A biogeographic distribution of magnetotactic bacteria influenced by salinity.

Abstract

Magnetotactic bacteria (MTB), which synthesize intracellular ferromagnetic magnetite and/or greigite magnetosomes, have significant roles in global iron cycling in aquatic systems, as well as sedimentary magnetism. The occurrence of MTB has been reported in aquatic environments from freshwater to marine ecosystems; however, the distribution of MTB across heterogeneous habitats remains unclear. Here we examined the MTB communities from diverse habitats across northern and southern China, using comprehensive transmission electron microscopy and comparison of 16S rRNA gene analyses. A total of 334 16S rRNA gene sequences were analyzed, representing the most comprehensive analysis on the diversity and distribution of MTB to date. The majority (95%) of sequences belong to the Alphaproteobacteria, whereas a population of giant magnetotactic rod is affiliated with the Nitrospirae phylum. By a statistical comparison of these sequence data and publicly available MTB sequences, we infer for the first time that the composition of MTB communities represents a biogeographic distribution across globally heterogeneous environments, which is influenced by salinity.

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SHORT COMMUNICATION
A biogeographic distribution of magnetotactic
bacteria influenced by salinity
Wei Lin1,2, Yinzhao Wang1,2, Bi Li1,2and Yongxin Pan1,2
1Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth’s
Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China and
2France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences,
Beijing, China
Magnetotactic bacteria (MTB), which synthesize intracellular ferromagnetic magnetite and/or
greigite magnetosomes, have significant roles in global iron cycling in aquatic systems, as well
as sedimentary magnetism. The occurrence of MTB has been reported in aquatic environments from
freshwater to marine ecosystems; however, the distribution of MTB across heterogeneous habitats
remains unclear. Here we examined the MTB communities from diverse habitats across northern and
southern China, using comprehensive transmission electron microscopy and comparison of 16S
rRNA gene analyses. A total of 334 16S rRNA gene sequences were analyzed, representing the most
comprehensive analysis on the diversity and distribution of MTB to date. The majority (95%) of
sequences belong to the Alphaproteobacteria, whereas a population of giant magnetotactic rod is
affiliated with the Nitrospirae phylum. By a statistical comparison of these sequence data and
publicly available MTB sequences, we infer for the first time that the composition of MTB
communities represents a biogeographic distribution across globally heterogeneous environments,
which is influenced by salinity.
The ISME Journal advance online publication, 25 August 2011; doi:10.1038/ismej.2011.112
Subject Category: microbial population and community ecology
Keywords: magnetotactic bacteria; biogeography; microbial diversity; salinity
Magnetotactic bacteria (MTB) are a diverse group of
microorganisms, which are ubiquitous in aquatic
environments from freshwater to marine ecosystems
(Bazylinski and Frankel, 2004). These bacteria can
mineralizeintracellular
(Fe3O4) and/or sulfides (Fe3S4) named magneto-
somes (Jogler and Schu ¨ler, 2009). Based on the
analysis of 16S rRNA genes, all known MTB are
affiliated within Proteobacteria and Nitrospirae
phyla (Amann et al., 2006). Considering their high
abundance (104–106cellsperml) near the oxic–anoxic
transition zone and high intracellular iron content
(10?13to 10?15g per cell), MTB have been attributed as
an important role in iron cycling in aquatic systems
(Faivre and Schu ¨ler, 2008). Moreover, fossil magne-
tosomes preserved in sediments may significantly
contribute to the bulk magnetization of sediments
and serve as potential archives of paleoenviron-
mental information (Kopp and Kirschvink, 2008; Lin
and Pan, 2009). However, due to the lack of
nanosizedironoxides
comprehensive study on the distribution of MTB
across different ecosystems thus far, we know little
about the biogeography of MTB communities.
In the present study, we analyzed the MTB
communitiesfromdifferent
northern and southern China, including four fresh-
water lakes, two mangrove swamps, two estuaries
and one intertidal zone, with a salinity gradient
ranging from 0.18 to 28.6 parts per thousand (p.p.t.)
and spanning latitudes of 191N–401N. MTB were
magnetically enriched solely using the ‘MTB trap’
method,whichsimultaneously
north- and south-seeking MTB (Jogler et al., 2009).
After magnetic collection, the enriched north- and
south-seeking MTB from same sample were pooled.
The diversity of MTB communities in each site was
examined by transmission electron microscopy and
comparison of 16S rRNA genes. Detailed descrip-
tions of sampling sites and experimental procedures
are given as Supplementary Information. MTB
communities from different sites in this study, along
with publicly available data, were further compared
using statistically phylogenetic methods.
Live MTB were enriched from all nine sampling
sites. Only coccoid MTB were observed in the saline
samples from the mangrove swamps, estuaries and
intertidal zone (Figures 1a–c). However, great mor-
phological variability was observed in the MTB
ecosystems across
collectedboth
Received 9 February 2011; revised 18 July 2011; accepted 18 July
2011
Correspondence: W Lin or Y Pan, Biogeomagnetism Group,
Paleomagnetism and Geochronology Laboratory, Key Laboratory
of the Earth’s Deep Interior, Institute of Geology and Geophysics,
Chinese Academy of Sciences, Bei Tu Cheng Xi Lu 19, Chaoyang
District, Beijing 100029, China.
E-mails: weilin0408@gmail.com or yxpan@mail.iggcas.ac.cn
The ISME Journal (2011), 1–5
& 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11
www.nature.com/ismej

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enrichment from the freshwater lakes, including
cocci (Figures 1d–f), vibrios (Figures 1g and h) and a
giant rod-shaped bacterium (Figure 1i); this rod was
morphologically similar to ‘Candidatus Magneto-
bacterium bavaricum’, found in Lake Chiemsee
(Spring et al., 1993; Jogler et al., 2010, 2011), and
‘Ca. Magnetobacterium bavaricum’-like MTB found
in Lake Miyun previously (Lin et al., 2011).
The 16S rRNA genes were directly amplified from
magnetically enriched MTB, using the bacterial
universal primers 27F (50-AGAGTTTGATCCTGGCT
CAG-30) and 1492R (50-GGTTACCTTGTTACGAC
TT-30) as previously described (Lin et al., 2008).
Randomly selected clones were sequenced using a
27F primer (Beijing Genomics Institute, Beijing,
China). After removing sequences of insufficient
length (o400bp) and low quality, nearly 400
sequences were retrieved in this study. The presence
of potential chimeras was checked using the Green-
genes chimera-check tool (Huber et al., 2004).
Twenty-six sequences, which were most similar to
non-MTB bacteria, but unrelated to known MTB
(o80%sequenceidentity), were
contaminationbynon-magnetotactic
(SupplementaryInformation
Table 3), and were thus removed from the analyses.
In this way, a total of 334 high quality 16S rRNA genes
were retrieved, which covered V1 to V3 hypervariable
regions (450–500bp) and sufficed for accurate micro-
bial diversity analysis (Liu et al., 2007).
These sequences were composed of 43 operational
taxonomic units (OTUs) defined as 98% similarity
level, representing only 3–11 OTUs per location
(Figure 2a and Supplementary Table 1). Although
the potential limit of the magnetic enrichment
approach (Lin et al., 2008) and/or the strict MTB
sequences assignment applied in this study may
restrict the assessment of MTB diversity, our results
were similar to the diversity level reported else-
where (Simmons et al., 2004; Flies et al., 2005).
Rarefaction curves for all nine libraries nearly
reached an asymptote, indicating that we have
attributed
organisms
Supplementary
to
and
Figure 1
(a–c) are MTB from saline environments, including the mangrove swamps, estuaries and intertidal zone. (d–i) are MTB from freshwater
lakes. Bars¼500nm.
Representative transmission electron micrographs of various MTB from nine locations across northern and southern China.
Biogeography of magnetotactic bacteria
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captured
(Figure 2a). Therefore, our results likely reflect the
true situation that the sequence diversity of MTB
communities in nature, compared with the whole
bacterial community (Whitman et al., 1998), is not
very high. Out of 334 sequences, 318 sequences (42
OTUs) were affiliated within the Alphaproteo-
bacteria, whereas the residual 16 sequences (1
OTU) detected from freshwater sediments belonged
to the Nitrospirae phylum and were 97.9% similar to
‘Ca. Magnetobacterium bavaricum’ (Figure 2b). The
phylogeneticstructure
here suggestedabiogeographic
MTB communities. For example, out of 43 OTUs,
31 OTUs were endemic, whereas none were cosmo-
politan (Figure 2b). In addition, there was no
overlap in OTUs between freshwater and saline
environments.
To understand the global biogeographic pattern of
MTB communities, we compared each community
of this study and publicly available MTB sequence
sets from Itaipu lagoon (saline) in Brazil, Jiaozhou
Bay (saline) in China
(freshwater) in Germany, with a matrix of UniFrac
themajor extent of MTBdiversity
ofallOTUs
distribution
retrieved
of
and LakeChiemsee
distances (Hamady et al., 2010) through principal
coordinates analysis (Supplementary Table 2). Of
particular interest, all MTB communities were
grouped by salinity rather than geographic distances
or continents (Figure 2c). Among them, MTB
communities from freshwater environments, even
those from Lake Chiemsee in Germany, which is
geographically distant from China, clustered to-
gether along principal coordinate 1. On the other
hand, MTB communities from the saline sediments,
including Itaipu Lagoon in the Southern Hemi-
sphere, were more similar to each other than to their
freshwater counterparts. The salinity-dependent
distribution of MTB was further confirmed by
Spearman rank correlations analysis, which demon-
stratedthatthesalinity
(Spearman’s r¼0.619, P¼0.003) correlated with
the degree of community distance across the nine
Chinese sampling sites. These community distances
were not significantly related to other factors that
were measured, such as pH, oxygen concentration
andtemperature(P40.05).
number of samplings, to our knowledge, this is the
most comprehensive study on the diversity and
wassignificantly
Despitethesmall
Figure 2
phylogenetic tree and relative abundances of 43 OTUs (98% sequence similarity) retrieved from the nine locations across northern and
southern China. Bootstrap values were indicated at nodes. (c) Principal coordinates analysis of unweighted UniFrac distance matrix
showing the overall phylogenetic similarity of the MTB communities examined in this study. In this analysis, previously reported MTB
communities from Itaipu Lagoon in Rio de Janeiro (Brazil), Jiaozhou Bay in Shandong Province (China) and Lake Chiemsee near Munich
(Germany) were included to compare their phylogenetic relationships with the MTB communities retrieved in this study. The first
principal axis (PC1) is dominated by salinity, indicating the key effect of salinity on the distribution of MTB communities.
(a) Rarefaction curves for individual libraries of the highest, medium and lowest number of OTUs. (b) Neighbor-joining
Biogeography of magnetotactic bacteria
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distribution of dominant MTB clades across a large
spatial scale to date, which, for the first time, shows
that salinity has a strong influence on the bio-
geography of MTB. Our results support the view
that bacteria, like plants and animals, are not
globally homogeneous, but represent biogeographies
(Martinyet al.,2006),
influenced by salinity (Lozupone and Knight, 2007).
Thecorrelation between
communities observed here raises the question:
why can salinity influence the distribution of
MTB? One hypothesis is that different salinities
(and their related osmotic pressure) can affect the
energetic cost and metabolic pathways of micro-
organisms (Oren, 2001), including MTB commu-
nities. In addition to salinity, it is possible that other
geochemical factors that co-vary with salinity, or
even local competitors and predators, may affect the
distribution of MTB. The geographic distance
among sites does not seem to significantly influence
MTB community composition according to our
results. High dispersal capacity, making geographic
distance irrelevant to the incidence of MTB, is a
possible explanation. This result represents the
famous microbiological tenet ‘everything is every-
where, but, the environment selects’, the so-called
Baas-Becking hypothesis (de Wit and Bouvier,
2006). That is, MTB are probably widely dispersed
over great distances or may be robust over long-
distance transport, and environmental heterogeneity
(like salinity) determines their ability to thrive
within specific environments. Nevertheless, the true
causes for salinity-dependent distribution of MTB
communities across different continents needs to be
further studied. Knowledge of the biogeographic
distribution of MTB will help to better understand
the global iron dynamics in aquatic environments,
and perhaps can also be applied towards the
reconstruction of the paleoenvironment, based on
the fossil magnetosomes.
which areprimarily
salinityandMTB
Nucleotide sequence accession numbers
The sequence data has been submitted to the DDBJ/
EMBL/GenBank databases under accession numbers
HQ437323-HQ437656.
Acknowledgements
We would like to thank Jing Zhang, Zhuoyi Zhu, Ruifeng
Zhang and Hongyan Bao in the East China Normal
University, for help in field sampling. We are grateful to
the anonymous reviewers for their very useful comments
on an earlier version of the manuscript. We also thank Dirk
Schu ¨ler for valuable comments, and Andrea Cheung for
improving the English grammar on the revised version of
the manuscript. This work was funded by the CAS/
SAFEA International Partnership Program for Creative
ResearchTeams(KZCX2-YW-T10)
(40821091).
andNSFCgrant
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