DOI: 10.5061/dryad.ttdz08m9w
title: Data from: Bark microbiota modulate climate-active gas fluxes in Australian forests

description: The global surface area of tree bark is approximately equal to the total
 global land surface area. Though recent studies suggest microbes inhabit
 tree bark, little is known about their identities, functions, and
 environmental roles. Here, we reveal, through genome-resolved
 metagenomics, that tree bark hosts abundant and specialized microbial
 communities. The predominant bacteria are hydrogen-cycling facultative
 anaerobes adapted to dynamic redox and substrate conditions. Furthermore,
 bark-associated methanotrophs are abundant and can coexist with
 hydrogenotrophic methanogens. Microcosm experiments demonstrated that bark
 microorganisms rapidly aerobically consume methane, hydrogen, and carbon
 monoxide at in planta concentrations, but can produce these gases under
 anoxia. Combined with in situ field measurements, we show tree-dwelling
 microbiota process multiple climate-active gases at significant rates
 within tree stems, highlighting an important research frontier within
 global atmospheric cycles.
description: # Data from: Bark microbiota modulate climate-active gas fluxes in
 Australian forests Dataset DOI:
 [10.5061/dryad.ttdz08m9w](https://doi.org/10.5061/dryad.ttdz08m9w) ##
 Description of the data and file structure The data includes all multiple
 sequence alignment and maximum likelihood phylogenetic tree files reported
 in the Science publication "Bark microbiota modulate climate-active
 gas fluxes in Australian forests". ### Files and variables #### File:
 Fig_3E._McrA_with_ref2_mafft_linsi.fasta **Description:** Multiple
 sequence alignment of methyl-CoM reductase (McrA) sequences from unbinned
 contigs dereplicated at 97% identity and aligned using MAFFT-L-INS-i
 v7.505. This file was used to produce Fig. 3E. #### File:
 Fig_3E._McrA_with_ref2_mafft_linsi.fasta.contree **Description:** Maximum
 likelihood phylogenetic tree of methyl-CoM reductase (McrA) constructed
 using IQTREE2 v2.2.0 (LG+I+G4 model; 1000 ultrafast bootstrap replicates,
 -bnni). This file was used to produce Fig. 3E. #### File:
 Fig_3C._PmoA_with_ref_mafft_linsi.fasta **Description:** Multiple sequence
 alignment of particulate CH~4~ monooxygenase (PmoA) sequences from
 metagenome-assembled genomes and unbinned contigs dereplicated at 97%
 identity and aligned using MAFFT-L-INS-i v7.505. This file was used to
 produce Fig. 3C. #### File:
 Fig_3C._PmoA_with_ref_mafft_linsi.fasta.contree **Description:** Maximum
 likelihood phylogenetic tree of particulate CH~4~ monooxygenase (PmoA)
 constructed using IQTREE2 v2.2.0 (LG+G4 model; 1000 ultrafast bootstrap
 replicates, -bnni). This file was used to produce Fig. 3C. #### File:
 Fig_3D._SDIMO97_with_ref_mafft_linsi.fasta.contree
 **Description:** Maximum likelihood phylogenetic tree of soluble diiron
 monooxygenase family (SDIMO) constructed using IQTREE2 v2.2.0
 (Q.pfam+I+I+R5 model; 1000 ultrafast bootstrap replicates, -bnni). This
 file was used to produce Fig. 3D. #### File:
 Fig_S5._NiFe_hydrogenase_MAG_and_contig_mafft_linsi.fasta.contree
 **Description:** Maximum likelihood phylogenetic tree of the catalytic
 subunits of [NiFe]-hydrogenase from metagenome-assembled genomes and
 unbinned contigs constructed using IQTREE2 v2.2.0 (LG+F+I+I+R7 model; 1000
 ultrafast bootstrap replicates, -bnni). This file was used to produce Fig.
 S5. #### File: Fig_3D._SDIMO97_with_ref_mafft_linsi.fasta
 **Description:** Multiple sequence alignment of soluble diiron
 monooxygenase family (SDIMO) sequences from metagenome-assembled genomes
 and unbinned contigs dereplicated at 97% identity and aligned
 using MAFFT-L-INS-i v7.505. This file was used to produce Fig. 3D. ####
 File: Fig_3A._NiFe_hydrogenase_MAG_only_mafft_linsi.fasta.contree
 **Description:** Maximum likelihood phylogenetic tree of the catalytic
 subunits of [NiFe]-hydrogenase from metagenome-assembled genomes
 constructed using IQTREE2 v2.2.0 (LG+F+I+I+R7 model; 1000 ultrafast
 bootstrap replicates, -bnni). This file was used to produce Fig. 3A. ####
 File: Fig_2B._Treethane.bac120.user_msa.treefile **Description:** A
 concatenated multiple protein sequence alignment was built using the 120
 GTDB bacterial marker genes in all bacterial metagenome-assembled genomes
 by GTDB-Tk v2.3.2. This file was used to produce Fig. 2B. #### File:
 Fig_S6._CoxL_with_ref_mafft_linsi.fasta.contree **Description:** Maximum
 likelihood phylogenetic tree of the catalytic subunits of carbon monoxide
 dehydrogenase (CoxL) from metagenome-assembled genomes and unbinned
 contigs constructed using IQTREE2 v2.2.0 (LG+F+R5 model; 1000 ultrafast
 bootstrap replicates, -bnni). This file was used to produce Fig. S6. ####
 File: Fig_3A._NiFe_hydrogenase_MAG_only_mafft_linsi.fasta
 **Description:** Multiple sequence alignment of the catalytic subunits of
 [NiFe]-hydrogenase sequences from metagenome-assembled genomes aligned
 using MAFFT-L-INS-i v7.505. This file was used to produce Fig. 3A. ####
 File: Fig_S5._NiFe_hydrogenase_MAG_and_contig_mafft_linsi.fasta
 **Description:** Multiple sequence alignment of the catalytic subunits of
 [NiFe]-hydrogenase sequences from metagenome-assembled genomes and
 unbinned contigs dereplicated at 97% identity and aligned
 using MAFFT-L-INS-i v7.505. This file was used to produce Fig. S5. ####
 File: Fig_S6._CoxL_with_ref_mafft_linsi.fasta **Description:** Multiple
 sequence alignment of the catalytic subunits of carbon monoxide
 dehydrogenase (CoxL) sequences aligned using MAFFT-L-INS-i v7.505. This
 file was used to produce Fig. S6. #### File:
 Fig_2B._Treethane.bac120.user_msa.fasta **Description:** A maximum
 likelihood phylogenomic tree of all bacterial metagenome-assembled
 genomes constructed using IQTREE2 v2.2.0 (WAG+G20 model; 1000 ultrafast
 bootstrap replicates). This file was used to produce Fig. 2B. #### File:
 Fig_3B._FeFe_hydrogenase_MAG_with_contig_mafft_linsi.fasta.contree
 **Description:** Maximum likelihood phylogenetic tree of the catalytic
 subunits of [FeFe]-hydrogenase from metagenome-assembled genomes and
 unbinned contigs constructed using IQTREE2 v2.2.0 (Q.pfam+I+I+R5 model;
 1000 ultrafast bootstrap replicates, -bnni). This file was used to produce
 Fig. 3B. #### File:
 Fig_3B._FeFe_hydrogenase_MAG_with_contig_mafft_linsi.fasta
 **Description:** Multiple sequence alignment of the catalytic subunits of
 [FeFe]-hydrogenase sequences from metagenome-assembled genomes and
 unbinned contigs dereplicated at 97% identity and aligned
 using MAFFT-L-INS-i v7.505. This file was used to produce Fig. 3B. ####
 File: MAGs_114.tar.gz **Description:** 114 metagenome-assembled genomes
 constructed tree bark. ## Code/software Multiple sequence alignment files
 can be viewed in any multiple sequence alignment viewers such as MEGA. The
 phylogenetic trees were visualized in iTOL v6. ## Access information Other
 publicly accessible locations of the data: * None Data was derived from
 the following sources: * None