DOI: 10.5061/dryad.ksn02v7hp
title: Environment-mediated interactions cause an externalized and collective memory in microbes

description: Microbes typically live in complex communities, interacting with numerous
 other microbial species. These interactions determine who can persist in a
 community and how the overall community forms and functions. Microbes
 often exert interactions by chemically changing the environment, like
 taking up nutrients or producing toxins. These environmental changes can
 persist over time. We demonstrate here that such lasting environmental
 changes can induce a “memory effect,” where current growth conditions
 influence interaction outcomes in the future. This memory is only stored
 in the environment and not inside bacterial cells. Only the collective
 effort of many bacteria can build up this memory, making it an emergent
 property of bacterial populations. This externalized and collective memory
 can also impact the assembly of more complex communities and lead to
 different final compositions depending on the system's past. Overall,
 we show that to understand interaction outcomes fully, we not only have to
 consider the interacting species and abiotic conditions but also the
 system's history
description: # Environment-mediated interactions cause an externalized and collective
 memory in microbes Dataset DOI:
 [10.5061/dryad.ksn02v7hp](10.5061/dryad.ksn02v7hp) ## Description of the
 data and file structure -&gt; CFU/mL data with 1/2x or 1/100x along with
 species corresponds to mildly-diluted co-culture or Highly-diluted
 co-culture, respectively. -&gt; The term Ca 35 corresponds to
 *Corynebacterium ammoniagenes* grown in preferred conditions, i.e., at
 35degreesCelsiusus and oxic conditions, while Lp 18 refers to
 Lactobacillus plantarum grown in unpreferred conditions, i.e, at 18
 degrees Celsius and oxic conditions. -&gt; In the community's
 composition data, species codes correspond to the following species: 1\.
 4: *Bacillus toyonensis (Bt)* 2\. 6: *Bacillus flexus(Bf)* 3\. 27:
 *Rouxiella badensis (Rb)* 4\. 66: *Pseudomonas veronii (Pv)* 5\. 79:
 *Pseudomonas protegens (Pp)* 6\. 81: *Sphingobacterium multivorum (Sm)*
 7\. 107: *Rhodococcus qingshengii (Rq)* 8\. Myb27: *Arthrobacter
 nitroguajacolicus (An)* -&gt; In the communities' composition data,
 the Sup4 column corresponds to the community composition data of the
 community assembled in Supernatant of Species 4 (*Bacillus toyonensis*).
 -&gt; 'NoSup' columns in community composition data refer to the
 communities assembled without any supernatant. ### Files and variables
 #### File: Fig_1_cfu_counts_CaUnwashed-LpW-Set1.csv **Description:** 
 ##### Variables * Ca%: Final Percentage of *Corynebacterium ammoniagenes*
 * Lp_1/2x-W: CFU/mL of *Lactobacillus plantarum* (washed/without memory)
 in mildly diluted final co-culture  * Lp_1/6x-W: CFU/mL of *Lactobacillus
 plantarum* (washed/without memory) in 1/6x diluted final co-culture  *
 Lp_1/20x-W: CFU/mL of *Lactobacillus plantarum* (washed/without memory) in
 1/20x diluted final co-culture  * Lp_1/100x-W: CFU/mL of *Lactobacillus
 plantarum* (washed/without memory) in highly diluted final co-culture  *
 Ca_1/2x-Un: CFU/mL of *Corynebacterium ammoniagenes* (Unwashed/with
 memory) in mildly diluted final co-culture  * Ca_1/6x-Un: CFU/mL of
 *Corynebacterium ammoniagenes* (Unwashed/with memory) in 1/6x diluted
 final co-culture  * Ca_1/20x-Un: CFU/mL of *Corynebacterium ammoniagenes*
 (Unwashed/with memory) in 1/20x diluted final co-culture  *
 Ca_1/100x-Un: CFU/mL of *Corynebacterium ammoniagenes* (Unwashed/with
 memory) in 1/100x-highly-diluted final co-culture  #### File:
 Fig_1_cfu_counts_CaUnwashed-LpW-Set2.csv #### File:
 Fig_1_cfu_counts_CaUnwashed-LpW-Set3.csv #### File:
 Fig_1_cfu_counts_CaWashed-LpUN-Set1.csv **Description:**  ##### Variables
 * Ca%: Final Percentage of *Corynebacterium ammoniagenes* *
 Lp_1/2x-Un: CFU/mL of *Lactobacillus plantarum* (Unwashed/with memory) in
 mildly-diluted final co-culture  * Lp_1/6x-Un: CFU/mL of *Lactobacillus
 plantarum* (Unwashed/with memory) in 1/6x diluted final co-culture  *
 Lp_1/20x-Un: CFU/mL of *Lactobacillus plantarum* (Unwashed/with memory) in
 1/20x diluted final co-culture  * Lp_1/100x-Un: CFU/mL of *Lactobacillus
 plantarum* (Unwashed/with memory) in highly diluted final co-culture  *
 Ca_1/2x-W: CFU/mL of *Corynebacterium ammoniagenes* (washed/without
 memory) in mildly diluted final co-culture  * Ca_1/6x-W: CFU/mL of
 *Corynebacterium ammoniagenes* (washed/without memory) in 1/6x diluted
 final co-culture * Ca_1/20x-W: CFU/mL of *Corynebacterium ammoniagenes*
 (washed/without memory) in 1/20x diluted final co-culture *
 Ca_1/100x-W: CFU/mL of *Corynebacterium ammoniagenes* (washed/without
 memory) in 1/100x (highly) diluted final co-culture #### File:
 Fig_1_cfu_counts_CaWashed-LpUN-Set3.csv #### File:
 Fig_1_cfu_counts_CaWashed-LpUN-Set2.csv #### File:
 Fig_2B_cfu_counts_Ca18-Lp35-Set1.csv **Description:**  ##### Variables *
 Ca%: Final Percentage of *Corynebacterium ammoniagenes* * Lp_1/2x: CFU/mL
 of *Lactobacillus plantarum* (with memory and grown in preferred
 conditions) in 1/2x (mildly) diluted final co-culture * Lp_1/6x: CFU/mL of
 *Lactobacillus plantarum* (with memory and grown in preferred conditions)
 in 1/6x diluted final co-culture * Lp_1/20x: CFU/mL of *Lactobacillus
 plantarum* (with memory and grown in preferred conditions) in 1/20x
 diluted final co-culture * Lp_1/100x: CFU/mL of *Lactobacillus plantarum*
 (with memory and grown in preferred conditions) in 1/100x (highly) diluted
 final co-culture * Ca_1/2x: CFU/mL of *Corynebacterium ammoniagenes* (with
 memory and grown in unpreferrred conditions) in 1/2x (mildly) diluted
 final co-culture * Ca_1/6x: CFU/mL of *Corynebacterium ammoniagenes* (with
 memory and grown in unpreferred conditions) in 1/6x diluted final
 co-culture * Ca_1/20x: CFU/mL of *Corynebacterium ammoniagenes* (with
 memory and grown in unpreferred conditions) in 1/20x diluted final
 co-culture * Ca_1/100x: CFU/mL of *Corynebacterium ammoniagenes* (with
 memory and grown in unpreferred conditions) in 1/100x diluted final
 co-culture #### File: Fig_2B_cfu_counts_Ca18-Lp35-Set2.csv #### File:
 Fig_2B_cfu_counts_Ca18-Lp35-Set3.csv #### File:
 Fig_2B_cfu_counts_Ca35-Lp18-Set1.csv **Description:**  ##### Variables *
 Ca%: Final Percentage of *Corynebacterium ammoniagenes* * Lp_1/2x: CFU/mL
 of *Lactobacillus plantarum* (with memory and grown in unpreferred
 conditions) in 1/2x (mildly) diluted final co-culture * Lp_1/6x: CFU/mL of
 *Lactobacillus plantarum* (with memory and grown in unpreferred
 conditions) in 1/6x diluted final co-culture * Lp_1/20x: CFU/mL of
 *Lactobacillus plantarum* (with memory and grown in unpreferred
 conditions) in 1/20x diluted final co-culture * Lp_1/100x: CFU/mL of
 *Lactobacillus plantarum* (with memory and grown in unpreferred
 conditions) in 1/100x (highly) diluted final co-culture * Ca_1/2x: CFU/mL
 of *Corynebacterium ammoniagenes* (with memory and grown in preferred
 conditions) in 1/2x (mildly) diluted final co-culture * Ca_1/6x: CFU/mL of
 *Corynebacterium ammoniagenes* (with memory and grown in preferred
 conditions) in 1/6x diluted final co-culture * Ca_1/20x: CFU/mL of
 *Corynebacterium ammoniagenes* (with memory and grown in preferred
 conditions) in 1/20x diluted final co-culture * Ca_1/100x: CFU/mL of
 *Corynebacterium ammoniagenes* (with memory and grown in preferred
 conditions) in 1/100x diluted final co-culture #### File:
 Fig_2C_Ca_Lp_Pref_Unpref.csv **Description:**  ##### Variables * pH
 values: pH values of cultures after growth in respective conditions for 24
 hrs. #### File: Fig_2B_cfu_counts_Ca35-Lp18-Set2.csv #### File:
 Fig_2B_cfu_counts_Ca35-Lp18-Set3.csv #### File:
 Fig_4_cfu_counts_Day_5_Community_1_triplicates.csv **Description:** 
 Community composition of Community 1 at Day 5 (in triplicate) #####
 Variables * Species: CFU/mL counts of given species * Sup4: Community
 assembled in the presence of supernatant of *Bacillus toyonensis* *
 Sup6: Community assembled in the presence of the supernatant of *Bacillus
 flexus* * Sup27: Community assembled in the presence of supernatant
 of *Rouxiella badensis* * Sup66: Community assembled in the presence of
 supernatant of *Pseudomonas veronii* * Sup79: Community assembled in the
 presence of supernatant of *Pseudomonas protegens* * Sup81: Community
 assembled in the presence of supernatant of *Sphingobacterium multivorum*
 * Sup107: Community assembled in the presence of supernatant
 of *Rhodococcus qingshengii* * SupMyb27: Community assembled in the
 presence of supernatant of *Arthrobacter nitroguajacolicus* #### File:
 Fig_4_cfu_counts_Day_5_Community_2_triplicates.csv
 **Description:**  Community composition of Community 2 at Day 5 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_5_Community_3_triplicates.csv
 **Description:** Community composition of Community 3 at Day 5 (in
 triplicate #### File: Fig_4_cfu_counts_Day_5_Community_4_triplicates.csv
 **Description:**  Community composition of Community 4 at Day 5 (in
 triplicates) #### File: Fig_4_cfu_counts_Day_5_Community_5_triplicates.csv
 **Description:** Community composition of Community 5 at Day 5 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_10_Community_2_triplicates.csv
 **Description:** Community composition of Community 2 at Day 10 (in
 ttriplicate #### File: Fig_4_cfu_counts_Day_5_Community_6_triplicates.csv
 **Description:** Community composition of Community 6 at Day 5 (in
 triplicates) #### File:
 Fig_4_cfu_counts_Day_10_Community_1_triplicates.csv
 **Description:** Community composition of Community 1 at Day 10 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_10_Community_3_triplicates.csv
 **Description:** Community composition of Community 3 at Day 10 (in
 triplicate #### File: Fig_4_cfu_counts_Day_10_Community_4_triplicates.csv
 **Description:** Community composition of Community 4 at Day 10 (in
 triplicates) #### File:
 Fig_4_cfu_counts_Day_10_Community_5_triplicates.csv
 **Description:** Community composition of Community 5 at Day 10 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_10_Community_6_triplicates.csv
 **Description:** Community composition of Community 6 at Day 10 (in
 ttriplicate #### File: Fig_4_cfu_counts_Day_12_Community_1_triplicates.csv
 **Description:** Community composition of Community 1 at Day 12 (in
 triplicates) ##### Variables * noSup1: Community assembled in the presence
 of no supernatant replicate 1 * noSup2: Community assembled in the
 presence of no supernatant replicate 2 * noSup3: Community assembled in
 the presence of no supernatant replicate 3 * noSup4: * noSup5: * noSup6: *
 noSup7: * noSup8: Community assembled in the presence of no supernatant
 replicate 8 #### File: Fig_4_cfu_counts_Day_12_Community_2_triplicates.csv
 **Description:** Community composition of Community 2 at Day 12 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_12_Community_3_triplicates.csv
 **Description:** Community composition of Community 3 at Day 12 (in
 triplicate #### File: Fig_4_cfu_counts_Day_12_Community_4_triplicates.csv
 **Description:** Community composition of Community 4 at Day 12 (in
 triplicates) #### File:
 Fig_4_cfu_counts_Day_12_Community_5_triplicates.csv
 **Description:** Community composition of Community 5 at Day 12 (in
 triplicate) #### File: Fig_4_cfu_counts_Day_12_Community_6_triplicates.csv
 **Description:** Community composition of Community 6 at Day 12 (in
 ttriplicate #### File: Supp_Fig_2_CaSup-CaW-LpW-Set1.csv
 **Description:** Modified media by *Ca* added to the assembled community
 is sufficient for the externalized memory effect ##### Variables * Ca%:
 Final percentage of *Corynebacterium ammoniagenes* * Lp_1/2x: CFU/mL of
 *Lactobacillus plantarum* (washed/without memory) in 1/2x (mildly) diluted
 final co-culture * Lp_1/6x: CFU/mL of *Lactobacillus plantarum*
 (washed/without memory) in 1/6x diluted final co-culture *
 Lp_1/20x: CFU/mL of *Lactobacillus plantarum* (washed/without memory) in
 1/20x diluted final co-culture * Lp_1/100x: CFU/mL of *Lactobacillus
 plantarum* (washed/without memory) in 1/100x diluted final co-culture *
 Ca_1/2x: CFU/mL of *Corynebacterium ammoniagenes* (washed/without memory)
 in 1/2x (mildly) diluted final co-culture * Ca_1/6x: CFU/mL of
 *Corynebacterium ammoniagenes* (washed/without memory) in 1/6x diluted
 final co-culture * Ca_1/20x: CFU/mL of *Corynebacterium ammoniagenes*
 (washed/without memory) in 1/20x diluted final co-culture *
 Ca_1/100x: CFU/mL of *Corynebacterium ammoniagenes* (washed/without
 memory) in 1/100x (highly) diluted final co-culture #### File:
 Supp_Fig_2_CaSup-CaW-LpW-Set2.csv #### File:
 Supp_Fig_2_CaSup-CaW-LpW-Set3.csv #### File:
 Supp_Fig_2_LpSup-CaW-LpW-Set1.csv **Description:** Modified media by *Lp*
 added to the assembled community is sufficient for the externalized memory
 effect #### File: Supp_Fig_2_LpSup-CaW-LpW-Set2.csv
 **Description:** Modified media by *Lp* added to the assembled community
 is sufficient for the externalized memory effect #### File:
 Supp_Fig_3_Data.csv **Description:** Limiting the nutrients during the
 formation of externalized memory leads to a decline in the memory effect.
 ##### Variables * Ca%: Final percentage of *Corynebacterium ammoniagenes*
 * CaUn-SBM: CFU/mL of *Corynebacterium ammoniagenes* (Unwashed/with memory
 formed from undiluted SBM) * LpW-SBM: CFU/mL of *Lactobacillus
 plantarum *(washed/without memory formed from undiluted SBM) * CaUn-1/2x
 SBM: CFU/mL of *Corynebacterium ammoniagenes* (Unwashed/with memory formed
 from 1/2x diluted SBM) * LpW-1/2x SBM: CFU/mL of *Corynebacterium
 ammoniagenes* (washed/without memory formed from 1/2x diluted SBM) *
 LpUn-1/2x SBM: CFU/mL of *Corynebacterium ammoniagenes* (unwashed/with
 memory formed from 1/2x diluted SBM) * CaW-1/2x SBM: CFU/mL of
 *Corynebacterium ammoniagenes* (washed/without memory formed from 1/2x
 diluted SBM) #### File: Supp_Fig_2_LpSup-CaW-LpW-Set3.csv #### File:
 Supp_Fig_4_single_parameter.csv **Description:** OD600, pH, and CFU/mL of
 single growth parameter change in externalized memory formation in both
 species. #### File: Supp_Fig_6_Ca18-Lp35-Set1.csv #### File:
 Supp_Fig_6_Ca18-Lp35-Set2.csv #### File: Supp_Fig_6_Ca35-Lp18-Set1.csv
 #### File: Supp_Fig_6_Ca35-Lp18-Set2.csv ## Code/software Jupyter
 notebooks containing code for simulations are accessible on our lab GitHub
 through the following link: 
 [https://github.com/RatzkeLab/Environment-mediated-interactions-cause-an-externalized-and-collective-memory-in-microbes-](https://github.com/RatzkeLab/Environment-mediated-interactions-cause-an-externalized-and-collective-memory-in-microbes-) ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * NA