Biogeochemical Cycling and Introductory Microbial Ecology Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Chapter 27 Biogeochemical Cycling and Introductory Microbial Ecology

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Microbial Ecology the study of community dynamics and the interaction of microbes with each other, with plants and animals, and with the environment in which they live Microbes make life possible microbes play a major role in life on earth, yet only ~ 1% of all species have been cultured, identified, and studied

Foundations of Microbial Ecology Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Foundations of Microbial Ecology populations assemblages of similar organisms communities mixtures of different populations ecosystems self-regulating biological communities and their physical environment

Biogeochemical Cycling Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Biogeochemical Cycling biogeochemical cycling of nutrients involves biological and chemical processes often involves oxidation-reduction reactions that change chemical and physical characteristics of nutrients all nutrient cycles are linked and make life on Earth possible

Carbon Cycle Carbon can be a variety of forms Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Carbon Cycle Carbon can be a variety of forms reduced e.g., methane (CH4) and organic matter oxidized e.g., CO and CO2

Carbon Cycle Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Carbon fixation can occur through the activities of photoautotrophic and chemoautotrophic organisms. Methane can be produced from inorganic substrates (CO2 and H2) or from organic matter. Carbon monoxide, produced by sources such as automobiles and industry, is returned to the carbon cycle by CO-oxidizing bacteria. Aerobic processes are noted with blue arrows, and anaerobic processes are shown with red arrows. Figure 27.2

Degradation of organic matter Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Degradation of organic matter influenced by several factors nutrients present in environment abiotic conditions microbial community present

nutrient immobilization Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Table 27.2 mineralization decomposition of organic matter to simpler inorganic compounds (e.g., NH4) protein to ammonium ions nutrient immobilization the nutrients that are converted into biomass become temporarily unavailable for nutrient cycling.

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Microorganisms form different products when breaking down complex organic matter aerobically than they do under anaerobic conditions. Under aerobic conditions oxidized products accumulate, while reduced products accumulate anaerobically. These reactions also illustrate commensalistic transformation of a substrate, where the waste products of one group of microorganisms can be used by a second type of microorganism. Figure 27.3

Nitrogen Cycle can be carried out by either autotrophs or heterotrophs Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Nitrogen Cycle can be carried out by either autotrophs or heterotrophs Flows that occur predominantly under aerobic conditions are noted with open arrows. Anaerobic processes are noted with solid bold arrows. Processes occurring under both aerobic and anaerobic conditions are marked with cross-barred arrows. The anammox reaction of NO2– and NH4+ to yield N2 is shown. Important genera contributing to the nitrogen cycle are given as examples. Figure 27.4

Nitrogen Cycle nitrogen fixation reduction of N2organic nitrogen Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Nitrogen Cycle nitrogen fixation reduction of N2organic nitrogen unique to procaryotes requires an expenditure of energy, source of electrons, and anaerobic environment carried out by aerobes or anaerobes aerobes use a variety of strategies to protect nitrogenase from oxygen

Nitrogen Cycle product of nitrogen fixation is ammonium (NH4+) Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Nitrogen Cycle product of nitrogen fixation is ammonium (NH4+) immediately incorporated into organic matter as an amine nitrification deamination of amino acids NH4+ NO2- NO2-  NO3-

More on the Nitrogen Cycle Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. More on the Nitrogen Cycle fate of NO3- assimilatory nitrate reduction NO3- is reduced and incorporated into organic nitrogen dissimilatory nitrate reduction NO3- serves as a terminal electron acceptor during anaerobic respiration NO3- removed from ecosystem and returned to atmosphere as dinitrogen gas (N2)

Phosphorous Cycle has no gaseous component Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Phosphorous Cycle has no gaseous component environmental phosphorus usually present in low concentrations; is often the growth limiting nutrient phosphorus exists in both organic and inorganic forms orthophosphate (+5 valence)complex forms of phosphorus, including polyphosphates

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Figure 27.5

Sulfur Cycle dissimilatory sulfate reduction Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Sulfur Cycle dissimilatory sulfate reduction the use of sulfate as a terminal electron acceptor assimilatory sulfate reduction the reduction of sulfate for use in amino acid and protein biosynthesis

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Sulfur Cycle Photosynthetic and chemosynthetic microorganisms contribute to the environmental sulfur cycle. Sulfate and sulfite reductions carried out by Desulfovibrio and related organisms (purple arrows) are dissimilatory processes. Sulfate reduction also can occur in assimilatory reactions, resulting in organic sulfur forms. Elemental sulfur reduction to sulfide is carried out by Desulfuromonas, thermophilic archaea, or cyanobacteria in hypersaline sediments. Sulfur oxidation can be carried out by a wide range of aerobic chemotrophs and by aerobic and anaerobic phototrophs. Figure 27.6

Interaction of Element Cycles Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Interaction of Element Cycles in nature cycles do not occur independently e.g., an autotroph that fixes CO2 also requires N, P and S for protein, nucleic acid and phospholipid synthesis

The Physical Environment Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. The Physical Environment influences interactions of microorganisms with each other and with other organisms

The Microenvironment and Niche Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. The Microenvironment and Niche microenvironment specific physical location of microorganism impacted by fluxes of nutrients and diffusion rates of waste products niche function of an organism in a complex system, including place of the organism, resources used in a given location, and time of use

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Creation of a niche from a microenvironment. As shown, 2 nearby particles create a physical microenvironment for possible use by microorganisms. Chemical gradients, as with oxygen from the aerobic region, and sulfide from the anaerobic region, create a unique niche. This niche thus is the physical environment and the resources available for use by specialized aerobic sulfide-oxidizing bacteria. Figure 27.10

Biofilms and Microbial Mats Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Biofilms and Microbial Mats biofilms organized microbial systems consisting of layers of microbial cells associated with surfaces (layers of organisms of different types) Catheters and dialysis units formation of biofilms creates microenvironments and niches hospitable to different types of microbes Antibiotic resistance, waste product - nutrient microbial mats thick biofilms having macroscopic dimensions often found in aquatic environments Photosynthetic zone (Cyanobacteria), sulfur reducing bacteria (Desulfovibrio), anoxygenic photosynthetic bacteria (Chromatium).

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Winogradsky column

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Figure 27.11

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Microbial mat Figure 27.12

Microorganisms and Ecosystems Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Microorganisms and Ecosystems ecosystems communities of organisms and their physical and chemical environments that function as self-regulating units

Roles of organisms in ecosystems Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. Roles of organisms in ecosystems primary production synthesis of organic matter from CO2 and other inorganic compounds primary producers organisms that carry out primary production decomposers decompose accumulated organic matter the microbial loop describes the interactions of microbial loop the multiple and overlapping roles played by microorganisms in nutrient cycling