Open Access

High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

  • Sivan Laviad1,
  • Alla Lapidus2, 3,
  • James Han4,
  • Matthew Haynes4,
  • TBK Reddy4,
  • Marcel Huntemann4,
  • Amrita Pati4,
  • Natalia N Ivanova4,
  • Konstantinos Mavromatis4,
  • Elke Lang5,
  • Manfred Rohde6,
  • Victor Markowitz7,
  • Tanja Woyke4,
  • Hans-Peter Klenk5,
  • Nikos C Kyrpides4, 8 and
  • Malka Halpern1, 9Email author
Standards in Genomic Sciences201510:29

DOI: 10.1186/s40793-015-0010-4

Received: 15 September 2014

Accepted: 16 April 2015

Published: 27 May 2015

Abstract

Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Keywords

Brachymonas chironomi Comamonadaceae Chironomid Chironomus Egg mass Toxicant

Introduction

Strain AIMA4T (= LGM 24400T = DSM 19884T), is the type strain of Brachymonas chironomi, one out of two species in the genus Brachymonas. The genus Brachymonas was formed by Hiraishi et al. [1] while characterizing rhodoquinone-containing bacteria that had been isolated from soybean crude waste sludge in Japan. Strain AIMA4T, was isolated from an insect egg mass (Chironomus sp.) that was sampled from a waste stabilization pond in northern Israel [2]. Chironomids (Arthropoda; Insecta; Diptera; Chironomidae; Chironomus sp.) inhabit virtually every type and condition of aquatic habitats. They undergo a complete metamorphosis of four life stages (egg, larva, pupa and adult that emerges into the air) [3]. Eggs are laid in an egg mass at the water’s edge. Each egg mass contains hundreds of eggs. Chironomid egg masses were found to harbor Vibrio cholerae and Aeromonas spp. [3-10]. V. cholerae degrades chironomid egg masses by the secreted haemagglutinin protease (HAP) [11,12]. Strain AIMA4T was isolated in the course of a study that investigated endogenous bacterial communities that inhabit chironomid egg masses [2,13,14]. The species epithet chironomi was derived from the non-biting midge insect Chironomus (Diptera; Chironomidae), from where this species was isolated. Strain AIMA4T didn’t show the ability to degrade the egg masses like it was found for V. cholerae.

Here we describe a summary classification and a set of the features of Brachymonas chironomi strain AIMA4T (DSM 19884T), together with the genome sequence description and annotation.

Organism information

Classification and features

A taxonomic study using a polyphasic approach placed B. chironomi strain AIMA4T in the genus Brachymonas within the family Comamonadaceae (Figure 1). The family Comamonadaceae comprises a larger number of genera (as shown in Figure 1) and a larger variety of species and phenotypes [15,16].
Figure 1

Phylogenetic tree highlighting the position of Brachymonas chironomi relative to the type strains of the other species within the family Comamonadaceae. The sequence alignments were performed by using the CLUSTAL W program and the tree was generated using the maximum likelihood method in MEGA 5 software. Bootstrap values (from 1,000 replicates) greater than 50% are shown at the branch points. The bar indicates a 1% sequence divergence.

B. chironomi strain AIMA4T is a Gram-negative, non-motile coccobacillus or rod (Figure 2). After 48 h incubation on LB agar at 30°C, colonies are beige colored (opaque) that turn to light brown after few days of incubation. Strain AIMA4T is aerobic, chemoorganotrophic and does not produce acid from carbohydrates (including glucose) [2]. Growth is observed at 18–37°C (optimum 30°C), with 0–2.5% (w/v) NaCl (optimum 0.5% NaCl) and at pH 5.0–9.0 (optimum pH 6.0–8.0) (Table 1). The following enzymatic activities were observed in strain AIMA4T: catalase and oxidase, alkaline and acid phosphatases, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, trypsin and naphthol-AS-BI-phosphohydrolase. Strain AIMA4T produces acetoin and reduces nitrate to nitrite [2].
Figure 2

Scanning electron micrograph of B. chironomi AIMA4T.

Table 1

Classification and general features of Brachymonas chironomi strain AIMA4T according to the MIGS recommendations [ 40 ], published by the Genome Standards Consortium [ 41 ] and the Names for Life database [ 42 ]

MIGS ID

Property

Term

Evidence code a

 

Classification

Domain Bacteria

TAS [43]

  

Phylum Proteobacteria

TAS [44]

  

Class Betaproteobacteria

TAS [45]

  

Order Burkholderiales

TAS [46]

  

Family Comamonadaceae

TAS [47]

  

Genus Brachymonas

TAS [1]

  

Species Brachymonas chironomi

TAS [2]

  

Type strain AIMA4T

TAS [2]

 

Gram stain

Negative

TAS [2]

 

Cell shape

Coccobacilli or rods

TAS [2]

 

Motility

Non-motile

TAS [2]

 

Sporulation

Non-sporulating

IDS

 

Temperature range

18-37°C

TAS [2]

 

Optimum temperature

30°C

TAS [2]

 

pH range; Optimum

5.0–9.0; 6.0–8.0

TAS [2]

 

Carbon sourceb

phenylacetic acid

TAS [2]

MIGS-6

Habitat

Aquatic/Insect host

TAS [2]

MIGS-6.3

Salinity

0-2.5% NaCl (w/v)

TAS [2]

MIGS-22

Oxygen requirement

Aerobic

TAS [2]

MIGS-15

Biotic relationship

Commensal (Insect, chironomid)

TAS [2]

MIGS-14

Pathogenicity

Non-pathogen

NAS

MIGS-4

Geographic location

Israel

TAS [2]

MIGS-5

Sample collection

July, 2006

TAS [2]

MIGS-4.1

Latitude

32.669167

TAS [2]

MIGS-4.2

Longitude

35.128639

TAS [2]

MIGS-4.4

Altitude

40 m

TAS [2]

aEvidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). Evidence codes are from the Gene Ontology project [48].

bThe only carbon source that was positive for this strain, out of all carbon sources that were tested (strain AIMA4T does not use carbohydrates, not even glucose) [2].

Chemotaxonomic data

The dominant cellular fatty acids are C16:1 ω7c, C16:0 and C18:1 ω7c. The main isoprenoid quinone is Q-8. Phosphatidylglycerol, phosphatidylethanolamine and phosphatidylserine occur as polar lipids [2].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [17-19]. Sequencing of B. chironomi strain AIMA4T is part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project [20] which aims in increasing the sequencing coverage of key reference microbial genomes [21]. The genome project is deposited in the Genomes OnLine Database [22] and the permanent draft genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI) using state of the art sequencing technology [23]. A summary of the project information is shown in Table 2.
Table 2

Genome sequencing project information

MIGS ID

Property

Term

MIGS 31

Finishing quality

Level 2: High-Quality Draft

MIGS-28

Libraries used

Illumina Std. shotgun library

MIGS 29

Sequencing platforms

Illumina HiSeq 2000

MIGS 31.2

Fold coverage

99.6×

MIGS 30

Assemblers

Velvet v. 1.1.04, ALLPATHS v. R37654

MIGS 32

Gene calling method

Prodigal 2.5

 

Locus Tag

C513

 

GenBank ID

ARGE00000000

 

GenBank Date of Release

September 16, 2013

 

GOLD ID

Gp0013605

 

BIOPROJECT

174982

MIGS 13

Source Material Identifier

DSM 19884T

 

Project relevance

Tree of Life, GEBA-KMG

Growth conditions and genomic DNA preparation

B. chironomi strain AIMA4T, DSM 19884T, was grown in DSMZ medium 1 (Nutrient Agar), at 28°C [24]. DNA was isolated from 0.5-1 g of cell paste using JetFlex Genomic DNA Purification Kit (GENOMED) following the standard protocol as recommended by the manufacturer, however with additional 50 μl protease K (20 mg/ml) during digest for 60 min. at 58°C. Protein precipitation was done with additional 200 μl Protein Precipitation Buffer, followed by over night incubation on ice. DNA is available through the DNA Bank Network [25].

Genome sequencing and assembly

The draft genome of B. chironomi strain AIMA4T was generated using the Illumina technology [23,26]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 14,014,260 reads totaling 2,102.1 Mb. All general aspects of library construction and sequencing performed at the JGI can be found at the institute website [27]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts [28]. Following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet [29], (2) 1–3 Kbp simulated paired end reads were created from Velvet Contigs using wgsim [30], (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG [31]. Parameters for assembly steps were: (1) Velvet (velveth: 63 –shortPaired and velvetg: −very clean yes –export-Filtered yes –min contig lgth 500 –scaffolding no –cov cutoff 10) (2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) (3) Allpaths–LG (PrepareAllpathsInputs: PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True). The final draft assembly contained 36 contigs in 36 scaffolds. The total size of the genome is 2.5 Mbp and the final assembly is based on 249.2 Mbp of Illumina data, which provides an average 99.6 × coverage of the genome.

Genome annotation

Genes were identified using Prodigal [32] as part of the DOE-JGI genome annotation pipeline [33,34], following by a round of manual curation using the JGI GenePRIMP pipeline [35]. The predicted CDSs were translated and searched against the Integrated Microbial Genomes (IMG) non-redundant database, UniProt, TIGERFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) platform [36].

Genome properties

The assembly of the draft genome sequence consists of 36 scaffolds amounting to 2,509,395 bp, and the G + C content is 63.5% (Table 3). Of the 2,450 genes predicted, 2,382 were protein-coding genes, and 68 RNAs. The majority of the protein-coding genes (85.5%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Table 3

Genome statistics

Attribute

Value

% of Total

Genome size (bp)

2,509,395

100.00%

DNA coding (bp)

2,294,427

91.43%

DNA G + C (bp)

1,593,935

63.52%

DNA scaffolds

36

100.00%

Total genes

2,450

100.00%

Protein coding genes

2,382

97.22%

RNA genes

68

2.78%

Pseudo genes

0

0

Genes in internal clusters

1,788

72.98%

Genes with function prediction

2,095

85.51%

Genes assigned to COGs

1,829

74.65%

Genes with Pfam domains

2,129

86.90%

Genes with signal peptides

171

6.98%

Genes with transmembrane helices

505

20.61%

CRISPR repeats

0

0

Table 4

Number of genes associated with the general COG functional categories

Code

Value

% age

Description

J

149

7.44

Translation, ribosomal structure and biogenesis

A

1

0.05

RNA processing and modification

K

104

5.19

Transcription

L

106

5.29

Replication, recombination and repair

B

1

0.05

Chromatin structure and dynamics

D

26

1.30

Cell cycle control, cell division, chromosome partitioning

V

32

1.60

Defense mechanisms

T

60

3.00

Signal transduction mechanisms

M

122

6.09

Cell wall/membrane/envelope biogenesis

N

15

0.75

Cell motility

U

60

3.00

Intracellular trafficking, secretion, and vesicular transport

O

95

4.75

Posttranslational modification, protein turnover, chaperones

C

137

6.84

Energy production and conversion

G

66

3.30

Carbohydrate transport and metabolism

E

182

9.09

Amino acid transport and metabolism

F

54

2.70

Nucleotide transport and metabolism

H

113

5.64

Coenzyme transport and metabolism

I

103

5.14

Lipid transport and metabolism

P

115

5.74

Inorganic ion transport and metabolism

Q

52

2.60

Secondary metabolites biosynthesis, transport and catabolism

R

227

11.34

General function prediction only

S

180

8.99

Function unknown

-

621

25.35

Not in COGs

Insights from the genome sequence

Strain AIMA4T was isolated from chironomid egg masses. Using pyrosequencing method, we have recently shown that the prevalence of Brachymonas in the endogenous bacterial communities of chironomid egg masses and larva was 0.04% and 0.006%, respectively [37]. Chironomid tolerance towards pollution is well documented [38]. Senderovich and Halpern [37,39], demonstrated by using Koch’s postulates that endogenous bacteria in chironomids have a role in protecting the insect from toxicants. Although B. chironomi was isolated from chironomid egg masses, its features regarding its protective potential have never been examined. Nevertheless, its genome reveals the potential of this species to protect its host in polluted environments. Genes encoding arsenate detoxification are present in B. chironomi strain AIMA4T. These genes include an arsenical resistance gene cluster with candidates for transcriptional regulator, ArsR; arsenical resistance operon trans-acting repressor, ArsD; arsenite efflux ATP-binding protein, ArsA and a hypothetical arsenic resistance protein (ACR3 family). A gene for arsenate reductase (ArsC family) is present in a different operon. More genes which may indicate the potential of this bacterium to tolerate or detoxify metals are: copper resistance protein D, CopD; copper chaperone, copper-resistance protein, CopA; copper (or silver) translocating P-type ATPase; uncharacterized lipoprotein NlpE involved in copper resistance; magnesium Mg(2+) and cobalt Co(2+) transport protein, CorA. Moreover, two genes encoding ABC-type transport system involved in resistance to organic solvents, auxiliary and periplasmic components are also present.

The genome of B. chironomi strain AIMA4T reveals the potential of the species to produce a polysaccharide capsule. It includes two gene clusters with candidates for capsule polysaccharide export protein, periplasmic protein involved in polysaccharide export, ABC-type polysaccharide/polyol phosphate transport system, ATPase component, ABC-type polysaccharide/polyol phosphate export systems, permease component and predicted glycosyltransferase involved in capsule biosynthesis. Another feature that is found in the genome of B. chironomi AIMA4T is its potential to produce a pilus (or pili). The following predicted genes indicate this ability; type IV pilus assembly protein PilB; type IV pilus secretin PilQ; Tfp pilus assembly proteins PilP, PilO and PilV; type IV prepilin peptidase; prepilin-type N-terminal cleavage/methylation domain and pilus retraction ATPase PilT (indicating the ability of twitching motility).

Tolerance of 2.5% NaCl was described for strain AIMA4T by Halpern et al. [2]. The presence of ABC-type proline/glycine betaine transport system in the genome may explain the way this species can tolerate high salt concentrations. In respect to the ampicillin (beta-lactam) antibiotic resistance, the genome encodes one beta-lactamase class B and a negative regulator of beta-lactamase expression. Three genes encoding two component transcriptional regulators (LuxR family), can be found in the genome of strain AIMA4T and demonstrate quorum sensing skills.

Conclusions

In the current study, we characterized the genome of B. chironomi strain AIMA4T that was isolated from a chironomid egg mass [2]. B. chironomi belongs to the family Comamonadaceae (order Bukholderiales; class Betaproteobacteria) (Figure 1). Members of this family are known for their ability to cope with harsh environmental condition such as high concentration of toxic metals and other pollutants like aromatic compounds or polymers [e.g. poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [16]. Likewise, the genome of strain AIMA4T reveals the potential of this species to cope with toxic metals. These demonstrate that B. chironomi may have a role in protecting its aquatic host (chironomids) in polluted environments.

Abbreviations

KMG: 

One thousand microbial genomes

PHBV: 

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Nicole Reimann for growing B. chironomi cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 Genome analysis was supported by the National Basic Research Program of China (No. 2010CB833801). A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI Dr Stephen J O’Brien). M. H. was supported in part by a grant from the US Civilian Research and Development Foundation (CRDF grant no. ILB1-7045-HA).

Authors’ Affiliations

(1)
Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa
(2)
Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University
(3)
Algorithmic Biology Lab, St. Petersburg Academic University
(4)
DOE Joint Genome Institute
(5)
Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(6)
Helmholz Centre for Infection Research
(7)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(8)
Dept. of Biological Sciences, Faculty of Science, King Abdulaziz University
(9)
Dept. of Biology and Environment, Faculty of Natural Sciences, University of Haifa

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