BR I E F RE POR T
Genome analysis and description of Tunturibacter gen.
nov. expands the diversity of Terriglobia in tundra soils
Adriana Messyasz1 | Minna K. Männistö2 | Lee J. Kerkhof3 |
Max M. Häggblom1
1Department of Biochemistry and
Microbiology, Rutgers University, New
Brunswick, New Jersey, USA
2Natural Resources Institute Finland,
Rovaniemi, Finland
3Department of Marine and Coastal Sciences,
Rutgers University, New Brunswick, New
Jersey, USA
Correspondence
Max M. Häggblom, Department of
Biochemistry and Microbiology, Rutgers
University, 76 Lipman Drive, New Brunswick,
NJ 08901, USA.
Email: haggblom@rutgers.edu
Funding information
USDA National Institute of Food and
Agriculture, Grant/Award Numbers: Project
accession number 1012785, Hatch Project
NJ01160; US National Science Foundation,
Grant/Award Number: DEB 2129351;
Academy of Finland, Grant/Award Numbers:
130507, 310776
Abstract
Increased temperatures in Arctic tundra ecosystems are leading to higher
microbial respiration rates of soil organic matter, resulting in the release of
carbon dioxide and methane. To understand the effects of this microbial
activity, it is important to better characterize the diverse microbial communi-
ties in Arctic soil. Our goal is to refine our understanding of the phylogenetic
diversity of Terriglobia, a common but elusive group within the Acidobacter-
iota phylum. This will help us link this diversity to variations in carbon and
nitrogen usage patterns. We used long-read Oxford Nanopore MinION
sequences in combination with metagenomic short-read sequences to
assemble complete Acidobacteriota genomes. This allowed us to build
multi-locus phylogenies and annotate pangenome markers to distinguish
Acidobacteriota strains from several tundra soil isolates. We identified a
phylogenetic cluster containing four new species previously associated with
Edaphobacter lichenicola. We conclude that this cluster represents a new
genus, which we have named Tunturibacter. We describe four new species:
Tunturibacter lichenicola comb. nov., Tunturibacter empetritectus sp. nov.,
Tunturibacter gelidoferens sp. nov., and Tunturibacter psychrotolerans
sp. nov. By uncovering new species and strains within the Terriglobia and
improving the accuracy of their phylogenetic placements, we hope to
enhance our understanding of this complex phylum and shed light on the
mechanisms that shape microbial communities in polar soils.
INTRODUCTION
Approximately one third of the global soil carbon stock is
stored in Arctic soils (Hugelius et al., 2014; Loya &
Grogan, 2004), and despite sub-zero temperatures,
microbial activity persists throughout the long winters,
albeit at a slower rate (Gadkari et al., 2020; Natali
et al., 2014; Nikrad et al., 2016; Oechel et al., 1997;
Pessi et al., 2022; Poppeliers et al., 2022; Welker
et al., 2000). Microbes play important roles in nutrient
cycling as they decompose soil organic matter (SOM).
As polar soils warm due to climate change, it is of con-
cern that enhanced microbial activity will increase the rate
of SOM degradation and consequently greenhouse gas
emissions (Campbell et al., 2010; Graham et al., 2012;
Natali et al., 2014; Welker et al., 2000). SOM degradation
usually increases in the short summer season, with cli-
mate change resulting in faster and longer soil decompo-
sition and increased greenhouse gas emissions that
contribute to a positive warming feedback loop (Bond-
Lamberty & Thomson, 2010; Koven et al., 2011; Schuur
et al., 2008). However, the mechanisms by which climate
change affects gas emissions are complex and site-
specific, likely determined by for example, vegetation type
and microbial community structure (Fry et al., 2023).
The microbial community diversity of Arctic environ-
ments, like the tundra, is shaped by soil abiotic factors
(e.g., pH, SOM, temperature and water activity) and the
Received: 3 December 2023 Accepted: 30 April 2024
DOI: 10.1111/1462-2920.16640
ENVIRONMENTAL MICROBIOLOGY
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium,
provided the original work is properly cited.
© 2024 The Authors. Environmental Microbiology published by John Wiley & Sons Ltd.
Environ Microbiol. 2024;26:e16640. wileyonlinelibrary.com/journal/emi 1 of 19
https://doi.org/10.1111/1462-2920.16640
extreme conditions of the Arctic (e.g., intense UV radia-
tion, drought, long periods of sub-zero temperatures
interspersed by freeze–thaw events; Männistö
et al., 2009; Tas¸ et al., 2018; Tveit et al., 2014;
Viitamäki et al., 2022; Weintraub & Schimel, 2003).
Despite these harsh conditions, there is tremendous
bacterial diversity in tundra soils, with the bacterial
communities dominated by Acidobacteriota, Actinomy-
cetota, and Pseudomonadota (Proteobacteria; Chu
et al., 2010; Kim et al., 2014; Männistö et al., 2007,
2013; Viitamäki et al., 2022; Vorˇísˇkov
a et al., 2019).
Members of these phyla change in abundance, compo-
sition, and activity in response to environmental vari-
ables such as seasonal changes (freeze–thaw cycles),
vegetation, and soil pH (Männistö et al., 2009, 2013;
McMahon et al., 2011; Viitamäki et al., 2022; Zinger
et al., 2009). The ubiquitous but elusive Acidobacteriota
are particularly susceptible to changes in soil pH and
different members of the phylum thrive at different pH
levels. Members of the Class Terriglobia (formerly Acid-
obacteriia; Sub-division 1 [SD1] Acidobacteriota) are
particularly abundant in the cold, nutrient-poor, acidic
soils such as those in Arctic tundra and boreal forest
biomes (Belova, Ravin, et al., 2018; Campbell
et al., 2010; Ivanova et al., 2020; Kim et al., 2014;
Männistö et al., 2007, 2009, 2018).
The Acidobacteriota is one of the most abundant
phyla in soils around the globe; however, the diversity
within this phylum is still largely uncharacterized (Zhang
et al., 2022). Initial culture-independent methods initially
delineated 26 subdivisions of Acidobacteria (Barns
et al., 2007). More recently, these subdivisions were
refined into 15 class-level units (Dedysh &
Yilmaz, 2018). Of these, the classes Terriglobia, Blasto-
catellia, and Vicinamibacteria are most abundant in soils
(Janssen, 2006; Jones et al., 2009). Furthermore, mem-
bers of the Terriglobia have been the most successfully
cultivated group with over 40 named and published spe-
cies to date (Göker, 2023; Zhang et al., 2022).
The family Acidobacteriaceae currently encom-
passes over a dozen named genera; however with fas-
ter and more advanced sequencing technologies a
greater number of Acidobacteriota species and strains
are being described (Kalam et al., 2020; Zhang
et al., 2022). The analysis of multiple genes from isolate
genomes and environmental metagenomes has contrib-
uted towards a better understanding of the diversity of
Acidobacteriota in multiple ecosystems without the need
for cultivation (Dedysh et al., 2022; Kalam et al., 2020;
Kielak et al., 2016; Parsley et al., 2011). Genome analy-
sis has indicated a variety of metabolic functions within
the Acidobacteriota including complex carbohydrate
degradation (xylan, cellulose, hemicelluloses, pectin,
starch, and chitin), nitrogen metabolism (nitrate, nitrite,
and nitric oxide reduction), genes for oxygen utilization
in hypo- and hyperoxic conditions, as well as the ability
to oxidize methanol (Diamond et al., 2019; Eichorst
et al., 2007; Kalam et al., 2020; Rawat et al., 2012; Ward
et al., 2009). Some Acidobacteriota is equipped with reg-
ulatory genes in response to stressors like starvation,
oxidative stress, heat stress, as well as acid resistance
systems (Challacombe et al., 2011; Kalam et al., 2020;
Kielak et al., 2016; Ward et al., 2009). Secondary
metabolites from biosynthetic gene clusters were also
found within Acidobacteriota. Specifically, non-ribosomal
peptide synthetases and polyketide synthases were
found within Candidatus Angelobacter (a proposed Ter-
riglobia), indicating mechanisms for interbacterial com-
petition (Crits-Christoph et al., 2022).
There may be several reasons for such a high taxo-
nomic and functional diversity of Acidobacteriota in terres-
trial systems. Primarily, soils create complex and
spatially/temporally heterogeneous environments, with
this disequilibrium ensuring that no one species domi-
nates over others (Ghoul & Mitri, 2016; Lennon
et al., 2012). Additionally, ecological drivers, such as
resource partitioning, selective predation, and temporal
separation, most likely shape the diversity of Acidobacter-
iota and other soil phyla (Chesson, 2000; Chesson &
Huntly, 1997). To better understand how Acidobacteriota
activity is shaped by environmental and ecological factors
we need to identify the yet uncharacterized species/
strains within this phylum and compare their genomes to
elucidate metabolic potential. In this study, we sequenced
several new tundra soil Acidobacteriota isolates from
Malla Nature Reserve, Kilpisjärvi, Finland using both Illu-
mina short-read and Oxford Nanopore long-read technol-
ogies. Through rRNA operon and full genome analysis,
we expand the current phylogenetic diversity of the order
Terriglobales in the Acidobacteriota. We also delineate
and name a novel genus, Tunturibacter, containing four
new species in phylogenetic proximity to other species
within the genera Terriglobus (Eichorst et al., 2007;
Männistö et al., 2011; Podar et al., 2019; Rawat
et al., 2012), Granulicella (Männistö et al., 2012;
Pankratov & Dedysh, 2010; Rawat et al., 2013, 2014),
and Edaphobacter (Koch et al., 2008; Wang et al., 2016).
With functional annotation and comparison of this new
genus to known Acidobacteriota, the core and unique
genes of the genera within this group can be identified.
Our phylogenetic analysis demonstrates that a complex
diversity of the Terriglobales can be uncovered. Addition-
ally, understanding how novel genera differ within Acido-
bacteriota can help further elucidate why such diversity
exists in soil environments.
EXPERIMENTAL PROCEDURES
Acidobacteriota isolation and DNA
extraction
Acidobacteriota strains were isolated from tundra soil
samples collected from Malla Nature Reserve,
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Kilpisjärvi, Finland (69
010 N, 20
500 E) in July 2010
(strain codes that begin with ‘M’) and July 2012 (strain
codes that begin with ‘X’). Several carbon substrates
were tested in an attempt to isolate novel members of
the Acidobacteriota. Soil samples were diluted in
VL55 mineral medium (Davis et al., 2005) and dilution
plated on the different media. Plates were incubated at
4
C for up to 3 months and inspected every 2 weeks.
To isolate Acidobacteriota and other slow-growing oli-
gotrophs, only colonies that formed after 1–2 months of
incubation were picked and streaked to new media.
After purification, isolated strains were identified by
Sanger sequencing of the 16S rRNA gene. DNA was
extracted from the isolates using the DNeasy Ultra-
Clean Microbial Kit (Qiagen) according to the manufac-
turer’s instructions. 16S rRNA genes were amplified
using 27f and 1525r primers (Lane, 1991) and the poly-
merase chain reaction (PCR) products were
sequenced by LGC Genomics (Berlin, Germany) using
the forward primer 27 f. Approximately 800 bp
sequences were compared with those in the EzTaxon
database (Yoon et al., 2017) and those identified as
members of the Acidobacteriota were selected for fur-
ther studies.
Strains M8UP20, M8UP22, M8UP23, M8UP27,
M8UP28, M8UP30, and M8UP39 were isolated using a
mixture of carboxy methyl cellulose (CMC), xylan, pec-
tin, and starch (each 0.25 g L1) in VL55 mineral salt
medium amended with yeast extract (0.1 g L1) and
agar (20 g L1). Strain MP8S11 was isolated using cel-
lobiose, trehalose, and sucrose (each 0.25 g L1) in
VL55 mineral salt medium amended with yeast extract
(0.1 g L1) and agar (20 g L1). Strains X4BP1, X5P3,
X5P6, and X4EP2 were isolated using xylan (0.5 gL1),
cellobiose (0.25 g L1), and xylose (0.25 g L1) in
VL55 mineral salt medium amended with MEM essen-
tial and non-essential amino acids (Sigma-Aldrich®).
VL55 mineral salt solution was prepared as described
by Davis et al. (2005), pH was adjusted either to 4.0 or
5.5. All strains were maintained at pH 5.5 using GY
medium containing glucose (1 g L1) and yeast extract
(0.5 g L1) in VL55. Isolation of Granulicella arctica
MP5ACTX2 has been described earlier (Männistö
et al., 2012).
Phenotypic and chemotaxonomic analyses
Growth of strains M8UP23, M8UP39, and X5P6 on GY
medium was tested at different temperatures and
pH. The temperature range was evaluated by growth
on GY-agar incubated at 2, 4, 10, 15, 20, 25, and 30
C.
The plates were checked every 1–2 days for growth.
Visual differences in growth at different temperatures
were recorded. The effect of pH on growth was evalu-
ated by growing the strains in liquid GY medium at
pH 3.0–9.0 (in 0.5 pH unit increments) in 96 well plates.
Carbon source utilization of the three strains was ana-
lysed in 96-well plates for up to 10 days at 20
C with
VL55 mineral medium supplemented with 100 mg L1
yeast extract and 10 mM of each carbon source. Yeast
extract was required for good growth on single carbon
sources. The control contained only yeast extract.
Growth was measured at 620 nm using a Multiscan FC
microplate reader (Thermo Scientific). Hydrolysis of dif-
ferent polysaccharides (starch, CMC, xylan, lichenan,
pectin, xanthan, and gum arabic) was determined at
room temperature by observing CO2 production for up
to 20 days and analysed as described in Männistö
et al. (2012).
Cellular fatty acids were analysed by gas chroma-
tography as described in Männistö et al. (2012). Analy-
sis of respiratory quinones and polar lipids was carried
out by the Identification Service, DSMZ, Braunschweig,
Germany. For the analysis, cells were cultivated on GY
medium, collected by centrifugation, washed with PBS
buffer, and freeze-dried. Polar lipids were extracted
from 200 mg of freeze-dried cells and separated by
thin-layer chromatography (German Collection of
Microorganisms and Cell Cultures GmbH: Polar Lipids,
n.d. https://www.dsmz.de/services/microorganisms/bio
chemical-analysis/polar-lipids). Respiratory quinones
were extracted from 50 mg of freeze-dried cells and
analysed by HPLC (German Collection of Microorgan-
isms and Cell Cultures GmbH: Respiratory Quinones,
n.d. https://www.dsmz.de/services/microorganisms/bioch
emical-analysis/respiratory-quinones).
Genome sequencing and assembly
A total of 13 Acidobacteriota isolates were used for
whole genome sequencing via the Oxford Nanopore
MinION. Sequence libraries were prepared using R 9.4
chemistry and the MinION Rapid Sequencing kit
(SQK-RAD004). Libraries were run on a MinION R9.4
Flongle for 24 h. Fast5 files were basecalled using
Guppy (V 6.0.1; Oxford Nanopore Technologies Ltd.) in
high accuracy mode and the FastA reads were used for
genome assembly with the Trycycler assembler pack-
age (V 0.5.3; Wick et al., 2021), which allows for multi-
ple assemblies specific to Nanopore long read
sequences. For these genomes, the assemblers Flye—
nano-hq (V 2.9; Kolmogorov et al., 2019; Lin
et al., 2016), Minipolish (V 0.1.2; Wick & Holt, 2019),
and Raven (V 1.8.1; Vaser & Sˇiki
c, 2021) were
employed using default settings. The contigs were put
into clusters and multiple sequence alignments were
generated to produce a consensus or final assembly
using Medaka (V 1.6.0; © 2018 Oxford Nanopore Tech-
nologies Ltd.).
In addition, several of the assemblies were run
through PolyPolish (V 0.5.0; Wick & Holt, 2022) to close
and complete the genomes. Of the 13 isolates used for
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genome assembly, 6 also had Illumina short-read
sequences publicly available via the JGI Genome Por-
tal (see Project IDs in Table S1), and 4 (MP8S11,
M8UP39, X5P6, and M8UP23) were previously
sequenced via Illumina (see Supporting information S1,
Methods and Results). These short reads along with
our Trycycler-Medaka assemblies were used in the
PolyPolish pipeline (default parameters). Genome
assembly completeness and contamination for all
13 isolates were analysed via CheckM (V 1.0.18; Parks
et al., 2015). Percent GC was calculated via QUAST
(V 4.4; Gurevich et al., 2013). For each assembly with
greater than one contig, the second longest contig was
searched against the plasmid database PLSDB
(V 2023_11_03_v2; Schmartz et al., 2021). This search
was conducted via the PLSDB online API tool using
Mash (V 2.3; Ondov et al., 2016) to search against the
PLSDB database (parameters used: maximal p-value
0.1, maximal distance 0.1, minimal identity 0.70). Gene
prediction was run via Prokka (V 1.14.5;
Seeman, 2014). To find annotations to carbohydrate-
active enzymes (CAZy), genes annotated via Prokka
were scanned using a set of Hidden Markov Models
(HMMs) from the dbCAN2 CAZy collection (dbCAN
HMM database v10; Zhang et al., 2018) using HMMER
(v 3.3.2; Eddy, 2011). The minimum e-value for this
search was 1e15 and the minimum coverage of the
model length was set at 90%. The Genome Taxonomy
Database (GTDB; releases 207 and 214; GTDB
R07-RS207 and R08–RS214; Parks et al., 2022) was
used to taxonomically classify the genomes via the
GTDB-Tk tool (v 2.3.2).
Genome phylogenies and pangenome
analysis
A single-copy gene (SCG) phylogeny including the
13 new tundra soil isolate genomes and known Class
Terriglobia (SD1 Acidobacteriota) species was ana-
lysed via the GToTree program (V 1.7.05; Lee, 2019).
The program was run with default settings for alignment
(MUSCLE V 5.1; Edgar, 2021) and approximately
maximum-likelihood phylogenetic tree building
(FastTree V 2.1.11; Price et al., 2010). The ‘-H Bacte-
ria’ parameter was used to identify 74 bacterial SCGs
across all genomes analysed (listed in Supporting
information S1 and S2). Another multi-locus tree for the
same genomes was built via OrthoFinder (V 2.5.4;
Emms & Kelly, 2019). The Orthofinder tree also utilized
a MUSCLE (V 5.1; Edgar, 2021) alignment and phylo-
genetic tree building with FastTree (Price et al., 2010).
Both SCG and OrthoFinder trees were viewed via the
iTOL interface (V6; Letunic & Bork, 2021). These trees
were compared with 16S rRNA gene and rRNA-operon
trees, which included a more complete representation
of the Terriglobia and the novel Acidobacteriota isolates
included in the rRNA operon analysis (see Supporting
information S1, Methods and Results). Genome align-
ment visualizations were conducted via PGV-Mummer
(default setting; V 0.3.2; Shimoyama, 2022) and pro-
gressive MAUVE (Geneious plugin V 1.1.1) with
15 match seed weight, minimum 5000 Locally Collinear
Blocks score, full alignment, and MUSCLE 3.6 gapped
aligner (Darling et al., 2004).
Genome assemblies of the new tundra isolates
along with some select Terriglobia were further com-
pared through the Anvi’o pangenome analysis pipeline
(Eren et al., 2021). A contig database for each genome
was created with the following additions: HMM search,
SCG taxonomy, tRNAs scan, NCBI cogs search, and
KEGG Kofam search. Average nucleotide identity
across the compared genomes was calculated via
pyANI (Pritchard et al., 2015) program plugin within the
Anvi’o pangenome pipeline (command:
‘anvi-compute-genome-similarity’). The pangenome
was then visualized via the Anvi’o interactive display,
organizing samples by a gene cluster frequencies tree.
Functional enrichment between strain categories within
the pangenome analysis was computed via anvi-com-
pute-functional-enrichment-in-pan using the KEGG_-
Class and COG20_PATHWAY annotation sources
(Shaiber et al., 2020).
Analysis of Acidobacteriota community in
Malla tundra heath soils
Soil samples were collected from tundra heaths of
Mt. Pikku Malla in Malla Nature Reserve, Kilpisjärvi
(69
030 5000N, 20
4404000 E), with differences in topogra-
phy that dramatically influence snow accumulation.
Four plots representing windswept slopes and four
plots corresponding to snow-accumulating biotopes
were sampled at a depth of <5 cm in February 2013 as
described previously (Männistö et al., 2024). Compos-
ite soil samples of five soil cores were taken from each
plot with three subsamples from each composite sam-
ple used for DNA extraction with a CTAB-based
method.
Near full-length bacterial rRNA operons were ampli-
fied from extracted DNA using 16S rRNA-27 Forward
and 23S rRNA-2241R primers, <10 ng template DNA,
and a High-Fidelity Taq Polymerase (Biomake Inc., CA,
USA; Kerkhof et al., 2017). PCR conditions were: Initial
denaturation for 3 min at 94
C; followed by 25 cycles of
98
C/10 s denaturation, 60
C/15 s primer annealing
and 72
C/240 s extension; and a final extension at
72
C for 5 min. Barcoded rRNA operon amplicons were
visualized and quantified by agarose gel electrophore-
sis and stored at 20
C until library preparation. Library
construction utilized the SQK-LSK108 sequencing kit
and sequencing via the Oxford Nanopore MinION. The
fast5 files were basecalled using Guppy (3.2.0). Raw
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reads were demultiplexed with Guppy and sized
(3700–5000 bp) using Geneious (11.1.5). FastA files
were initially screened via MegaBLAST (2.10.0) against
the ribosomal RNA operon database (rOPDB; Kerkhof
et al., 2022) to determine the raw reads associated with
the Acidobacteriota. These Acidobacteriota reads were
re-screened against a modified database using the
original Acidobacteriota rRNA operons from
the rOPDB, amended with rRNA operons from the new
Tunturibacter and Granulicella strains described in this
study. Best BLAST hits (BBHs) were identified using
the following settings: word size 60, match/mismatch
cost 2/3, gap open/extend 0/4, and e-value of
1  1010. Relative abundance of the Acidobacteriota
BBHs to the updated database was calculated and
bubble plots were generated in RStudio (2023.06.0
+ 421) using ggplot2 and reshape2.
RESULTS AND DISCUSSION
Novel tundra Acidobacteriota isolates
Acidobacteriota strains were isolated from tundra heath
soil samples from Malla Nature Reserve using different
carbon substrate combinations. Initial analysis of partial
16S rRNA sequences (data not shown) indicated that
these were members of the Terriglobia, closely related
to Edaphobacter and Granulicella species. Physiologi-
cal comparisons of our isolates to known Edaphobacter
and Granulicella strains showed similarities in the utili-
zation of various organic compounds and slight differ-
ences in temperature and pH range. Further
investigation utilizing long-read Oxford Nanopore
sequencing to assemble full genomes uncovered phy-
logenetic differences between the isolates and other
members of the Terriglobia. The consistent phyloge-
netic placement across several comparative tools (sin-
gle-gene trees, multi-locus trees, pangenome analysis)
clearly separates the tundra heath isolates from known
Edaphobacter and Granulicella species. Therefore,
these isolates ultimately represent a novel genus within
Terriglobia for which we propose the name Tunturibac-
ter. Here, we present the genomic, phylogenetic, and
phenotypic characterization of four novel species within
the Tunturibacter genus.
Genome assemblies
The 13 new Acidobacteriota genome assemblies are
listed in Table 1. Of these, 10 included Illumina short
reads used to polish the genomes to >99% completion.
Three of the 10 complete genomes had only one scaf-
fold/contig, while the remainder had two or more scaf-
folds/contigs, with the longer scaffold representing the
bacterial chromosome and the shorter contigs
representing smaller genetic elements, that is, plas-
mids. To examine whether these shorter contigs could
be plasmids, we searched the shorter contigs from
assemblies with more than one contig against the
PLSDB plasmid database. For each assembly, the sec-
ond longest contig had one or more hits with an aver-
age of 75% identity to an already annotated plasmid
from the database (Table S2). Their predominant align-
ment to plasmids from Granulicella tundricola at only
around 75% identity indicates these are novel plasmids
belonging to the Tunturibacter. These plasmids may
code for a few extra genes that are not necessary for
Tunturibacter growth, reproduction, or existence, but
may offer some resistance strategies beneficial for
survival.
The assembled genomes of the Tunturibacter
strains had between 3600 and 7400 predicted genes,
of which >98% were protein-coding genes for each
assembly (Table 1). Of these genes, on average 44%
were annotated as non-hypothetical. Full assembly sta-
tistics for these genomes are included in Table S1.
Based on GTDB annotation, 10 out of 13 assemblies
were classified as most similar to Edaphobacter licheni-
cola DSM 104462 with ANI values ranging from 89% to
100% and amino acid (AA) similarities from 76%
to 94%. Of the remaining three assemblies, two were
classified as most similar to G. arctica MP5ACTX2
(DSM 23128; 79%–100% ANI and 86%–94% AA) and
one to Granulicella mallensis MP5ACTX8 (100% ANI
and 94% AA).
Multi-locus phylogeny of the SD1
Acidobacteriota
To determine the taxonomic placement of the new tun-
dra Acidobacteriota isolates we compared 16S rRNA
gene, rRNA operon, and single copy gene phylogenies.
Utilizing the full genomes of members of the Terriglo-
bia, we phylogenetically compared the genome assem-
blies using 74 selected SCGs (Figure 1A). The
resulting SCG tree more accurately groups the Eda-
phobacter, Granulicella, and Terriglobus species than
the rRNA operon or 16S rRNA gene trees alone
(Figures S1A,B and S2A,B). Importantly, the assem-
blies grouping together with E. lichenicola DSM 104462
were phylogenetically separated from the other Eda-
phobacter species, including the type species Edapho-
bacter modestus, and would thus represent the new
genus Tunturibacter. As can be seen from the SCG
tree, this new genus appears to comprise four species,
each with several strains.
The phylogeny is more evident in the SCG sub-tree
showing the members of the Terriglobia most closely
related to the proposed Tunturibacter genus
(Figure 1B). The SCG tree also more accurately clus-
ters the Granulicella species. Another potential new
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icro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16640 by Luonnonvarakeskus, W
iley Online Library on [27/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on W
iley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
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6 of 19 MESSYASZ ET AL.ENVIRONMENTAL MICROBIOLOGY
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iley Online Library on [27/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on W
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F I GURE 1 (A) Single copy gene phylogeny of Terriglobia genomes. (B) Sub-tree of the phylogenetic placement of the new Tunturibacter
genus with more closely related genera. Accession numbers for genomes available from NCBI are listed in Table S3.
TUNTURIBACTER GEN. NOV. IN THE ACIDOBACTERIOTA PHYLUM 7 of 19ENVIRONMENTAL MICROBIOLOGY
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icro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16640 by Luonnonvarakeskus, W
iley Online Library on [27/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on W
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genus may be represented by G. mallensis, Granuli-
cella paludicola, and Granulicella cerasi, which group
with Bryocella elongata, phylogenetically distinct from
the other species in the Granulicella cluster, including
the type species G. paludicola (Figure 1A). A compari-
son of these genomes via a multi-locus phylogeny
based on orthogroups and orthologs (Orthofinder) also
resulted in a similar phylogenetic structure as the SCG
tree (Figure S3).
Overall, compared with the rRNA operon tree, phy-
logenies built on multiple genes from fully assembled
genomes more accurately delineated the Acidobacter-
iota genera and species. However, the rRNA operon
tree was still able to differentiate the various novel clus-
ters, revealing the polyphyletic nature of some of these
genera, supporting the separation of E. lichenicola and
three new species as the proposed new genus
Tunturibacter.
Pangenome analysis
Pangenome analysis was used to compare gene fre-
quencies from the COG, KEGG, SCG, and Kofam
annotations of the input genomes (Figures 2 and 3).
The gene frequency tree created from this analysis
(Figure 2, right side) is similar to the SCG tree, again
supporting the separation of two new potential genera
in the Terriglobia. The proposed Tunturibacter genus is
present as its own cluster, as is the cluster which
groups several Granulicella species that affiliate with B.
elongata (Figure 2). The very last row indicating the
F I GURE 2 Pangenome analysis of the Terriglobia in the Acidobacteriota. Comparison of gene clusters between the 13 assembled tundra
soil isolates and known Terriglobia. Each row designating an Acidobacteriota strain starts with information on the presence of gene clusters
(gene clusters are marked by the darker-coloured regions within the row). This is followed by the red/maroon columns indicating levels of
genome total length, number of genes per kbp, singleton gene clusters, and number of gene clusters. These columns are followed by the ANI
data from the pangenome analysis, and the grouping of the Acidobacteriota based on gene cluster frequency (right-hand tree). Under the gene
cluster presence rows are rows indicating COG20, KEGG, and Kofam annotations, SCG clusters, and the number of genes and contributing
genomes in the gene cluster.
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number of contributing genomes (Figure 2, bottom left)
shows that the area of the pangenome comparison with
the most contributing genomes also includes the SCG
clusters, representing the core genome of the Acido-
bacteriota analysed (Figure 3; Bin 1, 337 clusters,
11,791 gene calls).
Except for strain M8UP15, ANI analysis clearly sep-
arated the proposed new Tunturibacter species from
the other Edaphobacter species, with E. modestus as
the type species. The ANI similarities, along with the
phylogenetic clusters of this new genus in the SCG tree
(Figure 1) support the separation of four species within
the new Tunturibacter genus with their respective type
strains: E. lichenicola DSM 104462 transferred to the
genus as Tunturibacter lichenicola comb. nov.
(includes strain MP8S11), Tunturibacter psychrotoler-
ans sp. nov. X5P6 (includes strains X4BP1 and X5P2),
Tunturibacter empetritectus sp. nov. M8UP23 (includes
strains M8UP22, M8US30, M8UP20, and M8UP27),
and Tunturibacter gelidoferens sp. nov. M8UP39
(includes strains M8UP30 and M8UP28). Bin 2 captures
the gene clusters unique to this new genus (Figure 3;
Bin 2, 147 clusters, 1903 gene calls).
One major difference in this analysis compared
with the SCG tree, is the grouping of genome M8UP15
with E. aggregans DSM 19364 rather than the Tunturi-
bacter genus. These two genomes have the highest
number of gene clusters, with one area sharing
F I GURE 3 Circularized Anvio pangenome of the Terriglobia.
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iley Online Library on [27/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on W
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multiple genes unique to these two genomes
(Figure 3; Bin 3, 1820 clusters, 3640 gene calls). The
high ANI similarity of these two genomes indicates that
strain M8UP15 is most closely related to E. aggregans
DSM 19364. However, out of all the genomes in this
analysis, M8UP15 and E. aggregans DSM 19364
share the highest number of partial genes (416), indi-
cating that their genomes are not complete. Since the
SCG and operon trees did not group these two
genomes closely, it is unclear whether this result is
driven by their unique genes or their incomplete
genomes. The taxonomic placement of strain M8UP15
may thus require future reassessment.
Physiological comparison of Tunturibacter
species
The phenotypic properties of the proposed type-strains
for the new species, Tunturibacter empetritectus
M8UP23, T. gelidoferens M8UP39, and T. psychroto-
lerans X5P6 were compared with Tunturibacter (Eda-
phobacter) lichenicola (Belova, Suzina, et al., 2018).
Similarities were found for all strains based on their utili-
zation of various organic compounds (Table 2), as well
as hydrolysis of polysaccharides, enzyme activities
(API ZYM tests), and composition of quinones and
major cellular fatty acids (Table S4). The temperature
growth range for strains T. empetritectus M8UP23, T.
gelidoferens M8UP39, and T. psychrotolerans X5P6
was 2–30
C, while the growth range of T. lichenicola
DSM 104462 was different at 7–37
C. These Tunturi-
bacter species/strains tolerate cold conditions, similar
to Terriglobus (4–30
C; Eichorst et al., 2007; Männistö
et al., 2011) and Granulicella species (4–28
C;
Männistö et al., 2012). The growth pH range for T.
empetritectus M8UP23, T. gelidoferens M8UP39, and
T. psychrotolerans X5P6 was 3.5–6.5 and for T. licheni-
cola DSM 104462 was 3.4–7.0. These ranges are most
similar to those of G. tundricola and G. mallensis
(pH 3.5–6.5; Männistö et al., 2011) and can tolerate
more acidic conditions than Terriglobus (pH 4.5–7.5;
Eichorst et al., 2007; Männistö et al., 2012).
Genome comparisons of Tunturibacter
species
Genome alignments at various taxonomic levels further
support the designations of the new Tunturibacter
TAB LE 2 Utilization of various carbon substrates by Tunturibacter species.
Utilization of
T. empetritectus
M8UP23
T. gelidoferens
M8UP39
T. psychrotolerans
X5P6
T. lichenicola
(Belova, Suzina et al., 2018)
Acetate   
Arabinose    
Benzoate   
Cellobiose + + + +
Dulcitol   
Xylose + + + +
Fructose + + + +
Fucose + + +
Galacturonic acid   
Glucosamine + + w
Glucose + + + +
Lactulose    +
L-glutamic acid w w w
L-glutamine   
Maltose + + + +
Mannose + + + +
Mannitol    w
N-acetyl-glucosamine + + w
Oxalate    +
Pyruvate   
Salicin + + + +
Sorbitol   
Trehalose + + + +
Note: +, positive reaction; , negative reaction; w, weak positive reaction.
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species and strains (Figure 4). Only the longest assem-
bled scaffold for each genome was used for the align-
ment. At the genus level we compared T. lichenicola
DSM 104462 (5,662,239 bp), G. arctica DSM 23128
(4,736,692 bp), E. modestus DSM 18191
(6,121,180 bp), and Terriglobus saanensis SP1PR4
F I GURE 4 Genome comparisons at various taxonomic levels. (A) Comparison of four SD1 Acidobacteriota including Tunturibacter
lichenicola. (B) Comparison of the four species within the Tunturibacter (each species represents the type strain). (C) Comparison of four strains
within the Tunturibacter empetritectus. Genome comparisons were viewed via PGV-Mummer. Black horizontal lines indicate the span of the
genome being compared, green lines connect homologous regions between the genomes in the same orientation (normal link), and brown lines
connect homologous regions between the genomes in reverse orientation (inverted link). The shade of green and brown indicate percent
homology (bottom right legend, dark colour means higher percent homology).
TUNTURIBACTER GEN. NOV. IN THE ACIDOBACTERIOTA PHYLUM 11 of 19ENVIRONMENTAL MICROBIOLOGY
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(5,095,225 bp). At the species level we compared T.
lichenicola DSM 104462 (5,662,239 bp), T. empetritec-
tus M8UP23 (4,898,072 bp), T. gelidoferens M8UP39
(5,453,280 bp), and T. psychrotolerans X5P6
(5,619,635 bp). At the strain level, we also compared T.
empetritectus strains M8UP23 (4,898,072 bp),
M8UP20 (4,830,045 bp), M8UP22 (5,076,618 bp), and
M8UP27 (4,842,676 bp).
These alignments show decreased homology when
comparing the Tunturibacter genomes against other
genera in the Terriglobia (Figure 4A), compared with
increased homology when comparing the genomes of
the Tunturibacter species against each other
(Figure 4B,C). The strength of homology increases with
species and strain level alignments, with strain level
alignments (within the T. empetritectus strains) showing
the least amount of genome rearrangements
(Figure 4C). These trends are also apparent when
using another genome alignment visualization tool,
Mauve (Figure S4A–C), which results in longer homol-
ogy segments within alignments at the proposed strains
compared with the species and genus level alignments.
Unique pathways and phenotypic data of
Tunturibacter species
The Tunturibacter strains had between 3600 and 7400
predicted genes, of which >98% were protein-coding
genes (Table 1). All strains had at least one successful
alignment to a gene family in the CAZy HMM database
within the following CAZy classes: glycoside hydro-
lases, glycosyl transferases, carbohydrate-binding
modules, carbohydrate esterases, polysaccharide
lyases, and auxiliary activities. For each assembled
genome the number of CAZy gene alignments includes
one or more hits to unique CAZy genes spanning
numerous functions (Table 1 and Figure S5). In the dif-
ferent strains, 8%–16% of the total number of predicted
genes was coded for modules of the CAZy family, with
genes for glycoside hydrolases being the most abun-
dant. While these hits represent mostly partial align-
ments to CAZy genes, this indicates a wide set of
unique genes involved in the build-up and breakdown
of complex carbohydrates.
Compared with the other Acidobacteriota genomes
in the pangenome analysis, several pathways were sig-
nificantly enriched (p < 0.05) in members of the Tunturi-
bacter genus (Table 3). Based on KEGG Class and
COG20 Functional annotations, Tunturibacter genomes
are more enriched in functional pathways involving the
metabolism of amino acids, such as tryptophan, betaine,
and lysine. The enriched GABA (γ-aminobutyric acid)
biosynthesis pathway suggests a pH resistance strategy
within the Tunturibacter spp. (Dhakal et al., 2012). This
genus is also enriched in genes within pathways involv-
ing the metabolism and biosynthesis of cofactors and
vitamins such as menaquinone, cobalamin, biotin, and
molybdopterin. These (COG20 Pathway) annotations do
not, however, support the presence of the full pathway
within the Tunturibacter. The specific KEGG and
COG20 genes annotated from the enriched functional
pathways can be found in Table S5.
Additionally, there is a lack of evidence for promi-
nent vitamin and cofactor biosynthesis genes within
many members of the Terriglobia. Menaquinone has
been found in Acidobacterium capsulatum (Kishimoto
et al., 1991), cobalamin (B12) transport has only been
speculated in SD4 and SD8 Acidobacteriota and Bryo-
cella species (Kielak et al., 2016). An uncultivated
TAB LE 3 Enriched functional pathways within the Tunturibacter species compared with other Acidobacteriota genomes.
Annotation Enrichment score Adjusted q-value Accession
KEGG module
Aromatic amino acid metabolism: Tryptophan
metabolism, tryptophan =
>kynurenine = >2-aminomuconate;
NAD biosynthesis,
tryptophan = >quinolinate = >NAD
15.51 0.01 M00038; M00912
Amino acid metabolism: Betaine biosynthesis,
choline = > betaine; Lysine degradation,
lysine = > saccharopine = > acetoacetyl-
CoA; GABA biosynthesis, eukaryotes,
putrescine = > GABA
10.79 0.03 M00555; M00032; M00135
COG20 pathway
COG20 Pathway: Menaquinone biosynthesis;
Lysine biosynthesis
31.02 <0.01 COG0318; COG3320
COG20 Pathway: Cobalamin/B12 biosynthesis 15.51 <0.01 COG1010; COG2243
COG20 Pathway: Pyrimidine salvage; Biotin
biosynthesis
10.79 0.02 COG0402; COG2226
COG20 Pathway: Molybdopterin biosynthesis 8.99 0.05 COG0314; COG1977
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group of Acidobacteriota, GAL08, from hot springs con-
tained a biotin-specific transporter; however, it was not
able to synthesize biotin (Ruhl et al., 2022). Although
more detailed analysis is needed, the enrichment of
vitamin/cofactor biosynthesis genes within the Tunturi-
bacter suggests that members of this genus may be
able to synthesize vitamins de novo and have
increased metabolic capabilities compared with the
Edaphobacter, Granulicella, and Terriglobus species.
Acidobacteriota community in Malla tundra
heath soils
We examined the distribution of the Terriglobia in a set
of snow-accumulating and windswept tundra heath soils
in Malla Nature Reserve, from which the novel Tunturi-
bacter species were isolated. At this site, areas in
depressions are sheltered from the winds with high
snow accumulation (up to ≥1 m), while windswept areas
remain essentially snow-free throughout the winter lead-
ing to distinctly different soil temperature profiles and dif-
ferences in the amplitude of annual temperature
variation (Männistö et al., 2024). The bacterial communi-
ties were assessed by rRNA operon profiling with the
Oxford Nanopore MinION, enabling strain-specific identi-
fication of bacterial community members. Overall, rRNA
operon reads from the Acidobacteriota represented
4.2%–18.4% of the >760 K total bacterial reads from
these tundra samples. Specifically, the Acidobacteriota
reads varied from 1524 to 18,818 reads per sample with
an average of 6536 ± 5478 per site. Re-screening of
these reads against the augmented Acidobacteriota
rRNA database, containing the new rRNA operons from
this study, indicated that 18%–38% of these Acidobac-
teriota reads have best BLAST matches to Tunturibacter
and Granulicella.
Furthermore, distinct differences in the relative
abundance of Edaphobacter, Granulicella, and Terri-
globus species/strains could be observed between
windswept and snow-accumulating tundra heaths
(Figure 5). Reads matching the various Tunturibacter
strains were generally more dominant in the windswept
plots, while the Granulicella strain was more abundant
in the snow-accumulating plots. These strain and spe-
cies distinctions correspond to the observed differ-
ences in the overall soil microbial communities
between windswept and snow-accumulating tundra
heaths (Männistö et al., 2024). Snow cover and the
linked vegetation shifts and soil C and N dynamics may
thus be an important microclimatic driver of bacterial
communities. The improved taxonomy of the Acidobac-
teriota combined with the genomic and phenotypic
information of cultivated strains will enable an improved
understanding of the community response to fluctuating
environmental conditions in a changing climate.
F I GURE 5 Terriglobia community in soils of windswept (K1, K3, K6, K8) and snow-accumulating (T2, T5, T6, T7) tundra heath plots of
Mt. Pikku Malla. rRNA operon reads from the Acidobacteriota represent 4.2%–18.4% of the total bacterial reads.
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Ecological context of Acidobacteriota in
tundra soils
Members of the Acidobacteriota are ubiquitous in acidic
Arctic tundra and sub-Arctic forest soils. The Kilpisjärvi
study site has representative tundra vegetation domi-
nated by dwarf shrub-rich Empetrum heaths over acidic
soils, or forb- and graminoid-rich Dryas heaths over
non-acidic soils (Eskelinen et al., 2009; Männistö
et al., 2007, 2009, 2013). These soils are organic-rich
and well-aerated, harbouring abundant aerobic hetero-
trophic microbiota where diverse Acidobacteriota make
up 10%–40% of the total bacterial community
(Männistö et al., 2009, 2013). The abundance and com-
position of the Acidobacteriota vary with topography
and exposure influence snow accumulation and soil
temperatures (Männistö et al., 2013) as well as bedrock
material which influences soil pH (Männistö
et al., 2007). Different species within the Acidobacter-
iota appear to respond to environmental conditions dif-
ferently, highlighting the wide functional diversity of
these organisms even within the Terriglobia. From the
tundra heath sites in Kilpisjärvi Finland, several species
of Terriglobus, Granulicella, and Tunturibacter have
been cultivated (Männistö et al., 2011, 2012, this
study). These species appear adapted to the break-
down, utilization, and biosynthesis of diverse polysac-
charides, and resilience to fluctuating temperatures and
nutrient-deficient conditions.
Increased competition between plants and microbes
and within the microbial community can occur due to
environmental factors such as the increased presence of
woody evergreen shrubs that immobilize nutrients as a
consequence of warming-induced ‘shrubification’ on Arc-
tic soil carbon storage (Stark et al., 2023). Tundra soil car-
bon and nitrogen cycles are strongly coupled with soil
nitrogen availability often decreasing over the growing
season, leading to the soil microbial communities becom-
ing increasingly N-limited (Jonasson et al., 1999; Stark &
Kytöviita, 2006). Methods to combat low nutrient concen-
trations include having the functional capacity for nutrient
assimilation and transport. Acidobacteriota is known to
contain genes involved in attaining nitrogen, which
include genes essential for ammonia assimilation, for
example, glutamine synthetase, and genes for the ammo-
nium channel transporter family (amtB gene; Eichorst
et al., 2018). In a recent study comparing microbial
responses to Arctic greening in Alaskan soils, Acidobac-
teriota most strongly expressed the glutamine synthetase
metaprotein, a large component of the proteins involved
in ammonia metabolism (Miller et al., 2023). Within our
study, glutamine synthetase (COG0174) was annotated
mainly within the core genome of the Tunturibacter pan-
genome (Figure 3; Bin 1).
Another adaptation to low nutrient concentrations
includes genes for high-affinity transport systems
(Eichorst et al., 2018; Kielak et al., 2016). Transporter
genes annotated within the Tunturibacter pangenome
include high-affinity Mn2+ porin (COG3659), high-
affinity iron transporter (COG4393), and high-affinity
nickel/cobalt permease (HoxN; COG3376). Acidobac-
teriota has been shown to contain a broad substrate
range of transporters, including the Drug/Metabolite
transporter superfamily, the Ammonia Transporter
Channel (Amt) Family, and the Metal Ion (Mn2+ Iron)
Transporter (Nramp; Kielak et al., 2016). This diversity
of transporters suggests that Acidobacteriota have an
advantage in nutrient assimilation in nutrient-poor
conditions.
Tundra soil Acidobacteriota appears to be oligo-
trophs with slow growth rates and low population turn-
over rates that are favoured by the presence of
recalcitrant carbon. The genomes of the tundra soil
Acidobacteriota contain an abundance of conserved
genes/gene clusters encoding for modules of the CAZy
families, predominately glycoside hydrolases and gly-
cosyltransferases (Figure S5; Eichorst et al., 2018;
Rawat et al., 2012). In our study, pangenome glycosyl-
transferase COGs involved in cell wall biosynthesis
(COG0438) and the glycosylation of proteins and lipid
IVA (COG1807) were found across all Acidobacteriota
analysed. Multiple alignments to various CAZy gene
families were also found within the Tunturibacter indi-
cating a wide ability for utilizing complex carbohydrates.
Another interesting feature of the Acidobacteriota is
their synthesis of hopanoid lipids, which may play a
role in regulating membrane stability. Additionally,
quorum-sensing associated genes, such as acyl-
homoserine lactone (acyl-HSL), were found within
several Tunturibacter and across Acidobacteriota
within our pangenome analysis (Parsek et al., 1999).
Signalling molecules like acyl-HSLs are known to
impact bacterial community dynamics in soils, particu-
larly in response to virulence genes (Parsek
et al., 1999; Riaz et al., 2008).
Members of the Acidobacteriota are known to play a
role in the decomposition of SOM, in particular various
biopolymers, and they participate in the global cycling
of carbon, iron, and hydrogen. While Acidobacteriota
constitutes from 5% to 50% of the total bacterial com-
munity in organic-rich, low pH, Arctic, and boreal soils
based on rRNA gene reads (Männistö et al., 2007,
2009, 2013) they continue to be notoriously difficult to
cultivate and are thus woefully under-represented in
culture collections. The description of new strains and
species provides key phenotypic and genomic informa-
tion to help us understand why they are so dominant
and how they maintain diversity within the group. There
is much to learn about their ecosystem functions in
soils, their interactions with other microbes, and their
adaptations to environmental stress and climate
change.
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Description of Tunturibacter gen. nov.
The results from the multiple lines of analyses pre-
sented above indicate that E. lichenicola is not a mem-
ber of the genus Edaphobacter and should be
reclassified as a species of the proposed new genus
Tunturibacter, with the proposed name T. lichenicola
comb. nov. The NCBI BioProject ID for the 10 newly
assembled Tunturibacter genomes is PRJNA1004338.
Accession numbers for all new Tunturibacter 16S rRNA
genes and genomes are in Table S6.
Tunturibacter (Tun’tu.ri.bac’ter. tunturi, referring to
the Arctic treeless fells in Finland, N.L. masc. n. bacter,
a short rod; N.L. masc. n. Tunturibacter rod-shaped
tundra fell bacterium).
Cells are Gram-negative aerobic rods. On agar
plates, cells form circular, mucoid colonies. Colony pig-
ment varies from light beige to pink. Produce extracellu-
lar polysaccharide-like substances. Sugars are
preferred carbon sources and the different strains
are capable of hydrolyzing various polysaccharides.
The major cellular fatty acids are iso-15:0, iso-13:0,
16:1ω7c, and 16:0. The predominant menaquinone is
MK-8. The DNA G + C content is 56%–58%. Strains
have been isolated from tundra soil and lichen thalli col-
lected from lichen-dominated forested tundra. The type
species is T. lichenicola comb. nov.
Emended description of T. lichenicola
comb. nov.
The description is as given by Belova, Ravin, et al.
(2018) and Belova, Suzina, et al. (2018). The type
strain is SBC68T (=DSM 104462T = VKM B-3208T).
Description of Tunturibacter empetritectus
sp. nov.
Tunturibacter empetritectus (em.pet.ri.tectus. empetri,
referring to the plant Empetrum nigrum ssp. hermaph-
roditum; L. adj. tectus, covered; L. part. Adj. empetritec-
tus, growing under tundra heath dominated by E.
nigrum ssp. hermaphroditum).
Cells are Gram-negative, non-motile, aerobic rods.
Colonies are light beige or pink, circular, and smooth
when grown on GY agar (Figure S6). Growth occurs at
2–30
C and pH 3.5–6.5. In VL55 mineral medium with
100 mg L1 yeast extract and 5–10 mM carbon source,
utilizes cellobiose, xylose, fructose, fucose, glucos-
amine, glucose, L-glutamic acid (weak), maltose, man-
nose, N-acetyl-glucosamine, salicin and trehalose.
Hydrolyzes xylan, pectin, xanthan and gum arabic. The
major cellular fatty acids are iso-15:0, iso-13:0,
16:1ω7c, and 16:0. The DNA G + C content
determined from the genome sequence of the type
strain is 57.82%.
The type strain is M8UP23T (= DSMZ
117310 = HAMBI 3810) isolated from tundra soil in Malla
Nature Reserve, Kilpisjärvi, Finland (69
010 N, 20
500 E).
NCBI accession numbers for the 16S rRNA gene
sequence and the draft genome sequence of the type strain
are OR449309 and CP132932-CP132934, respectively.
Description of T. gelidoferens sp. nov.
Tunturibacter gelidoferens (ge.li.do.ferens. L. adj.
gelido cold; L. pres. Part. Ferens, to endure; L. part.
Adj. gelidoferens, cold-enduring).
Cells are Gram-negative, non-motile, aerobic rods.
Colonies are pink, circular, and smooth when grown on
GY agar (Figure S6). Growth occurs at 2–30
C and
pH 3.5–6.5. In VL55 mineral medium with 100 mg L1
yeast extract and 5–10 mM carbon source, utilizes
cellobiose, xylose, fructose, fucose, glucosamine, glu-
cose, L-glutamic acid (weak), maltose, mannose, N-
acetyl-glucosamine, salicin, and trehalose. Hydrolyzes
carboxy methyl cellulose (weak), xylan, pectin, lichenin,
starch (weak), and gum arabic (weak). The major cellu-
lar fatty acids are iso-15:0, iso-13:0, 16:1ω7c, and 16:0.
The DNA G + C content determined from the genome
sequence of the type strain is 57.42%.
The type strain is M8UP39T (= DSMZ
117311 = HAMBI 3809) isolated from tundra soil in
Malla Nature Reserve, Kilpisjärvi, Finland (69
010 N,
20
500 E). NCBI accession numbers for the 16S rRNA
gene sequence and the draft genome sequence of the
type strain are OR449311 and CP132937–CP132938,
respectively.
Description of T. psychrotolerans sp. nov.
Tunturibacter psychrotolerans (psy.chro.to’le.rans.
Gr. Adj. psychros, cold; L. pres. Part. Tolerans, tolerat-
ing; N.L. part. Adj. psychrotolerans, cold-tolerating).
Cells are Gram-negative, non-motile, aerobic rods.
Colonies are light beige to light pink, circular, and
smooth when grown on GY agar (Figure S6). Growth
occurs at 2–30
C and pH 3.5–6.5. In VL55 mineral
medium with 100 mg L1 yeast extract and 5–10 mM
carbon source, utilizes cellobiose, xylose, fructose,
fucose, glucosamine (weak), glucose, L-glutamic acid
(weak), maltose, mannose, N-acetyl-glucosamine
(weak), salicin, and trehalose. Hydrolyzes carboxy
methyl cellulose (weak), pectin, lichenin, starch,
xanthan and gum arabic (weak). The major cellular fatty
acids are iso-15:0, iso-13:0, 16:1ω7c, and 16:0. The
DNA G + C content determined from the genome
sequence of the type strain is 56.72%.
TUNTURIBACTER GEN. NOV. IN THE ACIDOBACTERIOTA PHYLUM 15 of 19ENVIRONMENTAL MICROBIOLOGY
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iley Online Library on [27/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on W
iley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
The type strain is X5P6T (= DSMZ 117309 = HAMBI
3811) isolated from tundra soil in Malla Nature Reserve,
Kilpisjärvi, Finland (69
010 N, 20
500 E). NCBI accession
numbers for the 16S rRNA gene sequence and the draft
genome sequence of the type strain are OR449310 and
CP132942–CP132943, respectively.
AUTHOR CONTRIBUTIONS
Adriana Messyasz: Writing—original draft; formal
analysis; investigation; writing—review and editing;
visualization; data curation; methodology. Minna
K. Männistö: Investigation; writing—review and edit-
ing; funding acquisition; conceptualization; methodol-
ogy. Lee J. Kerkhof: Writing—review and editing;
supervision; funding acquisition; resources; methodol-
ogy; investigation. Max M. Häggblom: Supervision;
writing—review and editing; funding acquisition; con-
ceptualization; project administration; methodology;
investigation; resources.
ACKNOWLEDGEMENTS
We thank Sirkka-Liisa Aakkonen, Sari Välitalo, and
Marika Pätsi for their help in cultivating and characteriz-
ing the strains. We thank Kristina Chew and Serena
Connolly for their assistance with nomenclature. This
study was funded in part by the US National Science
Foundation (Award Number 2129351) to MMH and
LJK, the Academy of Finland (decision numbers
130507 and 310776) to MKM, and the USDA National
Institute of Food and Agriculture Hatch project acces-
sion number 1012785 through the New Jersey Agricul-
tural Experiment Station (Hatch Project NJ01160) to
MMH. Illumina sequencing of select strains was done
through the Community Science Program (CSP) of the
US Department of Energy Joint Genomes Institute
(Genomic Sequencing of Core and Pangenomes of Soil
and Plant-associated Prokaryotes; PI William
B. Whitman).
CONFLICT OF INTEREST STATEMENT
The authors declare no conflicts of interest.
DATA AVAILABILITY STATEMENT
The NCBI BioProject ID for the newly assembled Tun-
turibacter genomes is PRJNA1004338: https://www.
ncbi.nlm.nih.gov/bioproject/PRJNA1004338. Accession
numbers for 16S rRNA genes are OR449309–
OR449318. Accession numbers for genomes are
CP132926-CP132945. The rRNA operon reads from
Malla Nature Reserve soil samples are available in Bio-
Project ID PRJNA1093128: https://www.ncbi.nlm.nih.
gov/bioproject/PRJNA1093128.
ORCID
Max M. Häggblom https://orcid.org/0000-0001-6307-
7863
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How to cite this article: Messyasz, A.,
Männistö, M.K., Kerkhof, L.J. & Häggblom, M.M.
(2024) Genome analysis and description of
Tunturibacter gen. nov. expands the diversity of
Terriglobia in tundra soils. Environmental
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