1. Chapter 23 Microbial systems

2. I. Principles of Microbial Ecology  23.1 Ecological Concepts  23.2 Microbial Ecosystems and Biogeochemical Cycling

3. 23.1 Ecological Concepts  Ecosystem  The sum total of all organisms and abiotic factors in a particular environment  Habitat  Portion of an ecosystem where a microbial community could reside  An ecosystem contains many different habitats

4.  Microbes account for ~ 50% of all biomass on Earth  They are ubiquitous on the surface and deep within the earth

5.  Many microbes establish relationships with other organisms (symbioses)  Parasitism  One member in the relationship is harmed and the other benefits  Mutualism  Both species benefit  Commensalism  One species benefits and the other is neither harmed nor helped

6.  The diversity of microbial species in an ecosystem can be expressed in two ways  Species richness: the total number of different species present  Species abundance: the proportion of each species in an ecosystem  Microbial species richness and abundance is a function of the kinds and amounts of nutrients available in a given habitat

7. Microbial Species Diversity Figure 23.1 High Species Richness and Low to Moderate Abundance Low Species Richness and High Abundance

8. 23.2 Microbial Ecosystems and Biogeochemical Cycling  Guilds  Metabolically related microbial populations  Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem

9. Populations, Guilds, and Communities Figure 23.2

10.  Biogeochemistry: the study of biologically mediated chemical transformations  A biogeochemical cycle defines the transformations of a key element that is catalyzed by biological or chemical agents  Typically proceed by oxidation-reduction reactions  Microbes play critical roles in energy transformations and biogeochemical processes that result in the recycling of elements to living systems

11. II. The Microbial Habitat  23.3 Environments and Microenvironments  23.4 Biofilms: Microbial Growth on Surfaces  23.5 Biofilms: Advantages and Control

12. 23.3 Environments and Microenvironments  The growth of microbes depends on resources and growth conditions

13. Major Resources & Conditions Governing Microbial Growth

14.  Difference in the type and quantity of resources and the physiochemical conditions of a habitat define the niche for each microbe - Niche: an organism’s residence in a community  For each organism there exists at least one niche in which that organism is most successful (prime niche)  Microenvironment  The immediate environmental surroundings of a microbial cell or group of cells

15. Oxygen Microenvironment Figure 23.3

16.  Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally  Resources in natural environments are highly variable and many microbes in nature face a feast-or-famine existence  Growth rates of microbes in nature are usually well below maximum growth rates defined in the laboratory  Competition and cooperation occur between microbes in natural systems

17. 23.4 Biofilms: Microbial Growth on Surfaces  Surfaces are important microbial habitats because  Nutrients adsorb to surfaces  Microbial cells can attach to surfaces

18. Microorganisms on Surfaces Figure 23.4 Bacterial microcolonies on a microscope slide that was immersed in a river. Fluorescence photomicrograph of a natural microbial community living on a plant roots in soil.

19.  Biofilms  Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells  The matrix is typically a mixture of polysaccharides  Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

20. Examples of Microbial Biofilms Figure 23.5a Cross-sectional view of experimental biofilm

21. Figure 23.5b Natural biofilm on a leaf surface (Confocal laser scanning microscopy)

22. Figure 23.5c Biofilm of iron-oxidizing prokaryotes attached to rocks

23.  Biofilm formation is initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes  Genes encode proteins that synthesize intercellular signaling molecules and initiate matrix formation

24. Biofilm Formation Figure 23.6a

25. DAPI-Stained Biofilm That Developed on Stainless Steel Pipe Figure 23.6b

26. Biofilms of Pseudomonas aeruginosa Figure 23.7a Small “buttons” attached to the surface in the early stages of biofilm formation

27. A Mature Biofilm “Mushroom” of P. aeruginosa Figure 23.7b

28.  Intracellular communication (quorum sensing) is critical in the development and maintenance of a biofilm  The major intracellular signaling molecules are acylated homoserine lactones  Both intra- and interspecies signaling likely occurs in biofilms

29. 23.5 Biofilms: Advantages and Control  Bacteria form biofilms for several reasons  Self-defense  Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics)  Allows cells to remain in a favorable niche  Allows bacterial cells to live in close association with one another

30.  Biofilms are important in human health and commerce  Biofilms have been implicated in several medical and dental conditions  Including periodontal disease, kidney stones, tuberculosis, Legionnaire’s disease, and Staphylococcus infections  In industrial settings, biofilms can slow the flow of liquids through pipelines and can accelerate corrosion of inert surfaces  Few highly effective antibiofilm agents are available

31. III. Freshwater, Soil, and Plant Microbial Ecosystems  23.6 Freshwater Environments  23.7 Terrestrial Environments  23.8 Plants as Microbial Habitats

32. 23.6 Freshwater Environments  Freshwater environments are highly variable in the resources and conditions available for microbial growth  The balance between photosynthesis and respiration controls the oxygen and carbon cycles  Phytoplankton: oxygenic phototrophs suspended freely in water; include algae and cyanobacteria  Benthic species are attached to the bottom or sides of a lake or stream

33.  The activity of heterotrophic microbes in aquatic systems is highly dependent upon activity of primary producers; oxygenic phototrophs produce organic material and oxygen  Oxygen has limited solubility in water; once consumed in freshwater lakes the deep layers can become anoxic  Oxygen concentrations in aquatic systems is dependent on the amount of organic matter present and the physical mixing of the system

34.  In many temperate lakes the water column becomes stratified during the summer

35. Development of Anoxic Conditions in a Temperate Lake Figure 23.8 (Warmer and less dense) (Colder and more dense)

36.  Rivers  May be well mixed because of rapid water flow  Can still suffer from oxygen deficiencies due to high inputs of  Organic matter from sewage  Agricultural and industrial pollution

37. Effects of the Input of Organic-Rich Wastewaters Figure 23.9a

38. Figure 23.9b Blooming of phototrophs in an eutrophic lake

39.  Biochemical Oxygen Demand (BOD)  The microbial oxygen-consuming capacity of a body of water

40. 23.7 Terrestrial Environments  Soil  The loose outer material of Earth’s surface  Distinct from bedrock  Soil can be divided into two broad groups  Mineral soils  Derived from rock weathering and other inorganic materials  Organic soils  Derived from sedimentation in bogs and marshes

41. Profile of a Mature Soil Figure 23.10a

42. Photo of a Soil Profile Showing O, A, and B Horizons Figure 23.10b

43.  Soils are composed of  Inorganic mineral matter (~40% of soil volume)  Organic matter (~5%)  Air and water (~50%)  Living organisms

44.  Most microbial growth takes place on the surfaces of soil particles  Soil aggregates can contain many different microenvironments supporting the growth of several types of microbes

45. A Soil Microbial Habitat Figure 23.11

46. Scanning Electron Micrographs of Microbes on Soil Figure 23.12a A microcolony of coccobacilli

47. Figure 23.12b Actinomycete spores

48. Figure 23.12c Fungal hyphae

49.  The availability of water is the most important factor in influencing microbial activity in surface soils  Nutrient availability is the most important factor in subsurface environments

50. 23.8 Plants as Microbial Habitats  Rhizosphere  The region immediately outside the root  Zone where microbial activity is usually high  Phyllosphere  The surface of plant leaf  Microbial communities form in both the rhizosphere and phyllosphere of plants

51. Examples of Phyllosphere and Rhizosphere Microbial Life Figure 23.13a Fungus growing on the surface of a leaf

52. Figure 23.13b Bacteria on the rhizosphere/rhizoplane of clover Bacteria attached to the surface of root hair of clover

53.  Microbes can prove both beneficial and harmful to plants - Many bacterial and fungal phytopathogens are known

54. IV. Marine Microbial Ecosystems  23.9 Open Oceans  23.10 The Deep Sea and Barophilism

55. 23.9 Open Oceans  Compared with most freshwater environments, the open ocean environment is  Saline  Low nutrient; especially with respect to nitrogen, phosphorus, and iron  Cooler  Due to the size of the oceans, the microbial activities taking place in them are major factors in the Earth’s carbon balance

56.  Nearshore marine waters typically contain higher microbial numbers than the open ocean because of higher nutrient levels

57. Distribution of Chlorophyll in the Western North Atlantic Figure 23.14 Rich in phytoplankton

58.  Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophyte  Prochlorococcus accounts for  > 40% of the biomass of marine phototrophs  ~50% of the net primary production

59. Prochloroccocus, the Most Abundant Oceanic Phototroph Figure 23.15a FISH-stained cells in marine water sample Cell suspensions of Prochlorococcus

60.  The planktonic filamentous cyanobacterium Trichodesmium is an abundant phototroph in tropical and subtropical oceans  Small phototrophic eukaryotes, such as Ostreococcus, inhabit coastal and marine waters and are likely important primary producers Chloroplast

61.  Small planktonic heterotrophic prokaryotes are abundant (10 5 –10 6 cells/ml) in pelagic marine waters - The most abundant marine heterotroph is Pelagibacter, an oligotroph  Oligotroph: an organism that grows best at very low nutrient concentrations Pelagibacter ubique

62.  Pelagibacter and other marine heterotrophs contain proteorhodopsin, a form of rhodopsin that allows cells to use light energy to drive ATP synthesis  Aerobic anoxygenic phototrophs  Contain bacterichlorophyll a  Light is used for ATP synthesis via photophosphorylation in the presence of oxygen  Another class of marine microbes that use light energy but do not fix carbon dioxide Citromicrobium sp.

63.  Prokaryote densities in the open ocean decrease with depth - Surface waters contain ~10 6 cells/ml; below 1,000 m cell numbers drop to 10 3 –10 5 /ml  Bacterial species tend to dominate in surface waters and Archaeal species dominate in deeper waters

64. Percentage of Total Prokaryotes in the North Pacific Ocean Figure 23.19

65.  Viruses are the most abundant microorganisms in the oceans (10 7 virion particles/ml)  Viruses affect prokaryotic populations and are highly diverse

66. 23.10 The Deep Sea and Barophilism  > 75% of all ocean water is deep sea, lying primarily between 1000 and 6000 m  Organisms that inhabit the deep sea must deal with  Low temperature  High pressure  Low nutrient levels  Absence of light energy

67.  Deep sea microbes are  Psychrophilic (cold-loving) or psychrotolerant  Barophilic (pressure-loving) or barotolerant

68. Growth of Barotolerant and Barophilic Bacteria Figure 23.20

69. Sampling the Deep Sea Figure 23.21

70.  Adaptations to growth under high pressure are likely only seen for a few key proteins - e.g. OmpH: a type of porin synthesized only in cells grown under high pressure