Soil Biology CSS 360
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This 13 page Class Notes was uploaded by Rosalind O'Connell on Saturday September 19, 2015. The Class Notes belongs to CSS 360 at Michigan State University taught by Staff in Fall. Since its upload, it has received 38 views. For similar materials see /class/207207/css-360-michigan-state-university in Soil Science at Michigan State University.
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Date Created: 09/19/15
FINAL EXAM REVIEW CSS360 For the lab practical you should be familiar with the morphology of each of the examples given in class Be able to identify each type of organism and identify basic appendages from the class slides and the book The lab practical is worth 41 points and the final exam is worth 89 points for a total of 13 points We will go over slides on Wed Nov 30th 1 Name the three groups ofprotozoa and describe their morphology Ciliates move with hairs along body used like oars consume up to 10000 bacteria per day Flagellates whiplike organ used for movement common in a wide range of soils Amoeba move using a temporary foot or pseudopod can explore very small pores 2 What is the role ofprotozoa in the nitrogen cycle How is this related to the bacterial community Protozoa consume a lot of bacteria and excrete high N waste because their CN is higher than bacteria s The N released is NH4 and redeposition 3 What is endocytosis Endocytosis is a process by which cells absorb moleculessuch as proteins from the environment by engul ng them Protozoa use this 4 What food source can amoeba explore that other protozoa cannot Amoeba can explore micropores by squeezing through whereas other protozoa can t 5 What is the difference between naked and testate quottestquot amoeba Test amoeba cover themselves with excretions and soil matter to better withstand harsh conditions such as low water 6 What affect does soil moisture play on protozoa abundance and activity Since protozoa rely on water for movement low soil moisture will make it more difficult to move around to eat and mate and so on 7 What environmental factors play a role in encystment ofprotozoa Encystment ofprotozoans is triggered by food shortage oxygen depletion wetdry extremes and predation 8 Would you expect protozoa to more or less abundant in the rhizosphere Why Protozoans are more abundant in the rhizosphere because they feed on bacteria which are more abundant in the rhizosphere 9 What are the properties of rotifers Under what soil moisture conditions would they be most expected to be found Why Rotifers have cilia on heads and 39toes with glue secreting glands that can attach to substrate They are most likely found in environments of high soil moisture especially ooded soil They move water with their mouth organs to engulf bacteria and they also have primitive eyes 10 What is parthenogenesis Give an example In parthenogenesis females produce eggs that selffertilize no male needed Males that are born cannot feed only reproduce Rotifers are an example 11 What do nematodes feed on Nematodes feed on fungi bacteria plant roots other smaller nematodes 12 How are the feeding characteristics of nematodes identified through the microscope Lesion nematodes has a shorter thicker stylet in its mouth than the root feeder 13 Why may nematodes be good indicators of overall soil health and condition Nematodes are a good indicator of soil health because a high amount ofnematodes means that there is also a large number of their prey indicating high overall N and C in the soil 14 How does the Baermann funnel method work for the collection ofnematodes that we did in lab With the Baermann funnel nematodes migrated down the funnel tube along with water bears rotifers via gravity to be collected 15 What is the role ofnematodes in the soil N cycle Nematodes redistribute nutrients because they have lower N requirement than bacteria or fungi so net N release like protozoa 16 What is the relationship between nematode abundance and prey At low densities nematodes stimulate prey plants bacteria fungi at higher densities they may reduce prey populations altering fungalbacteria ratios and the structure of microbial communities 17 What is the difference between a root lesion nematode and a root feeder nematode Root feeders use their stylets to puncture the root and feed off the contents Root lesion nematodes are migratory endoparasites they can migrate in and out of the plant root Lay eggs in plant root 18 What is cryptobiosis Give an example of an organism that employs this strategy Cryptobiosis is a state ofno detectable metabolic activity Tardigrada employ this 19 What are some of the unique characteristics of Tardigrada Tardigrada are able to withstand extremes such as survive in a pure vacuum of space 20 How do the microarthropods play a central role in the food web Microarthropods feed on nematodes so top down pressure on bacteria fungi is changed Are prey for larger macroinvertebrates shred organic matter Oribatid mites ingest OM etc Mix and aerate soil Eat nematodes regulate the size of all other populations 21 What is the relationship between organic matter and microarthropod density What about soil structure and microarthropods Higher OM higher microarthropod higher soil structure is same bc generally more OM higher water holding capacity more protozoa more nematodes Microarthropods affect soil structure but play a lesser role when comparing to macroarthropods 22 What microarthropod is the most numerous in the rhizosphere Why do you think that is Collembolans are the most numerous microarthropod in the rhizosphere because they feed primarily on fungi which are more abundant in the rhizosphere 23 How do collembolans respond to disturbance Would they be considered to be R or Kstrategists Collembolans are able to come back in abundance after a disturbance because they multiply quickly They are Rstrategists 24 What is the general diet of collembolans Collemb olans eat fungi 25 What is the direct effect of collembolans on ecosystem energy ow Collembolans have effects on N mineralization soil respiration indirectly leaching of DOC plant growth Grazing on fungal hyphae is major contribution selectively change fungal community composition can stimulate fungal growth b c of this 26 How may the collembolan diet in uence the decomposition process Decomposition can be slowed because the collembolans feed on fungi which decompose They can also specifically feed on certain fungi which may change a component of the decomposition process 27 What three factors make Oribatid mites unique among the soil fauna Oribatid mites occur in huge numbers undergo juvenile polymorphism juveniles do not resemble their adult form reproduce very slowly can be parthenogenic and are K strategists 28 What ecosystem type supports the highest Oribatid numbers Forests have the highest Oribatid numbers 29 How do Oribatid mites affect litter decomposition and nutrient cycling Oribatid mites shred OM graze on fungi populations and store Ca 30 What are the main diets ofprostigmatic mites How does this differ among the quotsmallquot and quotlargequot prostigmatic mites Smaller prostigmatic mite eat nematodes and fungi larger one eat arthropods and their eggs 31 Which group of mites are the least common Where may they be found Astigmatic mites are least common and can be found in moist environments in high OM after manure application and after harvest 3 2 What are cryptozoans C ryptozoans are small generally microscopic animals that permanently live under conditions with high relative humidity They can be found hiding under things like bark rocks and litter 33 What are the Enchytraeidae How can they affect organic matter dynamics and soil structure Enchytraeidae are potvvorms they ingest OM and mineral soil Feeding on fungi and bacteria can increase bacterial metabolic activity and turnover accelerate release of nutrients change species composition Fecal pellets can occlude soil OM 34 How can collembolans affect plant fungal infection Collembolans sometimes selectively feed on fungal plant pathogens 35 What are the three ecological groups of earthworms How are they classified Anecic nightcrawler litter soil feeder Endogeic soil feeder Epigeic leaf worms litter feeder 36 What are the diplopoda How does their diet differ from centipedes Diplopoda are millipedes they are saprophages which consume organic debris where as centipedes are predators 37 Why would millipedes favor eating their own feces The millipedes eat their own poo to supply their gut with microbes for breaking down material 38 What is the role of spiders in the soil food web Spider predate on soil fauna like collembolans Feed on collembolans depress their size litter decomposition increases 39 What are some roles of beetles in agriculture and decomposition In agriculture beetles prey on pest insects early stages of wood decomposition root feeders predators 40 What are the roles of ants in the soil ecosystem Ants are ecosystem engineers major predators of soil mites esp oribatids activities reduce abundance of other predators such as spiders and some beetles in uence soil structure 41 Why are termites among the most important of the soil fauna in terms of decomposition and soil structure Termites have high biomass process large amounts of litter distribute OM grow fungus colonies and in deserts they process large amounts of dead and dying primary production 42 How do earthworms affect soil structure Earthworms create open channels with their burrows 43 What is the mode of reproduction for earthworms Earthworms are hermaphroditic each possess male and female organs sperm exchanged between worms and later released with eggs into cocoons SOME parthenogeniccan establish itself in new habitats 44 What is the role of earthworms in forest soils in terms of surface litter decomposition Earthworms bring surface litter down into the soil column 45 Compare and contrast the three groups of earthworms Anecic Litter and soil large size lives in burrows in soil permanent burrows cast on the surface Epigeic Live in the litter layer and surface soil feed on litter small size no burrows highly pigmented Endogeic A B C horizon unpigmented extensive horizontal burrows very large 46 What are earthworm casts How do they affect the soil Earthworm casts are produced after earthworms ingest soil matter mix them enrich them with organic secretions colonization by microbes can harden into soil aggregates enhance soil fertility 47 What is the interaction between residue type and earthworm abundance on water infiltration rates Permanent macroporesvia secretions and burrowing In the surface the epigeic earthworms have horizontal and vertical burrows water infiltration may be limited due to casts Anecic vertical burrows stable via OM and secretions continuous macropores 48 Why is it important to know the life cycle ofa soil pest before deciding on the treatment course This is important to determine whether to control the grub or adultmost control focuses on the juvenile 49 What are some ways that the Japanese beetle can be treated Some ways to control the Japanese beetle are the use of microbes or macroorganisms such as bt strains or parasitic nematodes or trap crops 50 What is phenol oxidase Phenol oxidase is an enzyme that catalyzes oxidation 51 Why is C02 measured when different substrates are added to a soil suspension like in lab C02 is measured to observe the metabolic potential of the soil 52 Why is selective media used for culturing bacteria What is the great plate anomaly Selective media is used to cultivate specific species The great plate anomaly is that there is a huge diversity of microbes on earth but only a few are cultivatable 53 Two soils have the same composition One is more aerated than the other Which one would be expected to have higher phenol oxidase activity and why The aerated soil would have a higher phenol oxidase activity because the enzyme uses C02 in its actions 54 What is the difference between glucoside and glucosidase Glucosidase catalyzes the hydrolysis of glucoside to produce smaller sugars 1 Why may earthworms be used for the reclamation ofpreviously nonarable lands Earthworms create permanent macropores with their burrowing which increases aeration They also move around nutrients withing the soil column 2 From what you know about nutrients bacteria fungi and micro and mesofauna differentiate what you would expect to find in the rhizosphere versus the bulk soil in terms of abundance not real numbers and distribution Rhizosphere V Bulk Soil Higher N and C phenolic compounds Higher bacterial abundance because of higher nutrients 02 Higher fungi abundance can feed on phenolic compounds Phenol oxidase breaks down phenolic compounds Fungal feeding nematodes will be higher can feed on plant pathogens Springtails collembola also feed on plant pathogens Prostigmatic mites will be higher It s going to be drier around the roots so less protozoa because of this buts lots of food for them so it depends Less earthworms 3 Why do the microbial decomposers have the largest impact on energy ow in a soil system Decomposers are very important because they break down the leaf litter initially bringing nutrients into the food chain 4 Why do mites have topdown control on the other soil biota Describe why this is Large mites eat smaller mites and nematodes mites eat nematodes fungi and bacteria 5 Draw a food web pyramid List what types of organisms would be present at each level of the pyramid em ms a What would happen lfyou Increased the blomass ofthe bottorn level7 ll lncrease b lee an example of decreaslngthe blomass of an upper level and how that would affect the levels above and below lt the fungal bacterlal and micro messy and rnaorofauna populatlons Forest v Fleld temperate o Forest has hlgher OM WHO and aggegahon o Forest has hlgherbaetenal and fungal dlverslty o ngher protozoa abundance tn forest because they feed on battena anol nernatooles feed on hyphae and wlll be hlgner ln forest o Tardlgrada are usually found where there ls lots of algae so posslbly wlll be found E w o Mltes onbatlol astlgrnaoe rnesosogrnatle prosogrnatle o hreololers Onbaods eause greater OM o s grnatle rnltes feed on battena so more ln forest 0 o Macrofa una Mlllpedes anol potworrns eat OM C853 60 Exam 1 Review Questions and Study Guide I Questions Based on Lecture Materials A Soil Properties What contributions to overall soil health do soil aggregates provide For example what soil properties are in uenced by the presence of aggregates What differentiates the O A and E horizons in a soil profile In a highly reduced soil eg a waterlogged or saturated soil what is the source of the small red dots as in slide 17 of lecture 1 Given the soil textural triangle below indicate what soil texture is composed of 60 silt and 20 sand 100 0 clay Silty clay loam 70 Clay loam 30 Sandy clay loam 20 Loam 80 4 Silt loam 10 09 Sandy loam 90 s 0 0 Sand 6 SIIt giIOtOA 0 100 90 8O 70 60 50 4O 30 20 10 sand Percent Sand A sample of soil reveals that 3 cm3 of soil has a mass of 630 g What is the bulk density of the soil What will happen to the bulk density and particle density of a mineral soil when organic matter is incorporated Why is this the case Differentiate between micropores and macropores What roles do they play in water holding capacity and water movement What is the matric potential of a soil What happens to the matric potential as soils begin to dry out What is the difference between gravitational water and field capacity B Soil Carbon Why is soil organic carbon important to overall soil health Why does tilling reduce soil organic carbon over time How does the active carbon pool differ from the slow and passive carbon pools What type of matter constitutes each pool Which carbon pool responds the fastest to changes in soil management What are some methods that can be used to build soil carbon 9 l 000 weww H Ch 7 8 9 How does the ON ratio ofa substrate eg manure compost plant litter that is incorporated into a soil in uence N availability to plants and the buildup of soil organic matter An N poor amendment is added to a soil with a CN ratio of 361 What happens to the nitrogen in the amendment and how does this affect the microbial community What is lignin How does the ligninN ratio affect the speed of decomposition Why What are some controls over soil aggregate formation and stability C Soil Bacterial Genetics and Gene Exchange What is the difference between prokaryotes and eukaryotes What are the 3 domains oflife How do archaea differ from bacteria Name three different types of bacterial shapes Why is endospore formation important in soils What is the difference between a Gram and Gram bacteria Bacteria A has a Ks of 40 mmol while bacteria B has a Ks of110 mmol while growing on glucose Based on this information which bacteria would you expect to have a competitive advantage at a substrate concentration of 30 What is the difference between a copiotroph and an oligotroph Assuming that both can grow on the same substrate which would quotwinquot when the limiting substrate is at a high concentration What is the central dogma ofmolecular biology What is the structural difference between RNA and DNA What is the ribosome and why is it important in cell function 10 What is the difference between transcription and translation 11 Why is the 165 rRNA gene the current basis for bacterial taxonomy 12 Name one problem encountered by using 165 rRNA gene for bacterial taxonomy 13 What is the role of the plasmid in bacteria 14 Name three methods by which genetic material is exchanged among soil bacteria 15 Why is conjugation the most important pathway of genetic exchange among bacteria D Bacterial Diversity Viruses and Metabolism What soil properties have been proposed to control bacterial diversity What are the properties of viruses How do they differ from bacteria What are the two life cycles ofbacteriophages How can bacteriophages increase bacterial genetic diversity Why are bacteriophages not as important in soil as they are in the aquatic environment A bacteria obtains its carbon from C02 and its energy from photosynthesis What is the class of this bacteria Differentiate between a chemoheterotroph and a chemoautotroph 8 What is being reduced accepting electrons and what is being oxidized donating electrons in the following reaction C6H1206 aq 6 02 g gt 6 C02 g 6 H20 9 Name four electron acceptors in bacterial metabolism and place them in order of the highest energy yielding to the lowest energy yielding 10 Where would you expect to find aerobic respiration occurring in a ooded soil 11 Where would you expect to find anaerobic respiration occurring in a well aerated soil 12 What are siderophores 13 How does sulfate reduction and C02 reduction methanogenesis differ from the other methods ofmetabolism in regard to their C source 14 What is the advantage of using enzymes in a chemical reaction 15 What is the role of cofactors in enzymes 16 How are enzyme kinetics Vmax and Km in the graphs related to bacterial growth kinetics 17 Name two environmental factors that control enzyme activities 18 What is the difference between an ectoenzyme and an exoenzyme E Nitrogen Cycling 1What is meant by quotredox power in terms of electron ow from a donor to an acceptor 2 Name three input sources of nitrogen to soil 3 What regulates N fixation 4 What is a heterocyst Who uses them 5 Name the three types of N fixation discussed in lecture 6 Discuss the general steps of Rhizobia infection of legume root hairs 7 What is the advantage to the plant and to the bacteria in symbiotic N fixation 8 Discuss the difference between N mineralization and N immobilization 9 What are the possible fates of NH4 released from N mineralization in soil 10 In what conditions would N loss from ammonia volatilization be most pronounced 11 What are some possible fates of nitrate produced from nitrification 12 Where in the soil under what conditions would you expect denitrification to occur 13 What is anammox How does anammox differ from denitrification 14 Why was the anammox process overlooked for so long 11 Questions Based on Reading Assignments Condron et al pp 8794 H LON 1 Condron et al discussed the effects plant communities have on the microbial community and how plant productivity is affected or affects the microbial community Brie y discuss this What is the relationship between soil organic matter and microbial biomass What are the general differences between soils that are dominated by fungi and those dominated by bacteria What is meant by quotfunctional redundancy in the microbial community Condron et al pp 98108 H N er According to this manuscript what is the consequence of nitrogen addition on the microbial community composition and abundance Compare the stoichiometric decomposition theory with the nitrogen mining hypothesis What is the affect of nitrogen fertilization on lignin degradation Give some examples of why the microbial biomass carbon is an important carbon source in soil Smith et al Eutrophication H N9f 9 Give some examples of how human activities have drastically impacted the global nitrogen cycle What are 3 fates ofN added to soil as fertilizer What is eutrophication What are some ways that eutrophication affects lakes How does eutrophication affect coastal marine systems How does eutrophication or overall N addition affect terrestrial systems What relationship did the authors show between the anthropogenic addition of N to the ecosystem and atmospheric C02 eg what affect may increased N additions have on C02 uptake and storage by soil The two nitrogen readings are supplementary to the lecture Use them to clear up any questions you may have The exam will only cover what is covered in the N lecture not the two reading assignments
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