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Salt marshes dominate the intertidal zone in temperate latitudes and present some unique features pertaining to measurement of primary production. Several destructive harvest and non-destructive methods for quantifying salt marsh production are described. Allometric methods that account for stem turnover are the recommended approach. Field and laboratory procedures illustrating the recommended protocol are detailed using examples from LTER sites.

Although there is a common perception that deserts support few species, some deserts have high local diversity, largely because organisms are able to exploit patches of high productivity. This chapter differentiates between local species richness (also called α diversity), β diversity, which is also known as species turnover or the change in species among sites, and γ diversity, which is regional species diversity. Productivity-diversity relationships have been well studied in some deserts and have helped us understand the factors controlling ecosystem function at a large spatial scale. Studies of convergence of desert communities and consideration of the similarity of desert communities with neighbouring mesic communities are some of the best elucidated of this genre. The chapter also considers the major differences and similarities among desert taxa in the various deserts of the world, to draw inferences on the major biogeographic patterns.

This chapter examines how phylogenetic diversity changes across spatial and temporal gradients. Spatial ecophylogenetic patterns can reveal how different processes shape ecological communities. Metacommunity ecology reinvigorated the search for general mechanisms that create diversity and structural differences among communities, and by using phylogenetic patterns we can understand how shared traits and evolution inform community differences. The chapter first considers phylobetadiversity as a measure of phylogenetic turnover before discussing two types of phylobetadiversity metrics, diversity partitioning and pairwise distances. It also analyzes the influence of spatial scale on phylogenetic patterns, focusing on the scale dependency of phylogenetic patterns, and concludes with an overview of phylogenetic diversity–area relationships.

This chapter focuses on the aerobic oxidation of organic material by microbes. Microbes account for about 50 per cent of primary production in the biosphere, but they probably account for more than 50 per cent of organic material oxidization and respiration (oxygen use). The traditional role of microbes is to degrade organic material and to release plant nutrients such as phosphate and ammonium as well as carbon dioxide. Microbes are responsible for about half of soil respiration while size fractionation experiments show that bacteria are responsible for about half of respiration in aquatic habitats. In soils, both fungi and bacteria are important, with relative abundances and activity varying with soil type. In contrast, fungi are not common in the oceans and lakes, where they are out-competed by bacteria with their small cell size. Dead organic material – detritus – used by microbes comes from dead plants and waste products from herbivores. This, and associated microbes, can be eaten by many eukaryotic organisms, forming a detritus food web. These large organisms also break up detritus to small pieces, creating more surface area on which microbes can act. Microbes in turn need to use extracellular enzymes to hydrolyze large molecular weight compounds, which releases small compounds that can be transported into cells. Photochemical reactions are also important in the degradation of certain compounds. Some compounds are very difficult to degrade and are thousands of years old.

The aerobic oxidation of organic material by microbes is the focus of this chapter. Microbes account for about 50% of primary production in the biosphere, but they probably account for more than 50% of organic material oxidization and respiration (oxygen use). The traditional role of microbes is to degrade organic material and to release plant nutrients such as phosphate and ammonium as well as carbon dioxide. Microbes are responsible for more than half of soil respiration, while size fractionation experiments show that bacteria are also responsible for about half of respiration in aquatic habitats. In soils, both fungi and bacteria are important, with relative abundances and activity varying with soil type. In contrast, fungi are not common in the oceans and lakes, where they are out-competed by bacteria with their small cell size. Dead organic material, detritus, used by microbes, comes from dead plants and waste products from herbivores. It and associated microbes can be eaten by many eukaryotic organisms, forming a detritus food web. These large organisms also break up detritus into small pieces, creating more surface area on which microbes can act. Microbes in turn need to use extracellular enzymes to hydrolyze large molecular weight compounds, which releases small compounds that can be transported into cells. Fungi and bacteria use a different mechanism, “oxidative decomposition,” to degrade lignin. Organic compounds that are otherwise easily degraded (“labile”) may resist decomposition if absorbed to surfaces or surrounded by refractory organic material. Addition of labile compounds can stimulate or “prime” the degradation of other organic material. Microbes also produce organic compounds, some eventually resisting degradation for thousands of years, and contributing substantially to soil organic material in terrestrial environments and dissolved organic material in aquatic ones. The relationship between community diversity and a biochemical process depends on the metabolic redundancy among members of the microbial community. This redundancy may provide “ecological insurance” and ensure the continuation of key biogeochemical processes when environmental conditions change.