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Phylogenetic Diversity of the Bacillus pumilus Group and the Marine Ecotype Revealed by Multilocus Sequence Analysis

  • Yang Liu ,

    Contributed equally to this work with: Yang Liu, Qiliang Lai

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Qiliang Lai ,

    Contributed equally to this work with: Yang Liu, Qiliang Lai

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Chunming Dong,

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Fengqin Sun,

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Liping Wang,

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Guangyu Li,

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

  • Zongze Shao

    shaozz@163.com

    Affiliation Key Laboratory of Marine Genetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography of State Oceanic Administration, Fujian Provincial Key Laboratory of Marine Genetic Resources, Xiamen, China

Phylogenetic Diversity of the Bacillus pumilus Group and the Marine Ecotype Revealed by Multilocus Sequence Analysis

  • Yang Liu, 
  • Qiliang Lai, 
  • Chunming Dong, 
  • Fengqin Sun, 
  • Liping Wang, 
  • Guangyu Li, 
  • Zongze Shao
PLOS
x

Abstract

Bacteria closely related to Bacillus pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus simply by 16S rRNA gene sequence. In this report, 76 marine strains were subjected to phylogenetic analysis based on 7 housekeeping genes to understand the phylogeny and biogeography in comparison with other origins. A phylogenetic tree based on the 7 housekeeping genes concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB was constructed and compared with trees based on the single genes. All these trees exhibited a similar topology structure with small variations. Our 79 strains were divided into 6 groups from A to F; Group A was the largest and contained 49 strains close to B. altitudinis. Additional two large groups were presented by B. safensis and B. pumilus respectively. Among the housekeeping genes, gyrB and pyrE showed comparatively better resolution power and may serve as molecular markers to distinguish these closely related strains. Furthermore, a recombinant phylogenetic tree based on the gyrB gene and containing 73 terrestrial and our isolates was constructed to detect the relationship between marine and other sources. The tree clearly showed that the bacteria of marine origin were clustered together in all the large groups. In contrast, the cluster belonging to B. safensis was mainly composed of bacteria of terrestrial origin. Interestingly, nearly all the marine isolates were at the top of the tree, indicating the possibility of the recent divergence of this bacterial group in marine environments. We conclude that B. altitudinis bacteria are the most widely spread of the B. pumilus group in marine environments. In summary, this report provides the first evidence regarding the systematic evolution of this bacterial group, and knowledge of their phylogenetic diversity will help in the understanding of their ecological role and distribution in marine environments.

Introduction

Bacillus is an important bacterial genus that consists of a heterogeneous group of aerobic or facultative anaerobic, endospore-forming, Gram-positive, rod-shaped organisms. Owing to their metabolic diversity and spore dispersal, Bacillus is ubiquitous in the environment. The genus Bacillus comprises 172 species recognized to date (http://www.bacterio.cict.fr/b/bacillus.html), most of which are from terrestrial environments. The strains in Bacillus are divided into the following 5 groups based on phylogenetic analysis of the 16S rRNA gene sequence: the B. cereus, B. megaterium, B. subtilis, B. circulans and B. brevis groups. Bacteria of B. pumilus belong to the B. subtilis group [1].

The bacteria of some Bacillus groups usually share high genetic homogeneity despite their phenotypic diversity, including the B. cereus group, with over 97 % 16S rRNA sequence similarity among B. anthracis, B. cereus, B. weihenstephanensis, B. thuringiensis, B. mycoides, B. pseudomycoides, B. cytotoxicus, B. gaemokensis and B. manliponensis [2]. However, the discrimination of these closely related bacteria has long been problematic. Many methods have been applied to identify and classify these Bacillus bacteria, including phenotypic characteristics, biochemical tests, fatty acid methyl ester (FAME) profiling [3], 16S rRNA gene sequencing [4,5], DNA fingerprinting [6], randomly amplified polymorphic DNA (RAPD) [7], restriction fragment length polymorphism (RFLP) [8], amplified fragment length polymorphism PCR (AFLP) [9] and multilocus enzyme electrophoresis (MLEE) typing. Recently, phylogenetic analyses based on single or multilocus sequence typing (MLST) of housekeeping genes, such as rpoB (RNA polymerase β subunit), gyrB (gyrase B subunit), 23S rRNA, gyrA and pycA, have been used frequently for this genus [10,11]. Indeed, these genes can effectively differentiate the strains of the B. cereus group and the B. subtilis group [12-15].

Due to the survivability of spores against harsh conditions, it remains unclear whether such spore-forming bacteria as Bacillus are indigenous to marine habitats. In fact, compared to their terrestrial relatives, little is known about the distribution and ecology of Bacillus, particularly in the deep sea [16,17]. According to biochemical tests, FAME profiling and partial 16S rRNA gene sequencing, B. pumilus was found to be the predominant species of cultivated Bacillus in the coastal environment of Cochin, India, followed by B. cereus and B. sphaericus [17,18].

In recent years, hundreds of Bacillus strains have been isolated in our lab from various marine environments of a wide geographic range, including deep sea, coastal and polar areas. We found that some Bacillus isolates closely related to B. pumilus are not easily distinguished from each other by 16S rRNA gene sequence alone. The B. pumilus group contains 5 species, B. pumilus, B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus, which are nearly identical in 16S rRNA gene sequence, sharing similarity over 99.5%. In a phylogenetic tree of 16S rRNA gene sequences, this group is a neighbor of B. atrophaeus DSM 7264T, sharing similarity of less than 97.6%. Thus far, no systematic data are available to evaluate the diversity and evolution of this group. In an effort to understand the phylogeny, ecology and biogeography of this group, 76 marine strains and 3 type strains of this group were subjected to Multilocus Sequence Analysis (MLSA) based on 7 housekeeping genes and compared to 73 terrestrial isolates.

Materials and Methods

Ethics statement

No specific permissions were required for collection of these the bacterial strains used in phylogenetic analysis in this study, as they are isolated from areas beyond national jurisdiction or from areas within the exclusive economic zone of China. Moreover, the sample sampling did not involve endangered or protected species.

Bacterial strains

A total of 76 strains of 5 species close to B. pumilus were chosen for the phylogeny study: 15 from the Pacific Ocean, 7 from the Indian Ocean, 3 from the Atlantic Ocean, 7 from the North Polar Region, 20 from the coast area of Fujian Province, 4 from the East China Sea and the Yellow Sea and 20 from the South China Sea (Table 1 and Figure S1 in File S1). These strains were deposited at Marine Culture Collection of China (MCCC).

Strain NoAccession NoaOriginal NoSpeciesbOriginRegionElevation (m)Types
11A00008HYC-10Bacillus sp.Intestinal tract contents of fishXiamen island0B1
21A00112HC21-AB. altitudinis Intestinal tract contents of fishXiamen island0A13
31A00242Cr20B. altitudinis SedimentPacific Ocean-5246A1
41A00249Cr30B. altitudinis SedimentPacific Ocean-5246A1
51A06451FO-36bTB. safensisClean-room air particulateCalifornia0F7
61A00400Mn48B. altitudinis SedimentPacific Ocean-5000A5
71A00401Mn12B. altitudinis SedimentPacific Ocean-5246A1
81A00412NHCd5-4B. altitudinis SedimentSouth China Sea-3649A15
91A0042002Co-3B. altitudinis SedimentPacific Ocean-2869A1
101A00439Co21B. pumilus SedimentPacific Ocean-5059D3
111A00440Co11B. altitudinis SedimentPacific Ocean-5246A4
121A00448Ni27B. altitudinis SedimentPacific Ocean-5059A1
131A00466Pb29B. altitudinis SedimentPacific Ocean-5246A2
141A00468Pb71B. altitudinis SedimentPacific Ocean-5059A1
151A00482Cr61B. altitudinis SedimentPacific Ocean-5059A1
161A01044PA1AB. altitudinis Bottom water Indian Ocean-2488A30
171A013648-C-1B. altitudinis surface waterXiamen island0A22
181A01381S70-5-12B. altitudinis Surface waterIndian Ocean0A20
191A02095S2-5(2)2B. altitudinis SedimentSouth China Sea-15A17
201A022272007/3/1B. altitudinis SedimentIndian Ocean-2434A26
211A02467DSD-PW4-OH8B. altitudinis Bottom water South China Sea-1762A9
221A02468mj01-PW1-OH23B. altitudinis Bottom water South China Sea-812A23
231A0248537-PW11-OH8B. altitudinis Bottom water South China Sea-1A10
241A02775IF1B. altitudinis Surface waterYellow Sea-30A1
251A03121A019B. altitudinis Surface waterEast China Sea0A11
261A03126A025B. altitudinis Surface waterYellow Sea-40A31
271A04035C16B11B. altitudinis Bottom water Pacific Ocean-1755A1
281A04046NH8D1B. altitudinis SedimentSouth China Sea-756A35
291A04073NH18E1B. altitudinis SedimentSouth China Sea-1550A18
301A04526NH21E_2B. safensisSedimentSouth China Sea-1184F3
311A04568NH21R_2B. altitudinis SedimentSouth China Sea-1184A7
321A04638NH24ETB. altitudinis SedimentSouth China Sea-1081A16
331A05427NH65BB. altitudinis SedimentSouth China Sea-1467A12
341A05787NH7I_1Bacillus sp.SedimentSouth China Sea-756E1
351A05840B204-B1-5B. safensisSedimentSouth China Sea-1467F1
361A05860BMJ03-B1-22B. safensisSedimentSouth China Sea-1100F2
371A06638CJWT7B. safensisSedimentSouth China Sea-11F5
381A06692HSGT11B. altitudinis SedimentSouth China Sea-11A27
391A06774HTZ_29B. altitudinis SedimentSouth China Sea-11A19
401A06831SCN16B. altitudinis SedimentSouth China Sea-11A8
411A06858SLN29B. safensisSedimentSouth China Sea-11F4
421A06991sxm20-2B. pumilus SedimentIndian Ocean-2089D6
431A06996B01-4B. pumilus Surface waterPacific Ocean0D2
441A07053B07-3B. pumilus Surface waterPacific Ocean0D1
451A07134BN04-13B. safensisSurface waterPacific Ocean0F9
461A07286P2-1BB. pumilus SedimentIndian Ocean-4735D2
471A07375S11-5B. altitudinis SedimentAtlantic Ocean-3217A14
481A07587C101B. altitudinis SedimentArctic Ocean-4000A32
491A07588D21B. safensisSedimentArctic Ocean-3566F8
501A07590D95B. safensisSedimentArctic Ocean-2500F8
511A07613A1-1B. pumilus SedimentAtlantic Ocean-3310D5
521A07638A23-8B. altitudinis SedimentIndian Ocean-3879A36
531A07644A29-3B. pumilus SedimentIndian Ocean-2368D4
541A012871A-5B. altitudinis CoralDongshan island-2A28
551A076062A-2B. altitudinis CoralDongshan island-2A33
561A07656P1C-6B. altitudinis CoralDongshan island-2A25
571A07600P3A-7B. altitudinis CoralDongshan island-2A34
581A05459P6A-8B. altitudinis CoralDongshan island-2A28
591A05490J33-1B. pumilus SedimentYellow Sea-31.5D4
601A00023HYg-9B. safensisIntestinal tract contents of fishXiamen island0F8
611A00118HYG-22B. altitudinis Intestinal tract contents of fishXiamen island0A24
621A07052NP-4B. safensisSurface waterArctic Ocean0F8
631A06453DSM 27TB. pumilus Soil//D7
41A0838515-B04 10-15-3B. safensisSedimentBering Sea-3873F6
51A08208R06B32Bacillus sp.SedimentArctic Ocean-44.5C1
661A08151C2-2B. pumilus SedimentAtlantic Ocean-3452D2
671A08152DW2J2B. pumilus White shrimpShrimp farm0D1
681A08153DW3XJ7B. pumilus White shrimpShrimp farm0D1
691A08154XW1-6B. pumilus Aquaculture waterShrimp farm0D1
701A08372DW5-4Bacillus sp.Aquaculture waterShrimp farm0C1
711A08155DW3-7B. safensisAquaculture waterShrimp farm0F8
721A08373BS1B. altitudinis Bottom water South China Sea-1762A1
731A00009HYC-12B. altitudinis Intestinal tract contents of fishXiamen island0A37
741A08369C70B. altitudinisSedimentArctic Ocean-2790A1
751A08156DW2-3B. altitudinis Aquaculture waterShrimp farm0A1
761A08157DW3XJ1B. altitudinis White shrimpShrimp farm0A1
771A08370DW2-4B. altitudinis White shrimpShrimp farm0A32
781A08371XW3XJ7B. altitudinis White shrimpShrimp farm0A6
791A0645241KF2bTB. altitudinis High-elevation air sampleHyderabad/India41000A21

Table 1. Bacterial isolates of the B. pumilus group strains used in MLSA analysis.

aThe deposit accession No in MCCC (Marine Culture Collection of China).
bThe name of these isolates were modified after phylogenetic analysis.
TThree type strains were marked.
/ The detailed information of B. pumilus DSM 27T can not be found from reference.
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In addition, 3 type strains, B. pumilus DSM 27T isolated from soil [19], B. safensis FO-36bT isolated by the Jet Propulsion Laboratory spacecraft-assembly facility of California in USA [20] and B. altitudinis 41KF2bT isolated from air samples of high elevations (41,000 m) in India [21], were also included in the phylogeny study; these strains were purchased from DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) in Germany. Unfortunately, 2 other type strains, B. stratosphericus and B. aerophilus, isolated from the same sample as B. altitudinis 41KF2bT, are no longer available in public collections or from the authors and therefore not included in the our analyses. The gyrB sequences of 73 strains were acquired from the NCBI database, and their detailed information is listed in Table S1 in File S1.

DNA extraction

The strains were reactivated on a modified solid Luria-Bertani medium (10 g peptone, 5 g yeast extract, 10 g NaCl, 15 g agar and 1 L double-distilled water, pH 7.5) [22] and incubated at 37°C for 24 h. A suitable amount of cells on the plates were selected and transferred to 1.5 mL centrifuge tubes using sterile pipette tips. Genomic DNA was extracted using the SBS extraction kit (SBS Genetech Co., Ltd. in Shanghai, China) according to the manufacturer's instructions.

PCR amplification and sequencing of 16S rRNA and housekeeping genes

The 16S rRNA gene was amplified by PCR using universal primers 27F and 1492R, and seven housekeeping genes were amplified using specific primers designed using Primer 5.0 (Table S2 in File S1). The genes were amplified under nearly the same conditions. In brief, each PCR mixture contained 1 µL genomic DNA, 1.25 U Ex TaqTM DNA polymerase (TaKaRa), 4 µL dNTP mixture (2.5 mM of each dNTP), 1 µL each primer (20 µM), 5 µL 10×Ex Taq buffer (Mg2+ Plus) and sterile deionized water to a total volume of 50 µL. PCR was performed using a My GenTM L Series Peltier Thermal Cycle (Hangzhou Long Gene Scientific Instruments Co., Ltd, China). Each PCR product was separated by electrophoresis on a 1% agarose gel. The target PCR products were purified with the AxyPrepTM PCR Clean up kit (Axygen Scientific, Inc., USA) according to the manufacturer's instructions and sequenced using the ABI3730xl platform (BGI Co., Ltd, China).

The assembly and modification of the DNA sequences, including the 16S rRNA gene and seven housekeeping genes, were performed using DNAMAN 5.0 software. All sequences were deposited into the GenBank database; the accession numbers were listed in Table S3 in File S1.

Phylogenetic analysis based on single gene analysis and MLSA

The determined sequences of the 16S rRNA gene and seven housekeeping genes were analyzed against sequences in the NCBI database using Blastn [23]. A substitution saturation assessment was performed for each gene sequence using DAMBE [24]. Recombination events in the DNA sequence alignments were evaluated using RDP 3.0 [25]. The genetic distances and sequence similarities of gene(s) were calculated using Kimura’s 2-parameter model [26] with the MEGA 5.0 software. The selective pressure on housekeeping gene was evaluated with the calculation of nonsynonymous (Ka) and synonymous (Ks) substitution rates (Ka/Ks)by the DnaSP 5.0 software [27].

The phylogenetic trees were constructed using the neighbor-joining (NJ) algorithm [28] with MEGA 5.0 [29]. The strengths of the internal branches of the resulting trees were statistically evaluated by bootstrap analysis with 1000 bootstrap replications. B. cereus ATCC 14579T (GenBank accession: AE016877) was used as the outgroup.

Results

Phylogenetic diversity revealed by 16S rRNA gene analysis

All the tested bacteria were subjected to a 16S rRNA gene analysis, even though they had been characterized (approximately 600 bp) prior to deposition in MCCC. Nearly the full-length 16S rRNA gene sequences (approximately 1513 bp) were obtained to further assess the taxonomic affiliation and phylogeny of the strains.

The results demonstrated that the genetic distance of the 16S rRNA gene ranged from 0-0.005 (mean 0.002). Moreover, the number of alleles and polymorphic sites were only 7 and 10, respectively, and the proportion of polymorphic sites was 0.7%. In addition, the intraspecies similarities of 16S rRNA gene ranged from 99.6% to 100%, while the interspecies similarities were 99.5%-100%. These features of the 16S rRNA gene were presented in Table 2 and Table S4 in File S1. The 16S rRNA genes of the strains were highly conserved, and their similarities had overlap in intraspecies and interspecies, therefore it was unsuitable for the differentiation of these closely related strains.

LocusLength (bp)Alleles NoPolymorphic site No /Percentage (%)Mean G+C content (mol%)K2P distance rangeK2P distance mean
16S rDNA1513710/0.7055.030.000-0.0050.002
gyrB71735170/23.7142.200.000-0.1100.053
rpoB9273494/10.1445.740.000-0.0450.021
aroE90031253/28.1142.200.000-0.1590.080
mutL82838202/24.4045.300.000-0.1350.068
pycA86437197/22.8042.930.000-0.1280.065
pyrE54633160/29.3046.510.000-0.1790.085
trpB86729232/26.7644.770.000-0.1490.072
MLSA5649541308/23.0044.200.000-0.1100.053

Table 2. Characteristics of the 16S rRNA gene, housekeeping genes and concatenated genes from 79 strains.

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Despite the high similarity, the phylogenetic tree of the 16S rRNA gene showed that the 79 strains were divided into two groups (Figure 1). The large group contained our 52 isolates, which were close to the type strain B. altitudinis; the small group contained 24 strains that we isolated, which were close to the type strains B. pumilus and B. safensis and cannot be distinguished by their 16S rRNA gene.

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Figure 1. Phylogenetic tree based on the 16S rRNA genes of marine bacteria belonging to the B. pumilus group.

The tree was constructed using the neighbor-joining method with MEGA 5.0. Bootstrap values over 50% (1000 replications) were shown at each node. Bar, % estimated substitution. B. cereus ATCC 14579T was used as the outgroup.

http://dx.doi.org/10.1371/journal.pone.0080097.g001

Characteristics of seven housekeeping genes

To discriminate among the closely related bacteria, the housekeeping genes gyrB, rpoB, aroE, mutL, pycA, pyrE and trpB were chosen for analysis; 79 strains, including the 3 type strains, were analyzed. The characteristics of each housekeeping gene, such as the gene length, number of alleles, polymorphic sites, the mean G+C content, the genetic distance and the similarity range were shown in Table 2 and Table S4 in File S1.

The correlation of genetic distance between two housekeeping genes was calculated (Table S5 in File S1). An analysis of the characteristics and genetic distance of the housekeeping genes (Table 2) demonstrated that all the housekeeping genes showed remarkably higher resolution than the 16S rRNA gene (Table 2). Among the 7 housekeeping genes, the pyrE gene exhibited the highest resolution, with 29.3% polymorphic sites and the largest genetic distance range (0-0.179), whereas rpoB exhibited the lowest resolution. Although mutL had a higher allele number (38) than other genes, its polymorphic site percentage was less than many others. Specifically, gyrB displayed a better differentiation among strains close to B. altitudinis; in contrast, aroE was more powerful for strains of B. pumilus, and pyrE was better for strains of B. safensis (Table S6 in File S1).

Further, DNA sequence similarity ranges of the 7 genes at intraspecies and interspecies levels were analyzed with the MEGA 5.0 software. These 79 strains were divided into 6 species, three of which were established species and others were potential novel species as documented below. The similarity ranges at intraspecies and interspecies levels were shown in Table S4 in File S1. An obvious gap between intraspecies and interspecies similarity ranges was observed in most housekeeping genes with exceptions of 16S rDNA and rpoB (Figure 2, Table S4 in File S1). For more details, the numbers of strain pairs within different similarity grades of the housekeeping genes of the 79 strains were shown in Table S7 and Figure S2 in File S1. These data indicates that 16S rDNA and rpoB were inappropriate for species discrimination among the bacteria of this group, while other genes showed a general interspecies similarity gap of 92% to 96%, and can serve in species discrimination, especially pyrE (92%-95%) and aroE (93-95%) Table S7 and Figure S2 in File S1),

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Figure 2. Intraspecies and interspecies similarity ranges of housekeeping genes in the B. pumilus group.

http://dx.doi.org/10.1371/journal.pone.0080097.g002

In addition, the Ka/Ks ratio of each housekeeping gene of different species and all the 79 strains was calculated, the results were displayed in Table S8 and Figure S3 in File S1. All the genes exhibited low Ka/Ks ratios ranging from 0.0000-0.1200 (Table S8 and Figure S3 in File S1), suggesting that they are under negative selection pressure. However, the ratios of Ka/Ks of each gene in different species were significant differences. The pyrE gene had the highest Ka/Ks ratio (0.1200) in B. altitudinis, while the gene aroE in B. pumilus and B. safensis were the highest, respectively 0.0800 and 0.0561. Even at interspecies level based on all the 79 strains, pyrE had the highest Ka/Ks ratio (0.0731). In contrast, rpoB had the lowest the Ka/Ks ratio, and was the most conserved among the seven housekeeping genes.

Phylogenetic diversity revealed by individual housekeeping genes

Prior to the phylogenetic analysis, these housekeeping genes were subjected to an examination of sequence substitution saturation and recombination events (data not shown). The saturation test of each housekeeping gene with DAMBE showed no sign of substitution saturation, and no recombination events were found in any of their tested housekeeping genes, as determined by program RDP-3.0. These results indicated that these sequences provided essential phylogenetic information.

Phylogenetic analyses based on each of the housekeeping genes were able to distinguish the strains at the species level. Moreover, the phylogenetic trees possessed nearly congruent topology structure (Figure S4-S10 in File S1). Specifically, the 79 strains were divided into 6 groups from A to F. Group A is the largest, containing 49 strains close to B. altitudinis; Group F is the second largest group, containing 13 strains belonging to B. safensis. Group D consisted of 13 strains attributed to B. pumilus. Additional three minor groups were revealed, Groups B, C and E, supported by only 1 to 2 strains each. These minorities represent putative novel taxa.

Slight differences were also observed in some groups among the topologies of the seven trees. For example, B. pumilus was close to B. altitudinis in the phylogenetic tree of gyrB; in contrast, B. pumilus is close to B. safensis in other trees. In addition, the position of Groups B, C and D varied in the trees of gyrB, rpoB and mutL. For instance, Group B was closer to Group A in the phylogenetic trees of gyrB, aroE, mutL, pyrE and trpB, whereas Group B was closer to the groups in the large cluster of B. safensis and B. pumilus in the tree of pycA. Other small differences were also observed in the trees, as shown in the supplementary materials (Figure S4-S10 in File S1).

Phylogeny based on the concatenated housekeeping genes

The seven housekeeping genes were concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB (5649 bp) to reexamine the phylogeny of the 79 strains (Figure 3). The new phylogenetic tree showed a similar topology as the trees described above based on a single gene but was more elaborate and stable.

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Figure 3. Phylogenetic tree based on seven housekeeping genes concatenated of marine isolates of the B. pumilus group.

The tree was constructed using the neighbor-joining method with MEGA 5.0. Bootstrap values over 50% (1000 replications) were shown at each node. Bar, % estimated substitution. B. cereus ATCC 14579T was used as the outgroup.

http://dx.doi.org/10.1371/journal.pone.0080097.g003

Specifically, Group A consisted of 49 strains belonging to B. altitudinis that could be divided into 37 genetic types from A1 to A37 (Table 1). Group D contained 13 strains belonging to B. pumilus, with 7 genetic types, D1 to D7 (Table 1); Group F also contained 13 strains of 9 genetic types, F1 to F9 (Table 1), and belonging to B. safensis. In contrast, fewer bacteria were allotted into Group B, Group C and Group E and could not be assigned to any the described species due to low similarity. For example, the only strain in Group B showed 92.12%, 89.22% and 89.50% similarity with B. altitudinis, B. pumilus and B. safensis and a genetic distance of 0.079, 0.108 and 0.105, respectively. Both strains in Group C shared 91.04%, 90.21% and 91.02% similarity with the above type strains, with a genetic distance 0.09, 0.098 and 0.09, respectively. Similarly, the only member of Group E shared 89.48%, 91.41% and 93.93% similarity with the three type strains and a genetic distance of 0.105, 0.086 and 0.061, respectively. These unassigned strains represent novel bacterial taxa.

Correlation between phylogenetic and geographic distribution

The geographical distribution of the 76 strains covered various marine environments: a subtropical coastal area, the Pacific Ocean, the Indian Ocean, the Arctic Ocean, the Atlantic and the South China Sea.

Among these bacteria, those belonging to B. altitudinis were in the majority and had the widest geographical distribution; 48 of our isolates were allocated to this group in the concatenated gene tree (Group A in Figure 3). These isolates were mainly from three areas, the coastal area (○), South China Sea (□) and Pacific ocean (△), though some were isolated from the Indian Ocean (▽), the Atlantic Ocean (☆) and the Arctic Ocean. (◇). Group D contained twelve strains that were isolated from a Fujian coastal area and pelagic areas; however, no strain originated from the Arctic Ocean (◇) or South China Sea (□). The 12 strains in Group F were mainly from the coast area (○),South China Sea (□) and Arctic Ocean (◇). Among the above-mentioned special clades composed of putative novel species, two of three are from marine aquiculture environments, one from fish gut (strain 1 in Group B) and another from a shrimp farm (strain 70 in Group C).

In addition, according to the water depth, the habitats were arbitrarily divided into the upper layer (0-1000 m) and deep layer (>1000 m) and marked in green and black, respectively, in the phylogenetic tree (Figure 3). According to the tree, it was observed that the strains tended to cluster together to some extent according to the water depth. For example, in the largest group (Group A, B. altitudinis), bacteria from shallow areas tended to cluster together (in green). On the other hand, bacteria from the deep sea (in black) tended to cluster. Further, a principal component analysis (PCA) based on all strains was carried out to examine the key factors influencing their distribution using unweighted UniFrac. However, the correlation of the phylogenetic and geographic distribution was not significant (data not shown). This may be due to the inadequate strain numbers in other species.

To compare with their terrestrial counterparts, more sequences of the gyrB gene of the B. pumilus group were retrieved from GenBank (much less data for other housekeeping genes are available), and a phylogenetic tree of 152 strains was constructed (Figure 4). In general, the topological structure of the tree was the same as that constructed with our bacteria alone (Figure 3), though the three clades containing the potential novel species remain as minorities in the new tree. Some mistakes in nomenclature were observed for some strains retrieved from NCBI, such as strains 99, 101, 107, 108, 113 and 116, which actually belong to B. altitudinis rather than B. pumilus, as described in NCBI.

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Figure 4. Phylogenetic tree based on gyrB genes of 152 strains of both marine and terrestrial origins.

The tree was constructed using the neighbor-joining method with MEGA 5.0. Bootstrap values over 50% (1000 replications) were shown at each node. Bar, % estimated substitution. B. cereus ATCC 14579T was used as the outgroup. The number represented the number of strains in each portion of the pie chart. The bacteria from marine environments were in blue, and the others were in red. The pie charts illustrated the proportions of marine and terrestrial origins in each large cluster.

http://dx.doi.org/10.1371/journal.pone.0080097.g004

Of note, based on the large tree of gyrB genes, the bacteria of marine origin tended to cluster together; with some exceptions, the strains of terrestrial origin also clustered together (Figure 4). Most of our marine isolates were placed in the large cluster of B. altitudinis, positioned as a separate clade (numbers in blue); a similar tendency was observed for the B. pumilus and B. safensis clusters. Most of the terrestrial bacteria were allotted to B. safensis, forming a distinct clade (in red).

Discussion

Many Bacillus strains have recently been isolated from marine environments, with bacteria of B. pumilus being frequently reported, in addition to B. subtilis, B. licheniformis and B. cereus [17,30-36]. Although the B. altitudinis, B. pumilus and B. safensis bacteria of the B. pumilus group cannot be differentiated by their 16S rRNA gene sequences, according to the data retrieved from PubMed, the bacteria from marine environments are generally placed in the B. pumilus group. To understand the diversity and systematic relationship of the bacteria in the B. pumilus group, we subjected 76 strains to MLSA based on seven housekeeping genes. Unexpectedly, most of our isolates actually belong to the species of B. altitudinis rather than B. pumilus. To our knowledge, this is the first report on the diversity and phylogeny of the B. pumilus group.

Our phylogenetic analysis showed that different housekeeping genes varied with regard to their discrimination resolution among the bacteria of the B. pumilus group. Among the seven housekeeping genes, the pyrE gene possessed, on average, the highest percentage of the polymorphic sites (29.30%) and the highest genetic distance (0.085), indicating that pyrE has the highest differentiation power. This was reconfirmed by the results of Ka/Ks ratios and intraspecies and interspecies similarity ranges. In addition, both aroE and gyrB also possesses a relative high resolution power. Considering the popularity of the gyrB gene in the GenBank database, we suggest pyrE and gyrB can be used as a standard marker to differentiate the closely related strains of the B. pumilus group. In the B. subtilis group, approximately 95% similarity of gyrB gene was accordant with 70% of DNA-DNA relatedness [15]. In other genera, for example, the gyrB gene also has been used as a marker to assign species. The genetic distance of the gyrB gene used to separate two species is 0.014, which was the equivalent of 70% DNA-DNA hybridization in Micromonospora species, as reported by Kasai et al. [36]. As another example, 0.02 genetic distance for the gyrB gene was used as a species boundary among the Amycolatopsis genus in a study by Everest et al. [37]. Similarly, Curtis et al. proposed using a genetic distance of 0.04 for five concatenated housekeeping genes to distinguish different species in Kribbella [38]. In the B. pumilus group, we found 95%-96% similarities of gyrB gene was the interspecies gap. Based on these results and further genome sequence data, we proposed three novel species of the genus Bacillus, represented by strain 1, 70 and 34. These bacteria shared low gyrB gene sequence similarity (89.50%-94.98%) with and large genetic distances (0.05-0.1) from the described type strains. The preliminary draft genome sequence analysis showed that their estimated DNA-DNA values (among 3 novel strains and 3 type strains) were below 70% (data unpublished), suggesting that they are potential novel species. Further phenotypic characterizations are needed to establish these bacteria as novel species.

The correlation analysis of phylogeny with geographical distribution indicated that the strains of Group A (B. altitudinis) were more widespread in marine environments than the other groups (Groups B-F) (Figure 3), suggests that Group A is adapted to a wide range of marine environments. Furthermore, our marine isolates tended to form clades corresponding to the water depth (Figure 3), and such distribution is in congruence with other reports. It has been shown that bacteria of Exiguobacterium tend to form genetic clusters by niche differentiation in water and sediment environments of the Cuatro Cienegas Basin [39]. As another example, Qian et al. found that there were significant differences in the diversity of microbial communities in the upper (2 and 50 m) and deeper layers (200 and 1500 m) of the Red sea, though there were no obvious differences within the same layer [40]. The distribution of bacteria is significantly influenced by environmental factors, such as salinity, temperature, oxygen and, in particular, water depth and pressure [41-43]. However, the mechanisms of ecological divergence require additional studies.

The phylogeny of the bacteria of diverse origins is shown in the expanded gyrB tree (Figure 4), reconfirming that the strains of B. altitudinis appear to be more widespread in marine environments, whereas the strains of B. pumilus and B. safensis tend to reside in terrestrial habitats. In fact, the type strain of B. altitudinis, which appeared randomly among our marine isolates, was isolated from an air sample from a high elevation (41 km), and a marine origin with seawater evaporation cannot be excluded. In the clade of B. altitudinis, the marine taxa appeared to have evolved from terrestrial taxa. So did a small marine branch (strains 45, 49, 50, 60, 62 and 71) in the B. safensis clade (Figure 4).

In summary, we analyzed the phylogeny of marine isolates closely related to the B. pumilus group using MLSA based on seven housekeeping genes. The bacteria of the B. pumilus group are frequently misnamed at the species level due to the high similarity in their 16S rRNA gene sequence. We found that both the gyrB and pyrE genes can be used as molecular marker to distinguish these closely related strains. Based on our MLSA results, we conclude that bacteria of B. altitudinis are most widely spread among the bacteria of the B. pumilus group in marine environment; while most bacteria from terrestrial habitats of this group actually belong to B. safensis. The results of this study provide the first report of the phylogenetic analysis of bacteria in this group and will help in the understanding of their ecological role, ecological evolution and adaptation to marine environments. However, the results based on MLSA are not enough to resolve these issues as the housekeeping genes used only occupy 0.1%~0.2% of the genome. Fingerprinting methods like RAPD, AFLP and Rep-PCR, and genome sequence analyses would differentiate them in more details. Currently, genome sequencing of 21 strains representing different branches of the B. pumilus group are undergoing, and further analyses will help to determine the taxonomic status of these species in this group, more important to gain insights into the evolution and adaption in marine environments.

Supporting Information

File S1.

Supplementary material of Figure S1-S10 and Table S1-S8.

doi:10.1371/journal.pone.0080097.s001

(DOCX)

Acknowledgments

We are grateful to Dr. Lei Wang and Dr. Yamin Sun of Nankai University for help with PCA analysis and Ka/Ks analysis.

Author Contributions

Conceived and designed the experiments: ZZS. Performed the experiments: YL QLL. Analyzed the data: YL QLL ZZS. Contributed reagents/materials/analysis tools: CMD FQS LPW GYL. Wrote the manuscript: YL QLL ZZS.

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