DOI: 10.5061/dryad.1c59zw44p
title: Data from: Strain identity effects contribute more to Pseudomonas community functioning than strain interactions

description: Microbial communities can shape key ecological services, but the
 determinants of their functioning often remain little understood. While
 traditional research predominantly focuses on effects related to species
 identity (community composition and species richness), recent work
 increasingly explores the impact of species interactions on community
 functioning. Here, we conducted experiments with replicated small
 communities of fluorescent Pseudomonas bacteria to quantify the relative
 importance of strain identity versus interaction effects on two important
 functions, community productivity and siderophore production. By combining
 supernatant and competition assays with an established linear model
 method, we show that both factors have significant effects on functioning,
 but identity effects generally outweigh strain interaction effects. These
 results hold irrespective of whether strains interactions are inferred
 statistically or approximated experimentally. Our results have
 implications for microbiome engineering, as the success of approaches
 aiming to induce beneficial (probiotic) strain interactions will be
 sensitive to strain identity effects in many communities.
description: # Data from: Strain identity effects contribute more to Pseudomonas
 community functioning than strain interactions
 [https://doi.org/10.1093/ismejo/wraf025](https://doi.org/10.1093/ismejo/wraf025) The accompanying datafiles contain all the data used in Kramer J, Maréchal S, Figueiredo ART, and Kümmerli R (2024) Strain identity effects contribute more to Pseudomonas community functioning than strain interactions.*The ISME Journal*, 2025; wraf025 ## Description of the data and file structure The four datafiles contain data from supernatant feeding and competition assays with natural *Pseudomonas* bacteria (Kramer_FunctioningDeterminants_Data) as well as sequencing data for phylogenetic analyses of the used strains (Kramer_FunctioningDeterminants_SoilIsolates, Kramer_FunctioningDeterminants_PondIsolates, Kramer_FunctioningDeterminants_Outgroups). Together with the "Kramer_FunctioningDeterminants_Rscript" (see below), this data can be used to replicate the analyses and figures presented in the manuscript and its supplementary material. ### **Description of variables** #### File: Kramer\_FunctioningDeterminants\_Data ##### Sheet: StrainNames Names and origin of strains used to construct the phlyogenetic trees [Fig. S1] * strain: ID of specific strain * habitat: origin of strain (soil or pond; none --&gt; reference strains) * community: ID of community from which focal strain originated ##### Sheet: TypesData Data on pyoverdine production and protease production of the full collection of 315 natural Pseudomonas strains [Fig. S2] * habitat: origin of strain (soil or pond) * community: ID of community from which focal strain originated * strain: ID of specific strain * sequenced: indicates whether focal strain has been sequenced (1 = yes, 0 = no) * PVDrel: pyoverdine production, relative to laboratory reference strain Pseudomonas aeruginosa PAO1 * PROrel: protease production, relative to laboratory reference strain Pseudomonas aeruginosa PAO1 * type: strain type (based on PVDrel and PROrel; PVDPRO, PVD, NONPRO, or NON) ##### Sheet: SupernatantData\_Donors Data on growth, pyoverdine production, and total iron-chelating activity of strains used in this study [Fig. 1, Fig. S3] * habitat: origin of strain (soil or pond) * community: ID of community from which focal strain originated * medium: medium in which strains were grown (CAAM = iron-limited, CAAP = iron-rich) * donor.type: strain type of focal strain (PVDPRO, PVD, NONPRO, or NON) * donor: ID of focal strain * OD: optical density [OD600] * PVD: pyoverdine production [RFU] * CAS: total iron-chelating activity [OD630] ##### Sheet: SupernatantData\_Receivers Data on the effects of donor supernatant on receiver growth [Fig. 2] * habitat: origin of strains (soil or pond) * community: ID of community from which focal strains originated * medium: medium in which strains were grown (CAAM = iron-limited, CAAP = iron-rich) * donor.type: strain type of supernatant donor (PVDPRO, PVD, NONPRO, or NON) * donor: ID of supernatant donor * receiver.type: strain type of supernatant receiver (PVDPRO, PVD, NONPRO, or NON) * receiver: ID of supernatant receiver * intpair: ID of supernatant donor-receiver pair * ODrelN: supernatant effect * statistic: t-value from t-test investigating whether ODrelN differs from neutral * df: degrees of freedom from t-test investigating whether ODrelN differs from neutral * estimate: estimate from t-test investigating whether ODrelN differs from neutral * p.value: p-value from t-test investigating whether ODrelN differs from neutral * signif: indicates whether t-test investigating whether ODrelN differs from neutral was significant (p &lt;= 0.05) ##### Sheet: SupernatantData\_IntType Data on supernatant-effect-based interaction types [Fig. 3] * habitat: origin of strains (soil or pond) * community: ID of community from which focal strains originated * medium: medium in which strains were grown (CAAM = iron-limited, CAAP = iron-rich) * set: focal set of strains (A,B,C,D, or pairwise combination thereof; A = PVDPRO, B = PVD, C = NONPRO, D = NON) * interaction_type: interaction-type based on supernatant effects (positive, neutral, or negative for monocultures [see below]; mutualism, commensalism, neutralism, amensalism, parasitism, or competition for mixed cultures) * focal: focal strain (type) * nonfocal: nonfocal strain (type) * monoculture: indicates whether the focal set is a monoculture (1) or mixed culture (0) ##### Sheet: CompetitionData Data on co-culture (and monoculture) growth of different mixes of strains [Fig. 4-6] * habitat: origin of strains (soil or pond) * community: ID of community from which focal strains originated * medium: medium in which strains were grown (CAAM = iron-limited, CAAP = iron-rich) * richness: strain number (continuous) in focal set [see below] * facrichness: strain number (categorical) in focal set * set: focal set of strains (A,B,C,D, and all possible combinations of two, three, or all four strains; A = PVDPRO, B = PVD, C = NONPRO, D = NON) * setr: unique ID of focal set * Sp.1: presence of PVDDUO in focal set (1 = yes, 0 = no) * Sp.2: presence of PVD in focal set (1 = yes, 0 = no) * Sp.3: presence of NONPRO in focal set (1 = yes, 0 = no) * Sp.4: presence of NON in focal set (1 = yes, 0 = no) * posrat.int_24: ratio of positive supernatant effects among strains in focal set * absmean.int_24: average absolute magnitude of supernatant effects among strains in focal set * intscore_24: average interaction score among strains in focal set * AUC_OD48: growth (integral) of focal set * AUC_PVD48: (integral of) pyoverdine production of focal set * dev_growth48_1: deviation of growth of focal set from the growth expected based on the monocultures of the constituent strains * dev_PVD48_1: deviation of pyoverdine production of focal set from the pyoverdine production expected based on the monocultures of the constituent strains ## Code/Software The script "Kramer_FunctioningDeterminants_Rscript" can be used with the accompanying datafiles (in R [version 4.4.1]) to reproduce the analyses and figures of our manuscript.