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Wetlands harbor a variety of plants, particularly macrophytes, and animals, including birds, fish, reptiles, and mammals. These wetland plants and animals can adapt to an excess of water and often a lack of oxygen. This chapter examines the adaptations that have enabled a small number of vascular plants and vertebrate animals, the macrobiota, to thrive in wetlands. It discusses environmental and morphological characteristics of wetlands that can influence their use by various groups of animals, such as hydrology, water chemistry, water temperature, substrate, vegetation structure, and other species such as prey species, predators, and competitors. It also considers three characteristics that have made it possible for wetland plants to survive flooding and to spread in flooded environments: heterophylly, vegetative or clonal growth, and internal gas-space continuum.

In terms of energy base, wetlands appear to be hybrids of terrestrial and aquatic/marine habitats. Recognizing that the ecological functions of animals in wetlands share features with the faunas of terrestrial and aquatic/marine habitats, this chapter focuses on on some broadly applicable principles but highlights unique aspects of wetlands. The roles of animals in food webs are probably their most important contribution to overall wetland ecosystem function, and so the initial section of the chapter discusses animal trophic ecology. It then explores variation in wetland animal communities, emphasizing how communities change both spatially and temporally. The chapter also discusses the trophic basis for animal production, macrophytes and macrophyte herbivory, detritivory, algal herbivory, predation, community ecology, secondary succession, and biogeography. Finally, it analyzes the ecology of those animal populations that play especially important roles in wetland ecosystems or are of special interest to humans.

By definition, the water table of wetlands is near, at, or above the hydrosoil (sediment) surface. These changing hydrologic conditions are primary drivers of nutrient fluxes in the sediments and all aspects of plant biology: physiology, growth, and productivity. Because of the very nature of low elevational gradients within wetlands, there is a tendency for these regions of the whole ecosystem to retain organic matter either produced there by wetland plants or organic matter imported there from upland areas. The accumulated organic matter and associated nutrients promote two basic features of wetland ecosystems: an anoxic, reducing habitat of vigorously growing microbial communities on and within the sediments and organic debris, and very actively growing aquatic plants that are adapted to these growth conditions. This chapter discusses wetland ecosystem processes, focusing on periphyton as a critical metabolic component of aquatic ecosystems, nutrient retention and nutrient cycling in wetlands, modulation of periphyton by light availability, modulation of macrophytes and periphyton by mortality and losses, and potential effects of global climate change and related environmental conditions on ecosystem processes.

Microbe-mediated processes are crucial for biogeochemical cycles and the functioning of marine ecosystems (Azam and Malfatti 2007 ). If these processes are affected by ocean acidification, major consequences can be expected for the functioning of the global ocean and the systems that it influences, such as the atmosphere. In contrast to phytoplankton, which have been relatively well studied (see Chapter 6), there is comparatively little information on the effect of ocean acidification on heterotrophic microorganisms. Two reviews on the potential effects of ocean acidification on microbial plankton have recently been published (Liu et al. 2010 ; Joint et al. 2011) . In a recent perspective paper, Joint et al. (2011) concluded that marine microbes possess the flexibility to accommodate pH change and that major changes in marine biogeochemical processes that are driven by microorganisms are unlikely. Narrative reviews, which look at some of the relevant literature, are potentially biased and could lead to misleading conclusions (Gates 2002). Metaanalysis was developed to overcome most biases of narrative reviews. It statistically combines the results (effect size) of several studies that address a shared research hypothesis. Liu et al. (2010) used a metaanalytic approach to comprehensively review the current understanding of the effect of ocean acidification on microbes (including phytoplankton) and microbial processes, and to highlight the gaps that need to be addressed in future research. In the following, a brief digest on oceanic microbes and their role is provided for readers unfamiliar with this topic. Then the research that has been performed to assess the effects of ocean acidification on the diversity and activity of heterotrophic marine microorganisms is reviewed. Finally, scenarios are developed and potential implications are discussed. Microorganisms are defined as organisms that are microscopic, i.e. too small to be seen by the naked human eye, and mostly comprise single-celled organisms. Viruses are sometimes also included in this definition but it is hotly debated whether viruses are alive or not (Raoult and Forterre 2008). The current phylogeny considers three domains of cellular life, the Bacteria, the Archaea and the Eukarya.

Navigators visiting the Amazon during the fifteenth century provided the earliest descriptions of aquatic systems in the region, but it was not until mid twentieth century that systematic studies of the limnology of Amazon waters began (Sioli 1984). The inclusion of vegetation as an important part of the aquatic biota was only possible after the relatively recent change from traditional potamic limnology to wetlands limnology (Sioli 1975). The first studies of the vegetation of Amazon wetlands consisted mainly of species descriptions, and it is only recently that studies of floodplain vegetation have attained a level of importance equivalent to that of studies dealing with water chemistry, phytoplankton, zooplankton, and fishes. For the past thirty years, fertile floodplain systems along Whitewater rivers (várzea) have been focal areas of colonization. This fertility also supports high rates of primary production within the higher plants, especially of the herbaceous vegetation (Piedade et al. 1991, Junk and Piedade 1993a, 1997). Quickly turning-over pools of nutrients (Junk and Furch 1991, Furch and Junk 1992, 1997a) and direct connections with contiguous terra firme forest and river channels (Alves 1993, Furch and Junk 1997b) are also characteristic of these floodplain systems. As a consequence of the annual floodpulse (Junk et al. 1989), floodplain vegetation is subjected to aquatic and terrestrial phases, which hold important ecological implications for both the plant populations and related aquatic and terrestrial biota. Life cycles of the species and the time available for growing depend upon the duration of inundation and drought periods and the habit of the species. During the year, pulses of growth and dormancy occur and herbaceous vegetation changes its species composition according to the phase of the hydrological cycle. In this chapter we discuss the distribution and the development of plant communities in floodplain areas, mainly of the big Whitewater rivers, focusing on factors such as diversity, species composition, biomass and primary production. Based upon these factors, we also discuss the annual dynamics of bioelements stocks and their turnover through herbaceous and floodplain forest communities. Finally, we examine the implications of such nutrient dynamics and turnover for the aquatic biota.

Wetlands are land areas with shallow water or saturated soils that support a wide variety of plants not found somewhere else in the surrounding uplands. Although wetlands share a number of similarities with nearby aquatic and terrestrial ecosystems, they have two unique features: anaerobic soils and macrophytes. Wetlands are found in almost every climatic zone in every continent except Antarctica. They can be classified based on their hydrology, vegetation, and/or geomorphology.

Ecologists, conservationists, and managers frequently need to recognise and survey different aquatic plant species, vegetation types, plant communities, or habitat. It is, after all, the vegetation that defines the extent of a freshwater wetland. This chapter reviews the methods used to survey both ‘terrestrial’ and ‘aquatic’ freshwater plants and considers the approaches taken, some of the specialised equipment used, and technical expertise needed to conduct wetland vegetation surveys. The techniques and approaches used and associated sampling strategies are considered for field surveys; experiments including meso- and macrocosms; and surveys involving remote sensing techniques. The chapter ends by examining a series of examples that illustrate how different vegetation research questions in ecology, conservation, and management can be answered using a diversity of methods.

Freshwater ecosystems are particularly susceptible to invasions by invasive non-native species (INNS) across a range of taxa, largely as a consequence of anthropogenic influences on these systems, with a number of ecological and socio-economic impacts. This chapter reviews freshwater invasive non-native species across the globe, focusing on fishes, invertebrates, floating macrophytes, and submerged macrophytes emphasising the knowledge gaps in particular that have resulted in biases inherent in assessments of freshwater invasions. These include an ecological bias because the majority of studies focus on terrestrial invasions; a geographical bias as most studies are focused on temperate northern hemisphere systems; and a taxon bias where fish invasions, populate the literature. This chapter highlights some of the approaches needed to survey, monitor, and manage INNS.