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Ecological Indicators
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A R T I C L E I N F O A B S T R A C T
Keywords: Polar regions provide an ideal environment to investigate the succession of bacterial communities. In the present
Glacier foreland study, we investigated the bacterial diversity and community structure of the Midtre Lovénbreen glacier foreland
Soil development ecosystem using a chronosequence approach. The alpha diversity indices of the samples collected from recently
Bacterial succession
deglaciated sites comprised of less diverse, yet abundant bacterial groups compared to the samples from
Amplicon sequencing
comparatively older sites, where the bacterial diversity was very rich and evenly distributed. Bacterial phyla viz.
(a) Proteobacteria (14–44.58%) comprising classes of alpha- and gamma Proteobacteria along with (b) Acti
nobacteriota (8.8–33.8%) were predominantly distributed across the samples, while phyla Bacteroidota (up to
21%) was mainly distributed in the recently deglaciated samples and phyla Acidobacteriota (up to 24%) in
deglaciated samples which were older. Bacterial families (Sulfurovaceae and Sulfurimonadaceae) affiliated with
bio weathering of rocks for their energy metabolism was also detected in the present study from the recently
deglaciated region. Bacterial genera belonging to Luteolibacter (up to 10.25%), Polaribacter (up to 12.32%),
Acidimicrobium (6%) and Sulfitobacter (13.6%) were highly abundant in the recently deglaciated samples, while
Candidatus_Udaeobacter (up to 17%) and RB41 (up to 10.5%) were found to be abundant in the older stage
samples. Linear discriminant analysis revealed 121 Operational Taxonomic Units that could be attributed to the
differences in the community diversity between the two groups. Among the analyzed environmental variables,
pH, Cr, Cd and Ca significantly contributed to the differences in the bacterial community structure.
* Corresponding author.
E-mail addresses: venkatachalam@ncpor.res.in (S. Venkatachalam), krishnan@ncpor.res.in (K.P. Krishnan).
https://doi.org/10.1016/j.ecolind.2021.107704
Received 21 September 2020; Received in revised form 12 February 2021; Accepted 7 April 2021
Available online 25 April 2021
1470-160X/© 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
production is mostly restricted to the short summer season (Kosek et al., Spitsbergen Island (78◦ 55′ N, 12◦ 10′ E). The glacier is about 5 km long,
2019). Studies on ecological succession in the glacier forelands are located 50–650 m above sea level, and has been retreating since the end
mainly carried out by chronosequence method by investigating soil’s of the Little Ice Age (Seok et al., 2016). However, in the past few de
structure and development at a linear distance from the glacier edge cades, the glacier’s retreating ratio has accelerated rapidly, and current
(Walker et al., 2010). Most of the studies on succession mainly focused numerical modeling studies predict that the glacier could disappear in
on plant traits based on vegetation structure in the glacier forelands of the next 100 years (Ai et al., 2019; Schuler et al., 2020). Recently
polar and alpine environments (Hodkinson et al., 2003; Matthews, 1992; deglaciated sites in this glacier foreland are composed of different
Reiners et al., 1971; Sitzia et al., 2016). Studies focusing on microbes, bedrocks belonging to the Lower, Middle and Upper Proterozoic era
the primary colonizers of glacier forelands in the polar regions, have (Wynn et al., 2007), which are being weathered by microbes continu
been undertaken only since the last one decade (Mapelli et al., 2018) by ously, thereby providing optimal substrates for soil development and
using culture-independent amplicon sequencing based approaches to plant colonization (Mapelli et al., 2011). The gradually exposed soil is
assess bacterial community dynamics. Over the years, our understand subject to freeze-thaw cycles throughout the year (Wietrzyk et al., 2018;
ing of the microbial community structure and its functions has signifi Yoshitake et al., 2011), providing an excellent environmental setting for
cantly increased with the advancement in genomics. microbial ecologists to investigate changes in microbial communities in
The landscape of Svalbard has been undergoing rapid changes due to connection with soil exposure and environmental parameters that can
deglaciation. It has been reported that about 7% of the glaciers in help to predict the response of bacterial communities to changing
Svalbard have disappeared over the last 30 years (Hanna et al., 2020; environmental conditions during the process of deglaciation. With this
Nuth et al., 2013). Midtre Lovénbreen glacier is a polythermal valley background, the present study was undertaken to assess the bacterial
glacier located on the Brøggerhalvøya peninsula of the northwest community structure of the Midtre Lovénbreen glacier foreland
Fig. 1. Map showing the location of sampling coordinates along with Midtre Lovénbreen glacier foreland ecosystem. The map was generated in ArcGIS (v10.3)
software using source files obtained from (https://www.pgc.umn.edu/data/arcticdem/).
2
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
ecosystem using deep amplicon sequencing approach to determine the purification Kit (Invitrogen, USA). The isolated DNA was visually
distribution of bacterial communities across different deglaciation checked for quality assessment by agarose gel electrophoresis (1%
stages and to delineate further the influence of environmental parame agarose) and quantified using Biospectrometer (Eppendorf, Germany).
ters in shaping the community composition. The V3–V4 hyper-variable region of the bacterial 16S rRNA gene was
amplified using Pro341F/Pro805R primer sets (Takahashi et al., 2014).
2. Materials and methods The reaction mixture (25 µL) contained 10 ng genomic DNA, 12.5 µL of
AmpliTaq Gold® 360 PCR master mix (Invitrogen, USA) and 0.25 mM of
2.1. Sample collection each primer. The PCR conditions for amplification of DNA were as fol
lows: initial denaturation at 98 ◦ C for 2 min, followed by 25 cycles of
Samples were collected from the glacier foreland associated with 95 ◦ C for 30 s, annealing at 55 ◦ C for 1 min and extension at 72 ◦ C for 30
Midtre Lovénbreen glacier, Svalbard, during the Indian Arctic expedi s. The amplified PCR products were purified by using gel extraction kits.
tion (June 2019). A total of 8 soil samples (200 g) were collected The amplicon sequencing libraries were prepared using NEBNext®
(Fig. S1) from a transect using chronosequence approach from glacier Ultra™ II DNA Library Prep Kit (New England Biolabs, USA) according
snout to the fjord (Fig. 1, Table 1), which was about 1.8 km covering a to the manufacturer’s protocol and sequenced on Illumina HiSeq plat
deglaciation period of up to 1900 years (Hodkinson et al., 2003). Sam form 2500. The sequence datasets were submitted to the NCBI Sequence
ples (ML1–ML3) from recently de-glaciated sites (snout area) containing Read Archive (SRA) library under the accession number: PRJNA658121.
barren soil will be henceforth referred to as ’recent stage’ samples.
Samples (ML4–ML8) from older deglaciated sites where the soil is well
developed to support vegetation structure will be referred to as ’older 2.4. Bioinformatics and statistical analysis
stage’ samples. The present classification was adapted based on the
previous literature from this region (Mapelli et al., 2011). Larger gravel The raw sequence datasets were quality trimmed to remove primer
and other plant debris were removed before samples were taken. About and adapter sequences using Cutadapt (Martin, 2011). The trimmed
200 g of soil per sample was collected from the top layer (15 cm) using sequence datasets were further analyzed using Mothur (v.1.44.0) to
an ethanol-cleaned shovel and transferred to Whirl-Pak bags (Nasco, WI, characterize the bacterial community structure (Schloss et al., 2009).
USA). The samples were brought to the National Centre for Polar and The sequence analysis method includes, the removal of short sequences
Ocean Research, India, at − 20 ◦ C and further stored at the same tem of <300 nts, reads that contained ambiguous nucleotides and homo
perature till further analysis. polymeric runs of >7 from the dataset. Mitochondrial, chloroplast and
archaeal sequences were also excluded from the analysis. The chimeric
sequences were removed subsequent to identification using the
2.2. Trace metals chemical analysis VSEARCH algorithm (Rognes et al., 2016). Classification of the reads
was done to the genus level using the Naïve Bayesian classifier algorithm
Soil samples were dried, pulverized and then sieved (mesh size of (Cole et al., 2014; Wang et al., 2007) against the SILVA database version
1.70 mm – ASTM No .230) prior to analysis as described by Link et al. 138 (Quast et al., 2012) with a confidence threshold of 80% to assign
(1998) and Yuan et al. (2004). The samples were digested with suprapur taxonomic identity. A pairwise distance matrix was created from the
nitric acid (Sigma-Aldrich, USA), followed by filtration (0.2 μm nylon curated aligned datasets to group sequences into Operational Taxo
filter) and dilution of samples (25 parts). Trace metals were then nomic Units (OTUs) at a confidence level of 97%. The alpha diversity
quantified using an ICP-MS (iCAP Q, Thermo Fisher Scientific, USA). indices (observed species, Simpson, Shannon, and Chao1) were calcu
Continuous calibration was performed with standard and blank solu lated using the phyloseq package (McMurdie and Holmes, 2013) in R v-
tions during measurements. Standard solutions were prepared in 1% 4.0.2. The Linear discriminant analysis Effect Size (LEfSe) to identify the
HNO3 using ICP-multielement (30 elements) standard solution VI differentially abundant features (Segata et al., 2011) among the bacte
(Merck Millipore, Germany). The soil pH was measured in a 1:2 (w/v) rial taxa was calculated using the microbiome Analyst R server (Chong
ratio of soil: deionized water using a pH meter (Orion, Thermo scientific, et al., 2020) with described default parameters. Statistically significant
USA). groups were reported with nonparametric factorial Kruskal Wallis (KW)
rank-sum test (p < 0.05) and high LDA (Linear Discriminant Analysis)
2.3. Genomic DNA extraction and 16S rRNA gene sequencing threshold score values >2.0 (Segata et al., 2011). The OTU reads con
taining less than two numbers were discarded and the remaining OTUs
According to the manufacturer’s protocol, the total genomic DNA within each sample were converted into relative percentages, square-
was isolated from the soil samples using PureLink™ microbiome DNA root transformed and then Bray-Curtis resemblance matrix was
Table 1
Sampling locations along with details of the data obtained by high throughput sequencing from the Midtre Lovénbreen glacier foreland ecosystem.
Sample name GPS Coordinates Soil type Raw sequence reads Sub sampled reads Total number of OTUs Goods coverage (%)
ML1 78 53.906
◦ ′
N Barren 526,533 166,487 2482 99.86
12◦ 03.221′ E
ML2 78◦ 54.173′ N Barren 1,031,559 166,487 1760 99.82
12◦ 02.792′ E
ML3 78◦ 54.314′ N Barren 1,005,450 166,487 2276 99.37
12◦ 02.489′ E
ML4 78◦ 54.395′ N Developing 1,179,332 166,487 4603 99.04
12◦ 02.449′ E
ML5 78◦ 54.543′ N Mature 753,585 166,487 3163 99.37
12◦ 02.428′ E
ML6 78◦ 54.627′ N Mature 1,091,119 166,487 4086 99.22
12◦ 02.337′ E
ML7 78◦ 54.755′ N Mature 1,128,477 166,487 4513 99.01
12◦ 02.222′ E
ML8 78◦ 54.833′ N Mature 951,736 166,487 2630 99.49
12◦ 02.122′ E
3
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
calculated. A comparative nonmetric multidimensional scaling (nMDS) Species coverage indices (Goods coverage) of all the samples were above
analysis at the OTU level of 97% was performed among the sample 99%, which indicated an adequate level of sequencing had been carried
datasets to find the differences in the bacterial community composition out to identify most of the diversity within the samples.
by using the multivariate statistical software Primer (PRIMER E) version The alpha diversity indices (Observed, Chao-1, Shannon and Simp
7 (Clarke and Gorley, 2015). Distanced-based multiple linear regression son) revealed that richness and evenness of bacterial taxa in the samples
tests (Dist-LM) and distance-based constrained redundancy analysis (db- belonging to the recent stage samples were comparatively less than
RDA) were performed to analyze the contribution of environmental those of older stage samples from well-developed foreland ecosystem
physicochemical parameters attributed to the variability in bacterial (Fig. 2). Furthermore, the observed indices and Chao-1 richness indices,
community structure. which estimate the number of unobserved species in the given samples,
almost fell within the same range suggesting the present study described
3. Results near to complete diversity among the analyzed sequence datasets.
3.1. Environmental characteristics of Midtre Lovénbreen glacier foreland 3.3. Distribution of bacterial community structure
The samples were collected along the glacier foreland of Midtre Based on the phylogenetic classification of sequence datasets, a total
Lovénbreen glacier from glacier snout to the fjord mouth of Kongsfjor of 33 bacterial phyla were identified, of which Acidobacteriota
den. The vegetation structure was commonly observed among the older (4.1–23.8%), Actinobacteriota (8.8–33.8%), Proteobacteria
deglaciated regions of Midtre Lovénbreen glacier foreland, where the (14–44.58%), Chloroflexi (4.1–19%) and Verrucomicrobiota
soils are fully developed, whilst samples collected from the glacier snout (1.5–21.56%) were predominantly distributed among the samples with
area was classified as barren soil type (Table 1). Along the transect, soil different relative abundances (Fig. 3A). The phylum Proteobacteria,
pH decreased in a linear scale ranging from pH 8.5 in the vicinity glacier comprising mainly of alpha- and gamma Proteobacteria were dominant
snout to pH 6.7 near Kongsfjorden. At the time of sample collection, the among samples. Phyla Bacteroidota (2–22%) was mainly distributed in
mean air temperature was around 6.3–6.8 ◦ C (Norwegian Meteorolog the recent stage samples, whereas Acidobacteriota (18–24%) was
ical Institute, www.met.no). Elemental analysis revealed that except for commonly distributed in older stage samples. Likewise, a minor fraction
Na and P, all of the remaining analyzed elements were found to be of reads representing phyla Campilobacterota and superphylum Pates
highest at ML2 (Table 2), which was collected from a typical moraine cibacteria were also identified in recent and older late stage samples,
environment. Other elements like Ca (817.8–2352.8 µg g− 1) and Zn respectively. We also observed two other phyla, namely Myxococcota
(1040–1099.7 µg g− 1) were found to have the highest concentrations in and Gemmatimonadota, accounting for a small fraction (1–7%) of reads.
recent stage samples (ML1–3) in comparison to those of older stage Further taxonomic classification of sequence reads at 97% similarity
samples (ML4–8). We could not observe any specific patterns among the level showed about 93 different classes, 224 orders, 332 families and
remaining elements between recent and older stage sample groups. In 454 different genera among the samples. Class Bacteroidia
general, we observed that concentrations of metal elements varied (15.83–21.92%), Gammaproteobacteria (6.56–20.57%) and Actino
among collected samples across the studied transect (Table 2). bacteria (12.17–15.98%) were predominantly distributed in the recent
stage samples. However, older stage samples were equally dominated
3.2. Alpha diversity of glacier foreland samples (6–10% of reads) by class Acidimicrobiia, Vicinamibacteria, and Blas
tocatellia (Fig. 3B). The families, Rubritaleaceae (12.36%), Fla
A total of 7,667,791 good quality sequence reads were obtained from vobacteriaceae (9.82%), Microbacteriaceae (13.06%)
eight samples with an average length of 430 nucleotides that belonged Comamonadaceae (12.84%) were identified as dominant families in the
to the 16S rRNA V3–V4 region. The sequence data that was normalized recent stage group. Further, the families Sulfurovaceae (7.29%) and
to 1,66,487 reads per sample yielded a range of 1760–4513 OTUs per Sulfurimonadaceae (1.4%) were unique to sample ML1, which is located
sample (Table 1). At this defined sequencing depth, rarefaction curve near the glacier snout area (Supplementary Table 1). Similarly, Chtho
analysis revealed a reasonable coverage of bacterial richness among the niobacteraceae (18.7%), Pyrinomonadaceae (10.28%) were identified
datasets (Supplementary Fig. S2). In general, samples collected from as dominant families in the late stage samples, respectively. At the genus
recent stage sites contain fewer OTUs compared to the older stages. level, Luteolibacter, Polaribacter, Acidimicrobium, Candidatus_Aquiluna,
Table 2
Physico-chemical analysis of Midtre Lovénbreen glacier foreland samples. Given Data values are average of three technical replicates.
Element concentration (µg g− 1) ML 1 ML 2 ML 3 ML 4 ML 5 ML 6 ML 7 ML 8
4
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
Fig. 2. Alpha diversity indices from the soil samples of Midtre Lovénbreen glacier foreland. The samples ML1-ML3 is grouped as recent stage and samples ML4-ML8
is grouped as older stage based on their deglaciation time and phase.
Fig. 3. Distribution of bacterial community structure of the foreland of Midtre Lovénbreen glacier. Phylogenetic classification at (A) Phylum and (B) Class level. The
datasets were classified using Silva reference database v138 using the Naïve Bayesian classifier algorithm.
5
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
Fig. 4. Identification of dominant bacterial genera (A) from the glacier foreland samples and (B) their size effect by differential abundance analysis (LEfSe).
6
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
Fig. 5. Multivariate analysis of the glacier foreland samples. (A) Non-metric Multidimensional Scaling (NMDS) plot showing the relationship between bacterial
groups. (B) Distance-based Redundancy analysis (db-RDA) shows the best explained environmental variables in the glacier foreland’s bacterial community structure.
The samples ML1-ML 3 belong to recent stage, while ML 4-ML 8 are from older stage.
7
S. Venkatachalam et al. Ecological Indicators 126 (2021) 107704
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Declaration of Competing Interest
Matthews, J.A., 1992. The Ecology of Recently-Deglaciated Terrain: a Geoecological
Approach to Glacier Forelands. Cambridge University Press.
The authors declare that they have no known competing financial McMurdie, P.J., Holmes, S., 2013. phyloseq: an R package for reproducible interactive
analysis and graphics of microbiome census data. PLoS One 8, e61217.
interests or personal relationships that could have appeared to influence
Nuth, C., Kohler, J., König, M., Deschwanden, A.V., Hagen, J.O.M., Kääb, A.,
the work reported in this paper. Moholdt, G., Pettersson, R., 2013. Decadal changes from a multi-temporal glacier
inventory of Svalbard. Cryosphere 7, 1603–1621.
Pendleton, S.L., Miller, G.H., Lifton, N., Lehman, S.J., Southon, J., Crump, S.E.,
Acknowledgments Anderson, R.S., 2019. Rapidly receding Arctic Canada glaciers revealing landscapes
continuously ice-covered for more than 40,000 years. Nat. Commun. 10, 1–8.
The authors wish to express their gratitude to Director, NCPOR for Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J.,
Glöckner, F.O., 2012. The SILVA ribosomal RNA gene database project: improved
his support and encouragement. SV thanks Science and Engineering
data processing and web-based tools. Nucleic Acids Res. 41, D590–D596.
Research Board (SERB), Department of Science and Technology, Gov Reiners, W.A., Worley, I.A., Lawrence, D.B., 1971. Plant diversity in a chronosequence at
ernment of India for his Post-Doctoral Fellowship (No.: PDF/2018/ Glacier Bay, Alaska. Ecology 52, 55–69.
Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open
002088) and research running grant for carrying out the present work.
source tool for metagenomics. PeerJ 4, e2584.
This work was carried out as a part of the Indian scientific expedition to Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B.,
the Arctic-2019. We also thank Dr. N.S. Magesh, Project Scientist at Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., 2009. Introducing
NCPOR, for his assistance in the drawing sampling maps. This is NCPOR mothur: open-source, platform-independent, community-supported software for
describing and comparing microbial communities. Appl. Environ. Microbiol. 75,
contribution number: J- 2/2021-22. 7537–7541.
Schuette, U.M., Abdo, Z., Foster, J., Ravel, J., Bunge, J., Solheim, B., Forney, L.J., 2010.
Bacterial diversity in a glacier foreland of the high Arctic. Mol. Ecol. 19, 54–66.
Appendix A. Supplementary data
Schuler, T.V., Kohler, J., Elagina, N., Hagen, J.O.M., Hodson, A.J., Jania, J.A., Kääb, A.
M., Luks, B., Małecki, J., Moholdt, G., Pohjola, V.A., Sobota, I., Van Pelt, W.J.J.,
Supplementary data to this article can be found online at https://doi. 2020. Reconciling Svalbard glacier mass balance. Front. Earth Sci. 8, 156.
Schütte, U.M., Abdo, Z., Bent, S.J., Williams, C.J., Schneider, G.M., Solheim, B.,
org/10.1016/j.ecolind.2021.107704.
Forney, L.J., 2009. Bacterial succession in a glacier foreland of the High Arctic. ISME
J. 3, 1258–1268.
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