Environmental Microbiology, Second Edition

**The bestselling reference on environmental microbiology—now in a new edition** This is the long-awaited and much-anticipated revision of the bestselling text and reference. Based on the latest information and investigative techniques from molecular biology and genetics, this __Second Edition__ offers an in-depth examination of the role of microbiological processes related to environmental deterioration with an emphasis on the detection and control of environmental contaminants. Its goal is to further our understanding of the complex microbial processes underlying environmental degradation, its detection and control, and ultimately, its prevention. Features new to this edition include: * A completely new organization with topics such as pathogens in developing countries, effects of genetically modified crops on microbial communities, and transformations of toxic metals * Comprehensive coverage of key topics such as bacteria in the greenhouse and low-energy waste treatment * New coverage relating core book content to local, regional, and global environmental problems __Environmental Microbiology__, Second Edition is essential reading for environmental microbiologists and engineers, general environmental scientists, chemists, and chemical engineers who are interested in key current subjects in environmental microbiology. It is also appropriate as a textbook for courses in environmental science, chemistry, engineering, and microbial ecology at the advanced undergraduate and graduate levels.Content: Chapter 1 Bacteria in the Greenhouse: Marine Microbes and Climate Change (pages 1–31): Hugh W. Ducklow, Xose Anxelu G. Moran and Alison E. MurrayChapter 2 Control of Waterborne Pathogens in Developing Countries (pages 33–56): Tim Ford and Steve HamnerChapter 3 New Molecular Methods for Detection of Waterborne Pathogens (pages 57–94): Alison M. Cupples, Irene Xagoraraki and Joan B. RoseChapter 4 Microbial Transformations of Radionuclides in the Subsurface (pages 95–114): Matthew J. Marshall, Alexander S. Beliaev and James K. FredricksonChapter 5 Eutrophication of Estuarine and Coastal Ecosystems (pages 115–135): Nancy N. RabalaisChapter 6 Microbial Deterioration of Cultural Heritage Materials (pages 137–151): Christopher J. McNamara, Nick Konkol and Ralph MitchellChapter 7 Sorption and Transformation of Toxic Metals by Microorganisms (pages 153–176): Xu Han and Ji?Dong GuChapter 8 Bioremediation of Hazardous Organics (pages 177–212): Jennifer G. Becker and Eric A. SeagrenChapter 9 Biosensors as Environmental Monitors (pages 213–233): Steven Ripp, Melanie L. DiClaudio and Gary S. SaylerChapter 10 Effects of Genetically Modified Plants on Soil Microorganisms (pages 235–258): Nicole Weinert, Remo Meincke, Michael Schloter, Gabriele Berg and Kornelia SmallaChapter 11 Anaerobic Digestion of Agricultural Residues (pages 259–279): Vincent O'Flaherty, Gavin Collins and Therese MahonyChapter 12 Anaerobic Biodegradation of Solid Waste (pages 281–299): Morton A. Barlaz, Bryan F. Staley and Francis L. de los ReyesChapter 13 Low?Energy Wastewater Treatment: Strategies and Technologies (pages 301–318): Thomas P. CurtisChapter 14 Bioremediated Geomechanical Processes (pages 319–348): Eric A. Seagren and Ahmet H. Aydilek <h2>CHAPTER 1</h2> <p><b>Bacteria in the Greenhouse: Marine Microbes and Climate Change</b></p> <p>HUGH W. DUCKLOW</p> <p>Marine Biological Laboratory, The Ecosystems Center, Woods Hole, Massachusetts</p> <p>XOSÉ ANXELU G. MORÁN</p> <p>Centro Oceanográfico de Xixón, Instituto Español de Oceanografia, Xixón, Spain</p> <p>ALISON E. MURRAY</p> <p>Desert Research Institute, University of Nevada, Reno, Nevada</p> <br> <p><b>1.1 INTRODUCTION: A MICROBIAL OCEAN IN A WARMING WORLD</b></p> <p>The global ocean covers 70% of Earth's surface and comprises most of the volume of the biosphere (except the deep subsurface). It supports about half the annual net primary production (NPP) on the planet (Figure 1.1) (Field et al., 1998). This vast, interconnected network of marine ecosystems is warming in response to anthropogenic climate change, with uncertain consequences for human societies. In this chapter we address the possible responses of ocean warming on marine microbes (protists, phytoplankton, bacteria, and archaea, with emphasis on the bacteria). Other anthropogenic changes related to CO₂ accumulation in the atmosphere, such as ocean acidification (Orr et al., 2005), will also have uncertain effects on ocean microbes.</p> <p>The ocean is, and always has been, dominated by microbes. Microscopic unicellular phytoplankton and cyanobacteria inhabiting the sunlit upper approximate 100 m of the water column carry out nearly all the photosynthesis on which oceanic life depends (Falkowski et al., 1998, 2000). NPP on land and in the oceans is the process dominating solar energy and CO₂ fixation into organic matter, thus driving the global carbon cycle (Houghton, 2007). Nearly all of the approximately 50 Pg (1 petagram = 1 Pg = 10¹⁵ g = 10⁹ tons) of carbon fixed annually in marine photosynthesis is ultimately oxidized by bacterioplankton, protozoans, and zooplankton (Ducklow and Carlson, 1992) with a very small fraction (<0.1%) escaping heterotrophic metabolism in the deep water column to be buried in the sedimentary record and hydrocarbons. The myriad pathways by which marine organic matter is cycled through particulate and dissolved forms and back into CO₂ overwhelmingly involve microbial exchanges among organisms less than 1 to 5 µm in diameter—the microbial loop (Pomeroy, 1974; Azam et al., 1983; Azam and Worden, 2004; Azam and Malfatti, 2007). This large-scale view of global biogeochemistry makes the point that microbial ecology depends ultimately on the patterns and products of photosynthesis. In metabolizing the products of photosynthesis on land and in the sea, bacteria perform important ecosystem services, such as decomposition, nutrient cycling, regulating the composition of the atmosphere, enhancing soil fertility, and purifying water, on which human societies depend for healthy and sustainable existence (Ducklow, 2008). Here we review marine plankton and microbial ecology to understand how marine bacteria may respond to anthropogenic climate change, and suggest potential research directions for making more informed projections.</p> <p>Bacteria respond directly to changes in environmental temperature, but these responses occur in complex communities with phytoplankton and zooplankton and in a complex biogeochemical milieu. After reviewing the microbial loop to set the stage for a more detailed look at the connections between climate and plankton processes, we take two complementary approaches. First, we examine how bacterial activity varies as a function of temperature. Then we examine how marine phytoplankton respond to climate variability in the ocean and how these responses modulate the effects of climate change on bacterial and animal consumers. We have a reasonable understanding of the mechanisms by which phytoplankton (especially eukaryotes) will respond to climate change, based on physical theory and knowledge of past changes from the fossil record. But as Falkowski and Oliver (2007) stated in their review of phytoplankton and climate, "Whether this fundamental principle holds for marine prokaryotes remains to be seen, because the spatial and temporal distribution of prokaryotic taxa, as well as their relevant ecophysiological attributes, is not yet well characterized." Our knowledge of the mechanisms linking phytoplankton to bacterial variability is still fragmentary, but much new research is directed at this problem. We use this nascent understanding to suggest how bacterial carbon cycling may change and what knowledge is needed for better predictions of such changes. Finally, we synthesize these approaches and consider scenarios of how microbial communities will respond (or may allready be responding) to climate change in the coastal seas, cold polar seas, and in warm oligotrophic subtropical gyres. First, we sketch briefly the projected physical changes to the global oceans in response to anthropogenic climmmmate forcing.</p> <br> <p><b>1.1.1 Impact of Climate Change on the Oceans</b></p> <p>The world is warming in response to climate change driven by the accumulation of anthropogenic greenhouse gases (Kerr, 2007). The 2007 IPCC Assessment projects that the mean global surface atmospheric temperature will rise by 1 to 6°C by 2099, depending on various assumptions or scenarios of population growth, economic and technological development, energy use, and greenhouse gas emissions (IPCC, 2007b). The projected warming is not uniform in space or time, with different rates forecast for various regions and seasons. Surface ocean temperatures may rise by 3 to 7°C in some regions, with the largest increases (although not necessarily the largest <i>effects</i>; see below) in polar seas (Figure 1.2). Climate warming will take longer to percolate into the deep ocean. The surface ocean west of the Antarctic Peninsula has already increased by 1°C since the 1950s (Meredith and King, 2005), and Arctic sea ice has declined alarmingly in the past few years (Serreze et al., 2007). Enhanced greenhouse warming is projected to cause impacts ranging from changes in winds, clouds, sea level, precipitation, storm frequency and intensity to more complex alterations in long-term climate modes (e.g., ENSO), ecosystems, biodiversity, and human well-being (Millennium Ecosystem Assessment, 2005; IPCC, 2007a). The impact of changes in surface temperatures, clouds, and wind on ocean stratification, mixing, and circulation has been examined using coupled atmosphere–ocean general circulation models (AOGCM) (Meehl et al., 2007). In addition to atmospheric warming, major changes predicted by many different AOGCMs include increases in ocean surface stratification in the tropics and subtropics; and reductions in mixed-layer depth in the middle to upper latitudes (Figure 1.3; Boyd and Doney, 2002), Other changes include loss of sea ice in both hemispheres (especially in the north), and increases in westerly winds and coastal upwelling (Sarmiento et al., 2004). As the temperature fields shown in Figures 1.2 and 1.3 indicate, projected changes are far from uniform. Specification of the changes in any particular region is more uncertain than projections of the global means. Responses of ocean ecosystems and biogeochemistry are less certain than physical changes.</p> <br> <p><b>1.1.2 The Microbial Loop and Marine Bacterioplankton Communities</b></p> <p>A typical milliliter of seawater harbors about 10⁶ bacterial and archaeal cells, the great majority of which are revealed to be active based on fluorescent in situ hybridization and visualization of intact ribosomes (Church et al., 2003). This assemblage contains extraordinary genetic and metabolic diversity (Venter, 2004; Sogin et al., 2006), and with it the potential for adaptation to wide ranges and combinations of environmental conditions. The planktonic archaea make up a variable fraction of the prokaryote assemblage, comprising up to about 50% of the total abundance in deep-ocean waters, but less in the more active surface layer (Karner et al., 2001). Recent work has revealed new insights concerning the metabolism and ecological roles of planktonic GI marine crenarchaeota and GII marine euryarchaeota. Collective evidence suggests that perhaps a significant portion of the GI marine crenarchaeota are ammonia oxidizers (Francis et al., 2005; Konneke et al., 2005; Hallam et al., 2006; Wuchter et al., 2006), while the first environmental genomic sequence from a GII marine euryarchaeote identified a proteorhodopsin-encoding gene (Frigaard et al., 2006). Both of these metabolisms are consistent with the ecological distributions of these organisms in the ocean, where the GI marine crenarchaeota are typically found below the photic zone, and the GII marine euryarchaeota are found in oceanic surface waters. Marine aerobic heterotrophic bacteria directly take up and metabolize low-molecular-weight (LMW, <500 MW) dissolved organic matter (DOM) such as easily metabolized mono- and oligosaccharides, free amino acids, and small peptides (Kirchman et al., 2001). Most bacterial cells in the ocean are free-living and thus dependent on DOM (Azam and Hodson, 1977). Free and attached bacteria hydrolyze polymeric substances and particulate matter into LMW compounds that can be passed through cell membranes (Hoppe et al., 1993). Bacterial metabolism in the surface ocean depends predominantly on uptake of labile LMW and HMW compounds with turnover times of minutes to days (Fuhrman, 1990). However bacterial metabolism may be supplemented by a variable contribution from semilabile DOM that turns over on approximately seasonal time scales (Kirchman et al., 1993; Carlson and Ducklow, 1996). Bacterial turnover of DOM and the associated remineralization of micro- and macronutrients such as iron, nitrogen, and phosphorus close the major biogeochemical cycles of these elements in the sea (Falkowski et al., 2008).</p> <p>Marine net primary production is processed through a complex trophic network of consumers, with a global average 15 to 20% escaping microbial respiration in the euphotic surface layer (upper approximately 100 to 200 m) to be exported to the ocean interior. A change in this fraction would have a major impact on the global carbon cycle (Sarmiento and Toggweiler, 1984). In the open sea and in many coastal and shelf seas under stratified conditions, carbon and nitrogen flows are dominated by microbial food webs (Figure 1.4). The intensive recycling of the dissolved and particulate fractions of the NPP through consumers results in a large fraction (about 50%) of the NPP passing through bacteria and the dissolved pool (Pomeroy, 1974; Williams, 1981). In the open sea, most grazing is by microzooplankton (Landry and Kirchman, 2002; Calbet and Landry, 2004); thus most heterotrophic consumption and respiration is microbial. Microbial dominance of marine food webs appears to hold even for the Antarctic seas, previously thought to be the last bastion of the classical diatom–krill–whale food chain based on large plankton (Daniels et al., 2006).</p> <p>As this discussion and Figure 1.4 suggest, a large fraction of the organic matter fixed in marine NPP is cycled through dissolved pools and metabolized by bacteria. All organisms leak DOM into the environment via passive diffusion, cell lysis and breakage, and active metabolic processes (Bjrnsen, 1988; Nagata, 2000). Phytoplankton actively exude dissolved organic carbon (DOC) to dispose of excess photosynthetically fixed carbon not combined with nitrogen and phosphorus into biomass in the approximate Redfield ratio 106 : 16 : 1 (C/N/P). Phytoplankton exudation is the process most directly coupling primary to bacterial production (Moran et al., 2002), but not the only process. Larger-celled phytoplankton such as diatoms may be broken between capture and ingestion by crustacean predators, spilling their fluid contents, in a process known as <i>sloppy feeding</i> (Lampert, 1978). According to Nagata (2000), egestion and excretion during feeding by protistan grazers may be the greatest relative contribution to photosynthetically derived DOC fluxes. Clearly, passive diffusion across phytoplankton cell membranes, active exudation, egestion, and sloppy feeding will produce DOM with different chemical composition and at different rates. Following ingestion and digestion, zooplankton grazers excrete DOM, and it also diffuses out of fresh fecal material (Jumars et al., 1989). Additional DOM may be released during viral lysis, abiotic dissolution, or bacterial hydrolysis of suspended and sinking detrital particles and marine snow. Figure 1.4 suggests one scenario for the relative magnitudes of DOC fluxes from these diverse sources. This model explains how the level of bacterial production (BP) is limited by how much DOC flows through the food web to bacteria, and by the bacterial allocation of the carbon ingested between production and respiration (bacterial growth efficiency; see below). Phytoplankton extracellular release (PER) may vary widely even in healthy cells, ranging from less than 5 to more than 50% of the total (dissolved plus particulate) primary production (Moran and Estrada, 2002). Anderson and Ducklow (2001) outlined the importance of PER vs. grazer-related sources in setting the overall level of bacterial metabolism in the sea. Williams (1981) hypothesized a larger role for PER, whereas Jumars et al. (1989) emphasized the primacy of grazers as DOM sources. Depending on the season, location, and particular environmental conditions of nutrient and light levels, grazing intensity, and other factors, many different scenarios are possible. Specifying how bacteria may respond to climate change requires better understanding of these rates, and the chemical composition of DOM released from a multitude of sources. For example, DOM released by grazing activities is probably of lower quality for bacterial nutrition, due to enzymatic attack, than that released by phytoplankton or viral lysis (Nagata, 2000). Changes in the physical or ecological state of ocean ecosystems affecting herbivores may cascade to changes in bacterial activity or community composition.</p> <p>Our understanding of microbial life in the oceans has escalated rapidly following the application of molecular tools (e.g., gene or whole genome sequencing, molecular profiling, fluorescent in situ hybridization), many of which have targeted the SSU rRNA gene, a phylogenetically informative molecule in which all forms of life can be compared. Marine microbial communities are diverse, although moreso at finer taxonomic scales than at gross phylum levels. Overall at the phylum level, there are some differences between ocean realms and between coastal vs. open ocean. Some distribution and biogeographically-based patterns are now emerging following extensive surveys of the world's ocean with these new tools. The upper oceans are dominated (25 to 33%) by SAR11-related bacteria members of the -proteobacteria (Morris et al., 2002), and the deeper oceans below 150 m harbor abundant marine GI crenarchaeotal populations (20 to 40% of DAPI-stained cells; Karner et al., 2001; Teira et al., 2006). Another numerous group of α-proteobacteria, common to both coastal and open ocean regions, the Roseobacter clade is often abundant (about 15% of the community; Buchan et al., 2005). There is high phylogenetic and functional diversity of marine γ-proteobacteria, which comprise a significant fraction of the bacterioplankton. Interestingly, though, γ-proteobacteria are often the most commonly cultivated marine bacteria, yet the cultivated species are rarely detected in molecular surveys. The more commonly detected γ-proteobacteria in cultivation-independent surveys on global scale harbor diverse metabolisms, and are in a number of cases strictly oligotrophic (Cho and Giovannoni, 2004). Marine Bacteriodetes-related organisms are a third group that includes diverse members that are not well represented in culture collections but can be numerically dominant (Cottrell et al., 2000). Interestingly, we now also know that species in each of these major phylogenetic groups found in oceanic photic zones contain proteorhodopsin, a membrane-associated light-driven proton pump. How these organisms utilize proteorhodpsin to supplement growth is still not well understood, although it may be a theme for organisms living in the upper ocean. Campbell et al. (2008) estimated that at least 14% of organisms living in the photic zone contain proteorhodopsin homologs.</p> <p>Biogeographic, temporal, and spatial surveys have also revealed considerable diversity and dynamics in community composition. For example, Pommier et al. (2007) compared the diversity of bacterioplankton assemblage at nine different sites around the world. Their findings suggest that despite the fact that the major phyla detected were similar, there were very few sequences that were detected repeatedly. Seasonal variation in coastal Antarctic waters is dramatic, with bacterial richness shifting significantly (Murray et al., 1998; Murray and Grzymski, 2007) and archaeal populations increasing in relative proportions in winter (Massana et al., 1998; Murray et al., 1998; Church et al., 2003). Vertical density stratification in the ocean (see below) has the most apparent impact on gradients of diversity in the ocean, however, as community diversity shifts most significantly with depth rather than with longitude or latitude. One of the caveats of nearly all studies is that the diversity is undersampled but new technologies in massively parallel DNA sequencing promise to reshape our views of species richness and our ability to compare in detail community composition from many sites using the same deep sequencing approach (Sogin et al., 2006; Huber et al., 2007).
(Continues...) Excerpted from Environmental Microbiology by Ralph Mitchell, Ji-Dong Gu. Copyright © 2010 Wiley-Blackwell. Excerpted by permission of John Wiley & Sons.
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The bestselling reference on environmental microbiology—now in a new edition

This is the long-awaited and much-anticipated revision of the bestselling text and reference. Based on the latest information and investigative techniques from molecular biology and genetics, this Second Edition offers an in-depth examination of the role of microbiological processes related to environmental deterioration with an emphasis on the detection and control of environmental contaminants. Its goal is to further our understanding of the complex microbial processes underlying environmental degradation, its detection and control, and ultimately, its prevention.

Features new to this edition include:

• A completely new organization with topics such as pathogens in developing countries, effects of genetically modified crops on microbial communities, and transformations of toxic metals

• Comprehensive coverage of key topics such as bacteria in the greenhouse and low-energy waste treatment

• New coverage relating core book content to local, regional, and global environmental problems

Environmental Microbiology, Second Edition is essential reading for environmental microbiologists and engineers, general environmental scientists, chemists, and chemical engineers who are interested in key current subjects in environmental microbiology. It is also appropriate as a textbook for courses in environmental science, chemistry, engineering, and microbial ecology at the advanced undergraduate and graduate levels.

Bacteria in the greenhouse : marine microbes and climate change / Hugh W. Ducklow ... [et al.] Control of waterborne pathogens in developing countries / Tim Ford and Steve Hamner New molecular methods for detection of waterborne pathogens / Alison M. Cupples, Joan B. Rose, and Irene Xagoraraki Microbial transformations of radionuclides in the subsurface / Matthew J. Marshall, Alexander S. Beliaev, and James K. Fredrickson Eutrophication of estuarine and coastal ecosystems / Nancy N. Rabalais Microbial deterioration of cultural heritage materials / Christopher J. McNamara, Nick Konkol, and Ralph Mitchell Sorption and transformation of toxic metals by microorganisms / Xu Han and Ji-Dong Gu Bioremediation of hazardous organics / Jennifer G. Becker and Eric A. Seagren Biosensors as environmental monitors / Steven Ripp, Melanie L. DiClaudio, and Gary S. Sayler Effects of genetically modified plants on soil microorganisms / Nicole Weinert ... [et al.] Anaerobic digestion of agricultural residues / Vincent O'Flaherty, Gavin Collins, and Thérése Mahony Anaerobic biodegradation of solid waste / Morton A. Barlaz ... [et al.] Low-energy wastewater treatment : strategies and technologies / Thomas P. Curtis Bioremediated geomechanical processes / Eric A. Seagren and Ahmet H. Aydilek. Microbial carbon cycling and climate change / H. Ducklow Control of water-borne pathogens in developing countries / T. Ford New methods for detection of water-borne pathogens / J. Rose Microbial contamination of subsurfaces / J. Fredrickson Eutrophication of marine waters / N. Rabalais Microbial deterioration of cultural heritage materials / R. Mitchell Adsorption, transport and transformation of metals / J.D. Gu Bioremediation of hazardous organics / E. Seagren and J. Becker Biosensors as bioremediation monitors / G. Saylor and S. Ripp Genomics and proteomics in pollution control / T. Hazen Unintended microbiological effects of GM crops / K. Smalla Biotech application to agricultural waste treatment / V. O'Flaherty Novel treatment of domestic wastes / T. Curtis Biological treatment of solid wastes / M. Barlaz.