Microbial Terrestrial & Aquatic Environments

Microbiology

1. CEE 298: Advanced Biological Treatment Dr. Shakira Hobbs Assistant Professors Civil & Environmental Engineering Module 1.2 –Terrestrial & Aquatic Environments Lecture 3: April 16, 2024 Cavicchioli , R., Ripple, W.J., Timmis , K.N.  et al.  Scientists’ warning to humanity: microorganisms and climate change.  Nat Rev Microbiol   17 , 569–586 (2019). https:// doi.org /10.1038/s41579-019-0222-5

2. Objective(s) for today: (1) Understand terrestrial and aquatic environments along with relevant terminology. (2)Demonstrate knowledge of terrestrial and aquatic environments and characteristics.

3. Microbial species diversity: Richness vs. abundance Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

4. Energy Inputs to the Ecosystem Energy enters the system as sunlight, organic carbon and reduced inorganic substances Light is used by phototrophs to make ATP and synthesize new organic matter New organic matter contain N, S, P, Fe and other elements of life This newly synthesized material fuel catabolic activities of chemoorganotrophic organisms The activities oxidize organic matter to CO2 by respiration or ferment it to various reduced substances.

5. Population guilds, and communities Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

6. Resources and conditions that govern microbial growth in nature Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

7. Biofilms The matrix is typically a mixture of polysaccharides Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

8. Examples of Biofilms Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

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

10. Pseudomonas aeruginosa Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003.. Biofilm producer Intracellular communication (quorum sensing) is critical in the development and maintenance of a biofilm. The major intracellular signaling molecules are acylated hormones lactones. Both intraspecies signaling and interspecies signaling like to occur in biofilms.

11. Bacteria form biofilms for several reasons 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

12. Biofilms have been implicated in several medical and dental conditions Biofilms have been used to treat periodontal disease, kidney stones, tuberculosis, Legionnaires’ disease, Staphylococcus infections, others 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

13. Microbial Mats are very thick biofilms Phototrophic mats contain filamentous cyanobacteria Cyanobacterial mats are complete ecosystems Have existed for over 3.5 billion years Chemolithotrophic mats contains filamentous sulfur-oxidizing bacteria.

14. The layers are composed of species of different microbial guilds. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

15. Example of microbial mats on top of one another. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

16. Think, pair, share. Why might a biofilm be a good habitat for bacterial cells living in a flowing system? Give an example of a medically relevant biofilm that forms in virtual all healthy humans. How do different intercellular signaling molecules modulate biofilm formation and dispersal? Active Learning Take a minute to answer the following questions individually, then pair up and discuss.

17. Terrestrial Environments Consist of four distinct layers: O horizon at the surface, with undecomposed plant material A horizon , with most microbial growth, rich in organic material and nutrients B horizon , the subsoil where organic material leached from the A horizon gathers, little microbial activity C horizon , the base that is directly above the bedrock and forms from the bedrock

18. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

19. Soil can be divided into two broad groups Soils are composed of ~40% inorganic mineral matter ~ 5% organic matter ~50% air and water ~5% living organisms

20. 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. Very few microorganisms are free in the soil solution Most microorganisms reside in microcolonies attached to the soil particles. A soil Microbial Habitat. Taken from: Madigan et al. (2009)

21. Soil are formed by interdependent physical, chemical, and biological processes Carbon dioxide is formed by respiring organism that form carbonic acid that breaks down rock Physical processes such as freezing and thawing break a part rocks, allowing plant roots to penetrate and form an expanded rhizophore.

22. Availability of water and nutrients in environments

23. Water availability: Vegetated and Dryland Soils are Microbial Habitats Water availability is variable and dependent on rainfall, plant coverage, drainage, and soil composition. Soil water has many dissolved materials and is called a soil solution Well-drained soils have oxygen available, while waterlogged soils are typically anoxic, with the oxygen being consumed by the soil microbiota.

24. Arid soil are dry, have limited plant growth, and are home to microbial communities specialized for extreme conditions Arid soils lose more moisture from evapotranspiration than is gained from precipitation. Arid soils make up ~35% of the Earth’s land mass and are extreme environments, with low water availability and are variable temperatures (over 60 degrees and below -24 degrees C). Biological soil crusts are made up of photosynthetic cyanobacterial and filamentous fungi that stabilize the soil. Arid soils are very slow to form and are subject to desertification where the biological soil crust is damaged and soil fertility is decreased.

25. Example of Biological Soil Crust Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

26. Microbial diversity varies with soil type and geographical location Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

27. Terrestrial Subsurface The deep soil subsurface can extend for several hundred meters below the soil surface Archaea and Bacteria are believed to exist in deep subsurface in variable concentrations, depending on nutrient availability In general, subsurface microbial life grows in an extremely limited environment. The deep subsurface is home to a group of organism that may be the Archaea that are most closely related to eukaryotes, the Lokiarcheota .

28. Quick Video https:// education.nationalgeographic.org /resource/extremophiles-101/

29. Freshwaters 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 lake or streams.

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

31. Freshwaters In many temperate lakes, the water column becomes stratified during the summer. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

32. Rivers May be well mixed because of rapid water flow Can still suffer from oxygen deficiencies because of high inputs of organic matter from sewage and agricultural and industrial pollution Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

33. Biochemical oxygen demand (BOD) The microbial oxygen-consuming capacity of a body of water Increases with the influx of organic material (e.g. from sewage), then decreases over time. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

34. Marine Environment: Phototrophs and Oxygen Relationships Compared with most freshwater environments, the ocean environment is saline, low in nutrients, especially with respect to nitrogen, phosphorus, and iron, and cooler Because of the size of the oceans, the microbial activities taking place in them are major factors in Earth’s carbon balance. Near-shore marine waters typically contain higher microbial numbers than the open ocean because of higher nutrient levels Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

35. Deepwater Horizon oil spill Largest marine oil spill Oil released as a plume at great depths Blook of hydrocarbon-degrading Gammaproteobacteria , Colwellia , and Cycloclasticus Early growth of hydrocarbon-degrading bacteria may have reduced environmental impact. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

36. Oxygen Minimum zones Regions of oxygen-depleted waters at intermediate depths High oxygen demand Nutrient-rich areas High levels of denitrification and anammox (anerobic ammonium oxidation) Oxygen minimum zones are expanding

37. Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophytes Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003.. Contains chlorophylls a and b Prochlorococcus accounts for >40% of the biomass of marine phototrophs ~50% of the net primary production

38. Major Marine Phototrophs The planktonic filamentous cyanobacterium Trichodesmium is an abundant phototroph in tropical and subtropical oceans Small phototrophic eukaryotes, such as Ostreococcus , inhabit costal and marine waters and are likely important primary producers. Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

39. Aerobic anoxygenic phototrophs Another class of marine microbes that use light energy but do not fix carbon dioxide. Light is used for ATP synthesis via photophosphorylation.

40. Pelagic Bacteria, Archaea, and Virus Small planktonic heterotopic prokaryotes are abundant (10 5 -10 6 cells/ml) in pelagic marine waters. Prokaryote densities in the open ocean decrease with depth Surface waters contains ~10 6 cells/ml; cell numbers drop to 10 3 -10 5 /ml below 1000m in depth. Bacterial species tend to dominate surface waters. Bacteria and Archeae near equal in deeper waters Brock, T. D., Madigan, M. T., Martinko , J. M., & Parker, J. (2003).  Brock biology of microorganisms . Upper Saddle River (NJ): Prentice-Hall, 2003..

41. Deep-sea Microbes Adaptation for growth under high pressure are likely seen only for a few key proteins that are adapted for cold (short chain fatty acids in membranes and increased alpha helices in proteins).

42. Coming Up Class Tuesday, April 23 rd –in-person instruction (Lecture: Aquatic & Terrestrial Environments and Carbon Cycle) To-Do: Thursday, April 18 th –Work on Winogradsky Final Project Objective(s) for today: (1) Understand terrestrial and aquatic environments along with relevant terminology. (2)Demonstrate knowledge of terrestrial and aquatic environments and characteristics.