BISC209/S12: Lab4 - Revision history

Tucker Crum: /* LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior */

2012-02-22T20:57:19Z

LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior

←Older revision		Revision as of 20:57, 22 February 2012
Line 22:		Line 22:
	4. Count the number of colonies that show phosphate solubilizing activity as a clear zone or halo.<BR>		4. Count the number of colonies that show phosphate solubilizing activity as a clear zone or halo.<BR>

-	5. Calculate the prevalence (in %) of exoezyme secreting microbes out of the total in the culturable community for each assay (# positive colonies x dilution factor/total colony count x dilution factor on nutrient agar) X 100. This correction for dilution factor allows you to compare the CFUs counted from different dilutions on plates. If you are able to use control (NA) and test plates from the same dilution (each has between 30-300 colonies), you can omit the dilution factor. Be sure to show all your data and calculations ~~for the % of CFUs/gram of wet soil of microorganisms able to perform the role of interest~~ in your notebook. <BR><BR>	+	5. Calculate the prevalence (in %) of exoezyme secreting microbes out of the total in the culturable community for each assay (# positive colonies x dilution factor/total colony count x dilution factor on nutrient agar) X 100. This correction for dilution factor allows you to compare the CFUs counted from different dilutions on plates. If you are able to use control (NA) and test plates from the same dilution (each has between 30-300 colonies), you can omit the dilution factor. Be sure to show all your data and calculations in your notebook. <BR><BR>
-		+
-	~~6. Add your % data to the course spreadsheet. Be sure to click File Save after you enter your data if needed.<BR><Br~~>	+

	There should be time in lab today for you to brain storm with your partners about how you will use these results in a figure/table and in the results narrative to help the hypothetic reader of your research report on this investigation to understand what your data mean in terms of our experimental questions.		There should be time in lab today for you to brain storm with your partners about how you will use these results in a figure/table and in the results narrative to help the hypothetic reader of your research report on this investigation to understand what your data mean in terms of our experimental questions.

Tucker Crum: /* LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior */

2012-02-22T20:56:12Z

LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior

←Older revision		Revision as of 20:56, 22 February 2012
Line 22:		Line 22:
	4. Count the number of colonies that show phosphate solubilizing activity as a clear zone or halo.<BR>		4. Count the number of colonies that show phosphate solubilizing activity as a clear zone or halo.<BR>

-	5. Calculate the % ~~positive for~~ the ~~enzymatic activity~~ for each assay (# positive colonies x dilution factor/total colony count x dilution factor on nutrient agar) X 100. This correction for dilution factor allows you to compare the CFUs counted from different dilutions on plates. If you are able to use control (NA) and test plates from the same dilution (each has between 30-300 colonies), you can omit the dilution factor. Be sure to show all your data and calculations for the % of CFUs/gram of wet soil of microorganisms able to perform the role of interest in your notebook. <BR><BR>	+	5. Calculate the prevalence (in %) of exoezyme secreting microbes out of the total in the culturable community for each assay (# positive colonies x dilution factor/total colony count x dilution factor on nutrient agar) X 100. This correction for dilution factor allows you to compare the CFUs counted from different dilutions on plates. If you are able to use control (NA) and test plates from the same dilution (each has between 30-300 colonies), you can omit the dilution factor. Be sure to show all your data and calculations for the % of CFUs/gram of wet soil of microorganisms able to perform the role of interest in your notebook. <BR><BR>

	6. Add your % data to the course spreadsheet. Be sure to click File Save after you enter your data if needed.<BR><Br>		6. Add your % data to the course spreadsheet. Be sure to click File Save after you enter your data if needed.<BR><Br>

Tucker Crum: /* Assignment */

2012-02-22T16:11:28Z

Assignment

←Older revision		Revision as of 16:11, 22 February 2012
Line 77:		Line 77:
	This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>		This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>

-	Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates on solid medium (preferably NA) AND you must have a fresh nutrient broth (NB) culture of each isolate. Please make a broth culture of each of your isolates (MUST BE PURE CULTURE!) a day before your lab by adding a single well isolated colony from a plate with only ''one'' type of bacteria growing on it and incubate your broths at RT. Next week we will start our tests that characterize our isolates and we will also perform 16s rRNA gene amplification by PCR. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures no more than 24 hours prior to lab 5 and slower growing cultures, ~48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.	+	Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You '''must''' have pure cultures next week, preferably, young cultures of isolates on solid medium (preferably NA) AND you must have a fresh nutrient broth (NB) culture of each isolate. Please make a broth culture of each of your isolates (MUST BE PURE CULTURE!) a day before your lab by adding a single well isolated colony from a plate with only ''one'' type of bacteria growing on it and incubate your broths at RT. Next week we will start our tests that characterize our isolates and we will also perform 16s rRNA gene amplification by PCR. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures no more than 24 hours prior to lab 5 and slower growing cultures, ~48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-02-22T16:11:08Z

Assignment

←Older revision		Revision as of 16:11, 22 February 2012
Line 77:		Line 77:
	This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>		This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>

-	Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates. We will perform 16s rRNA gene amplification by PCR ~~in lab next week~~. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures 24 hours prior to lab 5 and slower growing cultures, 48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.	+	Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates on solid medium (preferably NA) AND you must have a fresh nutrient broth (NB) culture of each isolate. Please make a broth culture of each of your isolates (MUST BE PURE CULTURE!) a day before your lab by adding a single well isolated colony from a plate with only ''one'' type of bacteria growing on it and incubate your broths at RT. Next week we will start our tests that characterize our isolates and we will also perform 16s rRNA gene amplification by PCR. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures no more than 24 hours prior to lab 5 and slower growing cultures, ~48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-02-22T15:08:31Z

Assignment

←Older revision		Revision as of 15:08, 22 February 2012
Line 77:		Line 77:
	This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>		This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>

-	~~'''~~Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates. We will perform 16s rRNA gene amplification by PCR in lab next week. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures 24 hours prior to lab 5 and slower growing cultures, 48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.~~'''~~	+	Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates. We will perform 16s rRNA gene amplification by PCR in lab next week. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures 24 hours prior to lab 5 and slower growing cultures, 48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-02-22T15:08:14Z

Assignment

←Older revision		Revision as of 15:08, 22 February 2012
Line 73:		Line 73:

	==Assignment==		==Assignment==
-	'''Graded Assignment: '''Analyze prevalence of microbial starch & cellulose digesters and phosphate solubilizers in ~~the~~ soil community. Analyze ~~CLPP~~ data for carbon source utilization; turn in spreadsheet with calculations and make graphs turned into figures with legends. More information about this assignment and on how to use your data in these calculations can be found at [[BISC209/S12: Assignment_209_BIOLOG]].	+	'''Graded Assignment: '''Analyze prevalence of microbial starch & cellulose digesters and phosphate solubilizers in your soil community. Analyze your soil sample's community data for carbon source utilization; turn in spreadsheet with calculations and make graphs turned into figures/tables with legends. More information about this assignment and on how to use your data in these calculations can be found at [[BISC209/S12: Assignment_209_BIOLOG]].

	This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>		This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>

-	'''Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. ~~You will~~ need ~~young~~ pure culture isolates ~~for the PCR we~~ will perform next week ~~prior~~ to ~~sending out these isolates~~ for ~~identification~~. Please be sure to subculture fast growing cultures 24~~-48~~ hours prior to lab 5. Use your judgement or ask your instructor for advice ~~for the slower~~ growing groups such as Actinomycetes.'''	+	'''Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. If you need to subculture several times this week do achieve a pure culture, do so! You must have pure cultures next week, preferably, young cultures of isolates. We will perform 16s rRNA gene amplification by PCR in lab next week. If our amplifications are successful, we will send cleaned up pcr products to a DNA sequencing facility for sequencing of the 16srRNA gene of each of your isolates. When the sequences come back we will use a public data base to compare these DNA sequences to others submitted to this bacterial data base and, we hope, identify a few members of the bacteria in your soil community. Please be sure to subculture fast growing cultures 24 hours prior to lab 5 and slower growing cultures, 48 hours before lab so that we will have young cultures to work with. Use your judgement or ask your instructor for advice on how far in advance to subculture extremely slow growing isolates of groups such as ''Actinomycetes''.'''
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior */

2012-02-22T14:51:21Z

LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior

←Older revision		Revision as of 14:51, 22 February 2012
Line 6:		Line 6:
	<font size="+1">'''Community Level EXOENYMES PREVALENCE con't:'''</font size="+1"><BR>		<font size="+1">'''Community Level EXOENYMES PREVALENCE con't:'''</font size="+1"><BR>
	In Lab3 you started a quantitative assessment of the prevalence of microbial digesters of cellulose, starch, and for solubilizers of phosphates. Think about why we chose to test for your soil community's ability to process these particular nutrients. Why would it be advantageous for a soil microbial community to include members that '''secrete''' enzymes that process starch, cellulose or phosphorus into other forms of nutrients? Would it be advantageous for all of the community members to possess all of these abilities? Why or why not? What might be the cost? Would the microbial community be different if NONE of its members secreted these exoenzymes? If microbial community membership is always in flux, trying to maintain a balance where its members can all survive and thrive, do you think the prevalence of these exoenzyme producers is constant or variable? If variable, what are the conditions that might have an effect on prevalence?<BR><BR>		In Lab3 you started a quantitative assessment of the prevalence of microbial digesters of cellulose, starch, and for solubilizers of phosphates. Think about why we chose to test for your soil community's ability to process these particular nutrients. Why would it be advantageous for a soil microbial community to include members that '''secrete''' enzymes that process starch, cellulose or phosphorus into other forms of nutrients? Would it be advantageous for all of the community members to possess all of these abilities? Why or why not? What might be the cost? Would the microbial community be different if NONE of its members secreted these exoenzymes? If microbial community membership is always in flux, trying to maintain a balance where its members can all survive and thrive, do you think the prevalence of these exoenzyme producers is constant or variable? If variable, what are the conditions that might have an effect on prevalence?<BR><BR>
-	Today you will complete the colony counts from the differential media ~~(why are these media differential but not selective?)~~ that you inoculated with dilute soil extract last week. You and your group members will perform calculations that assess the prevalence of community members able to perform these valuable functions. Your data should provide evidence of co-operative behavior among members of this soil community. <BR><BR>	+	Today you will complete the colony counts from the differential media that you inoculated with dilute soil extract last week. You and your group members will perform calculations that assess the prevalence of community members able to perform these valuable functions. Your data should provide evidence of co-operative behavior among members of this soil community. <BR><BR>

	Examine the plates for evidence of digestion or processing of a particular nutrient (starch, cellulose or insoluble phosphates) in each of the differential culture medium. Remember that these differential media are not selective (they aren't designed to inhibit the growth of any groups of soil microorganisms), but they are differential media, in that they allow you to visibly SEE the difference in particular groups of microbes---in our case, between those that produce and secrete a functional exoenzyme and those that don't. You will count the number of individual colonies showing a clear zone (halo) around the colony (using the plate with 30-300 total colonies) and compare those numbers with the number at the same soil dilution that grew on NA- a general purpose, non-differential medium. Why does a halo indicate digestion of starch, cellulose, or processing of insoluble phosphate into a soluble form? <BR>		Examine the plates for evidence of digestion or processing of a particular nutrient (starch, cellulose or insoluble phosphates) in each of the differential culture medium. Remember that these differential media are not selective (they aren't designed to inhibit the growth of any groups of soil microorganisms), but they are differential media, in that they allow you to visibly SEE the difference in particular groups of microbes---in our case, between those that produce and secrete a functional exoenzyme and those that don't. You will count the number of individual colonies showing a clear zone (halo) around the colony (using the plate with 30-300 total colonies) and compare those numbers with the number at the same soil dilution that grew on NA- a general purpose, non-differential medium. Why does a halo indicate digestion of starch, cellulose, or processing of insoluble phosphate into a soluble form? <BR>

Tucker Crum: /* LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior */

2012-02-22T14:51:00Z

LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior

←Older revision		Revision as of 14:51, 22 February 2012
Line 5:		Line 5:
	==='''LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior '''===		==='''LAB 4: Community Level Testing for Richness as Functional Metabolic Diversity & for Community Co-operative Behavior '''===
	<font size="+1">'''Community Level EXOENYMES PREVALENCE con't:'''</font size="+1"><BR>		<font size="+1">'''Community Level EXOENYMES PREVALENCE con't:'''</font size="+1"><BR>
-	In Lab3 you started a quantitative assessment of the prevalence of microbial digesters of cellulose, starch, and for solubilizers of phosphates. Think about why we chose to test for your soil community's ability to process these particular nutrients. ~~Consider the difference in~~ soil ~~microbial communities in different habitats. Should your~~ microbial community ~~have the same prevalence of~~ starch, cellulose, or ~~phosphate processors as~~ other ~~habitats, such as a real tropical habitat (rather than an artificial one) or compared~~ to the ~~New England cold temperate soil outside~~ the ~~greenhouse~~? ~~What~~ are the ~~factors~~ that might ~~make the prevalences different~~?<BR><BR>	+	In Lab3 you started a quantitative assessment of the prevalence of microbial digesters of cellulose, starch, and for solubilizers of phosphates. Think about why we chose to test for your soil community's ability to process these particular nutrients. Why would it be advantageous for a soil microbial community to include members that '''secrete''' enzymes that process starch, cellulose or phosphorus into other forms of nutrients? Would it be advantageous for all of the community members to possess all of these abilities? Why or why not? What might be the cost? Would the microbial community be different if NONE of its members secreted these exoenzymes? If microbial community membership is always in flux, trying to maintain a balance where its members can all survive and thrive, do you think the prevalence of these exoenzyme producers is constant or variable? If variable, what are the conditions that might have an effect on prevalence?<BR><BR>
-	Today you will complete the colony counts from the differential media that you inoculated with dilute soil extract last week. You and your group members will perform calculations that assess the prevalence of community members able to perform these valuable functions.<BR><BR>	+	Today you will complete the colony counts from the differential media (why are these media differential but not selective?) that you inoculated with dilute soil extract last week. You and your group members will perform calculations that assess the prevalence of community members able to perform these valuable functions. Your data should provide evidence of co-operative behavior among members of this soil community. <BR><BR>

	Examine the plates for evidence of digestion or processing of a particular nutrient (starch, cellulose or insoluble phosphates) in each of the differential culture medium. Remember that these differential media are not selective (they aren't designed to inhibit the growth of any groups of soil microorganisms), but they are differential media, in that they allow you to visibly SEE the difference in particular groups of microbes---in our case, between those that produce and secrete a functional exoenzyme and those that don't. You will count the number of individual colonies showing a clear zone (halo) around the colony (using the plate with 30-300 total colonies) and compare those numbers with the number at the same soil dilution that grew on NA- a general purpose, non-differential medium. Why does a halo indicate digestion of starch, cellulose, or processing of insoluble phosphate into a soluble form? <BR>		Examine the plates for evidence of digestion or processing of a particular nutrient (starch, cellulose or insoluble phosphates) in each of the differential culture medium. Remember that these differential media are not selective (they aren't designed to inhibit the growth of any groups of soil microorganisms), but they are differential media, in that they allow you to visibly SEE the difference in particular groups of microbes---in our case, between those that produce and secrete a functional exoenzyme and those that don't. You will count the number of individual colonies showing a clear zone (halo) around the colony (using the plate with 30-300 total colonies) and compare those numbers with the number at the same soil dilution that grew on NA- a general purpose, non-differential medium. Why does a halo indicate digestion of starch, cellulose, or processing of insoluble phosphate into a soluble form? <BR>

Janet McDonough: /* Assignment */

2012-02-21T02:30:34Z

Assignment

←Older revision		Revision as of 02:30, 21 February 2012
Line 77:		Line 77:
	This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>		This assignment is due at the BEGINNING of Lab 5. Do not come late to lab because you are printing or otherwise completing this assignment and you may NOT work on it during lab. There is a 5% per day late penalty for work for this course and since you have a week or more to complete assignments, illness (unless it is lengthy and serious) does not excuse you from the late penalty.<BR><BR>

-	'''Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria.'''	+	'''Continue monitoring and following the appropriate protocols to isolate to pure culture our targeted bacteria. You will need young pure culture isolates for the PCR we will perform next week prior to sending out these isolates for identification. Please be sure to subculture fast growing cultures 24-48 hours prior to lab 5. Use your judgement or ask your instructor for advice for the slower growing groups such as Actinomycetes.'''
	<div class=noprint>		<div class=noprint>

Janet McDonough: /* Analysis of Carbon Source Utilization Data */

2012-02-21T02:25:08Z

Analysis of Carbon Source Utilization Data

←Older revision		Revision as of 02:25, 21 February 2012
Line 40:		Line 40:
	Your group should have a week of daily measurements recorded on the Excel workbook we provided as a template. This template is pre-formatted for the calculations you will do from these data. It includes the formulas to average replicate measurements each day and it will automatically subtract the background (readings in the water wells). There is a normalization for background that will be subtracted automatically (this threshold absorbance is provided by the manufacturer and was determined to be 0.25 absorbance units for each carbon source). These calculations are the first step in figuring out what you can learn from these data that provides evidence for one or more of our investigative goals.		Your group should have a week of daily measurements recorded on the Excel workbook we provided as a template. This template is pre-formatted for the calculations you will do from these data. It includes the formulas to average replicate measurements each day and it will automatically subtract the background (readings in the water wells). There is a normalization for background that will be subtracted automatically (this threshold absorbance is provided by the manufacturer and was determined to be 0.25 absorbance units for each carbon source). These calculations are the first step in figuring out what you can learn from these data that provides evidence for one or more of our investigative goals.

-	CMD is calculated by summing the number of positive responses (wells with a positive A<sub>595nm</sub> value after all the corrections) at each reading day. On your worksheet enter for each carbon source either a 0 or a 1. One indicates a positive value for absorbance at A<sub>590nm</sub> after correction for background. (Remember that this correction is built into the formulas embedded in the template spreadsheet.) Zero should be entered for carbon sources that have either a negative value or a zero absorbance after built-in correction. Zero means that the community was unable to use that particular carbon source for its metabolic needs. Once you have entered a 1 or a 0 for each substrate, the template will ~~average your three replicates and~~ sum the positive values. This number is your CMD for that day. It indicates the number of substrates usable by the community. Enter your daily CMD values into indicated column on the final page (CMD graph) of your worksheet template. A graph ~~will~~ be automatically generated showing average CMD on the y axis versus time (day) post-inoculation. Use the peak CMD value to calculate % of carbon sources utilized [number utilized divided by the total number available(31) x 100]. <BR><BR>	+	CMD is calculated by summing the number of positive responses (wells with a positive A<sub>595nm</sub> value after all the corrections) at each reading day. On your worksheet enter for each carbon source either a 0 or a 1. One indicates a positive value for absorbance at A<sub>590nm</sub> after correction for background. (Remember that this correction is built into the formulas embedded in the template spreadsheet.) Zero should be entered for carbon sources that have either a negative value or a zero absorbance after built-in correction. Zero means that the community was unable to use that particular carbon source for its metabolic needs. Once you have entered a 1 or a 0 for each substrate, the template will sum the positive values. This number is your CMD for that day. It indicates the number of substrates usable by the community. Enter your daily CMD values into indicated column on the final page (CMD graph) of your worksheet template. A graph should be automatically generated showing average CMD on the y axis versus time (day) post-inoculation. Use the peak CMD value to calculate % of carbon sources utilized [number utilized divided by the total number available(31) x 100]. <BR><BR>

	=='''What to do with your data:'''==		=='''What to do with your data:'''==