochthonous and autochthonous DOM masses bioavailable to natural marine phytoplankton communities. Bulk level analyses within these experiments quantified lower limits for the bioavailability of allochthonous and autochthonous DOM sources and the relative community response to each of these sources. This dissertation also represents the first molecular evaluation of the bacteria associated with a bloom and the first investigation of the allelopathic properties of brevetoxin. It has discussed and applied the use of ESI-MS to investigate the bioavailability of complex DOM, identified and quantified potential nutrient sources and linked marine toxin production to changes in bacterial community composition.

This book presents a comprehensive collection of articles illustrating the importance of microbial community structure and function for ecosystem sustainability and environmental reclamation. It addresses a diverse range of topics, including microbial diversity, physiology, genomics, ecosystem function, interaction, metabolism, and the fruitful use of microbial communities for crop productivity and environmental remediation. In addition, the book explores issues ranging from general concepts on the diversity of microorganisms in soil, and ecosystem function, to the evolution and taxonomy of soil microbiota, with future prospects. It covers cutting-edge methods in soil microbial ecological studies, rhizosphere microflora, the role of organic matter in plant productivity, biological nitrogen fixation and its genetics, microbial transformation of plant nutrients in soil, plant-growth-promoting rhizobacteria, and organic matter transformation. The book also discusses the application of microbes in biodegradation of xenobiotic contaminants. It covers bio-fertilizers and their role in sustainable agriculture and soil health, biological control of insect pests and plant pathogens, and the latest tools of omics in soil microbiology, i.e. genomics, proteomics, transcriptomics and metabolomics, which offer pioneering approaches to the exploration of microbial structure and function.