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Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chloroflexi)

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Norihisa Matsuura
Norihisa Matsuura
Norihisa Matsuura
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Dieter Tourlousse at National Institute of Advanced Industrial Science and Technology (AIST), Japan
Dieter Tourlousse
  • National Institute of Advanced Industrial Science and Technology (AIST), Japan
Akiko Ohashi
Akiko Ohashi
Akiko Ohashi
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Hugenholtz Philip at The University of Queensland
Hugenholtz Philip
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Abstract

Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a range of ecosystems but remain poorly understood. We present here the draft genome sequences of the type strains of five Anaerolineae species, Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, and Longilinea arvoryzae KOME-1.
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Draft Genome Sequences of Anaerolinea thermolimosa IMO-1,
Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2,
Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1,
Previously Described as Members of the Class Anaerolineae
(Chloroflexi)
Norihisa Matsuura,
a
Dieter M. Tourlousse,
a
Akiko Ohashi,
a
Philip Hugenholtz,
b,c
Yuji Sekiguchi
a
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
a
; Australian Centre for Ecogenomics,
School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
b
; Institute for Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland, Australia
c
Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a range of ecosystems but remain
poorly understood. We present here the draft genome sequences of the type strains of five Anaerolineae species, Anaerolinea
thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, and
Longilinea arvoryzae KOME-1.
Received 2 August 2015 Accepted 5 August 2015 Published 17 September 2015
Citation Matsuura N, Tourlousse DM, Ohashi A, Hugenholtz P, Sekiguchi Y. 2015. Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1,
Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi). Genome
Announc 3(5):e00975-15. doi:10.1128/genomeA.00975-15.
Copyright © 2015 Matsuura et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Yuji Sekiguchi, y.sekiguchi@aist.go.jp.
Members of the class Anaerolineae are cosmopolitan bacteria
found in various ecosystems, suggesting their functional im-
portance (1). Currently, 10 Anaerolineae species have been iso-
lated and characterized (2–8). However, the genome sequence of
only a single species, Anaerolinea thermophila (strain UNI-1), has
been available. To further expand the knowledge on the genomic
diversity of the Anaerolineae, we generated draft genomes of five
previously described isolates. Two represent the type strains of
thermophilic species, Anaerolinea thermolimosa (strain IMO-1)
and Bellilinea caldifistulae (strain GOMI-1), isolated from ther-
mophilic anaerobic waste/wastewater treatment systems (3,4).
The others are the type strains of mesophilic species, Leptolinea
tardivitalis (strain YMTK-2), Levilinea saccharolytica (strain KIBI-
1), and Longilinea arvoryzae (strain KOME-1), isolated from
mesophilic anaerobic wastewater treatment systems or Japanese
paddy field soil (3,4).
Nextera XT paired-end (300 to 700 bp) and Nextera mate-pair
(2 to 10 kbp) libraries were prepared from the genomic DNA of
each strain. Pooled libraries were sequenced on an Illumina MiSeq
(2 ⫻250-bp reads) at an expected coverage of ⬎50⫻and ⬎10⫻
per genome for the paired-end and mate-pair libraries, respec-
tively. The sequence reads were merged with SeqPrep with con-
current removal of sequencing adapters. Unmerged reads were
quality trimmed and filtered using Nesoni version 0.112. SPAdes
version 2.5.0 (9) was used for assembly, and further scaffolding
and refinement were performed as described previously (10). Ge-
nome annotations were generated within the Integrated Microbial
Genomes platform (11).
The assembly of the A. thermolimosa IMO-1 genome consists
of 81 contigs in 6 scaffolds (coverage, 180⫻); the total size is
4,173,865 bp, and the G⫹C content is 53.72%. The assembly of
the B. caldifistulae GOMI-1 genome consists of 43 contigs in a
single scaffold (coverage, 180⫻); the total size is 3,698,317 bp, and
the G⫹C content is 52.18%. The assembly of the L. tardivitalis
YMTK-2 genome consists of 15 contigs in 15 scaffolds (coverage,
230⫻); the total size is 3,687,036 bp, and the G⫹C content is
46.82%. The assembly of the L. saccharolytica KIBI-1 genome con-
sists of 196 contigs in 4 scaffolds (coverage, 200⫻); the total size is
4,249,622 bp, and the G⫹C content is 57.36%. The assembly of
the L. arvoryzae KOME-1 genome consists of 25 contigs in 2 scaf-
folds (coverage, 60⫻); the total size is 4,438,311 bp, and the G⫹C
content is 56.84%. The genomes are predicted to contain between
3,301 (L. tardivitalis YMTK-2) and 3,888 (L. arvoryzae KOME-1)
protein-coding genes and between 54 (L. tardivitalis YMTK-2)
and 64 (A. thermolimosa IMO-1) RNAs. The availability of these
genomes will contribute to our understanding of the metabolic
potential and possible ecological roles of members of the class
Anaerolineae.
Nucleotide sequence accession numbers. These whole-genome
shotgun projects have been deposited at DDBJ/EMBL/GenBank un-
der the accession numbers BBXW00000000,BBXX00000000,
BBXY00000000,BBXZ00000000, and BBYA00000000 for A. ther-
molimosa IMO-1 JCM 12577, B. caldifistulae GOMI-1 JCM
13669, L. arvoryzae KOME-1 JCM 13670, L. saccharolytica
KIBI-1 JCM 12578, and L. tardivitalis YMTK-2 JCM 12579,
respectively. The versions described in this paper are versions
BBXW01000000, BBXX01000000, BBXY01000000, BBXZ01000000,
and BBYA01000000.
crossmark
Genome AnnouncementsSeptember/October 2015 Volume 3 Issue 5 e00975-15 genomea.asm.org 1
ACKNOWLEDGMENT
This research was partly supported by a grant-in-aid for JSPS Fellows from
the Japan Society for the Promotion of Science (JSPS) to N.M.
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  • Nov 2013
  • INT J SYST EVOL MICR
A novel, anaerobic filamentous bacterium, strain MO-CFX1(T), was isolated from a methanogenic community, which was originally established from subseafloor sediments collected from off the Shimokita Peninsula, Japan. Cells were non-spore-forming, non-motile, Gram-negative, and filaments. The filaments were longer than 10 μm and 130-150 nm in width. Growth of the strain was observed at 10-37°C (optimum 25-30°C), at pH 5.5-8.5 (optimum pH 7.0), and in 0-50 g l(-1) (w/v) NaCl (optimum 15 g l(-1) NaCl). The strain was able to grow with a number of carbohydrates in the presence of yeast extract. The major cellular fatty acids were monounsaturated C18:1ω9, C16:1ω7, and saturated C18:0 and C16:0. The intact polar lipids of the strain were dominated by diacylglyceride and sphingolipid core lipid structures with monoglycosidic, mixed phospho-monoglycosidic, and fatty-acid modified monoglycosidic polar head groups. The G + C content of the genomic DNA was 52.4 mol%. Based on the comparative 16S rRNA gene sequence analysis, strain MO-CFX1(T) was affiliated with the class Anaerolineae within the phylum Chloroflexi and was most closely related to Leptolinea tardivitalis YMTK-2(T) (sequence identity of 91.0%). Based on phenotypic and genetic properties of the new isolate, we propose a new species representing a new genus Pelolinea submarina gen. nov., sp. nov., for strain MO-CFX1(T) (=JCM 17238(T), =KCTC 5975(T)). This is the first formal description of an isolate of the phylum Chloroflexi from the deep-sea sedimentary environment.
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IMG/M 4 version of the integrated metagenome comparative analysis system
Article
Full-text available
  • Oct 2013
  • NUCLEIC ACIDS RES
IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M’s data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M’s database architecture, annotation and data integration pipelines and analysis tools have been extended to copewith the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp).
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Isolation and Characterization of a Thermophilic, Obligately Anaerobic and Heterotrophic Marine Chloroflexi Bacterium from a Chloroflexi-dominated Microbial Community Associated with a Japanese Shallow Hydrothermal System, and Proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov.
Article
Full-text available
  • May 2013
  • MICROBES ENVIRON
A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7(T), was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7(T) was isolated from an enrichment culture at a high dilution rate. Strain SW7(T) was an obligately anaerobic heterotroph that grew with fermentation and had non-motile thin rods 3.5-16.5 μm in length and 0.2 μm in width constituting multicellular filaments. Growth was observed between 37-65°C (optimum 60°C), pH 5.5-7.3 (optimum pH 6.0), and 0.5-3.5% (w/v) NaCl concentration (optimum 1.0%). Based on the physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7(T) (=JCM15506(T)=KCTC5908(T)).
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Article
Full-text available
  • Apr 2012
  • J COMPUT BIOL
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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Ornatilinea apprima gen. nov., sp nov., a cellulolytic representative of the class Anaerolineae
Article
Full-text available
  • Feb 2012
  • INT J SYST EVOL MICR
A novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1T, was isolated from a microbial mat formed in wooden bath filled with hot water emerging from a 2775-m deep well in Tomsk region (Western Siberia, Russia). Cells of strain P3M-1T were rod-shaped, 0.3-0.7 µm in width, gathered in multicellullar filaments that reached up to 400 µm in length. Strain P3M-1T grew optimally at 42-45 °C, pH 7.5-8.0 and NaCl concentration of 1 g l-1. At the optimum conditions the doubling time was 6 hours. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H2 were the main products of glucose fermentation. G+C content of DNA was 55 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-1T was a member of class Anaerolinea with 16S rRNA gene sequence identity with the closest relative - Levilinea saccharolytica - being 92.8 %. Based on the phylogenetic analysis and physiological properties a new genus and species Ornatilinea apprima gen. nov., sp. nov. (type strain P3M-1T = DSM 23815T = VKM B-2669T) were proposed for the new isolate.
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Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level
Article
Full-text available
  • Dec 2003
Two thermophilic, Gram-negative, non-spore-forming, multicellular filamentous micro-organisms were isolated from thermophilic granular sludge in an upflow anaerobic sludge blanket reactor treating fried soybean-curd manufacturing waste water (strain UNI-1T) and from a hot spring sulfur-turf in Japan (strain STL-6-O1T). The filaments were longer than 100 μm and of 0.2-0.3 μm (strain UNI-1T) or 0.7-0.8 μm (strain STL-6-O1T) in width. Strain UNI-1T was a strictly anaerobic organism. The optimum temperature for growth was around 55 °C; growth occurred in the range 50-60 °C. The optimum pH for growth was around 7.0; growth occurred in the range pH 6.0-8.0. Strain STL-6-O1T was a facultatively aerobic bacterium. The optimum temperature for growth was around 55 °C; growth occurred in the range 37-65 °C. The optimum pH for growth was around 7.5-8.0; growth occurred in the range pH 7.0-9.0. The two organisms grew chemo-organotrophically on a number of carbohydrates and amino acids in the presence of yeast extract. The G + C content of the DNA of strains UNI-1T and STL-6-O1T was 54.5 and 59.0 mol%, respectively. Major cellular fatty acids for strain UNI-1T were C16:0, C15:0, C14:0, and C18:0, whereas those for strain STL-6-O1T were C18:0, C16:0, C17:0 and iso-C17:0. MK-10 was the major quinone from aerobically grown STL-6-O1T cells. Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria). These phenotypic and genetic properties suggested that each strain should be classified into a new independent genus; hence, the names Anaerolinea thermophila and Caldilinea aerophila are proposed for strains UNI-1T (=JCM 11387T = DSM 14523T) and STL-6-O1T(=JCM 11388T = DSM 14525T), respectively. These strains represent the type and sole species of the genera Anaerolinea and Caldilinea, respectively.
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Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi
Article
Full-text available
  • Jul 2006
One thermophilic (strain IMO-1(T)) and two mesophilic (strains KIBI-1(T) and YMTK-2(T)) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class 'Anaerolineae' of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 microm and the width was 0.3-0.4 microm for strain IMO-1(T), 0.4-0.5 microm for strain KIBI-1(T) and thinner than 0.2 microm for strain YMTK-2(T). Strain IMO-1(T) could grow at pH 6.0-7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1(T) was around 50 degrees C (growth occurred between 42 and 55 degrees C). Growth of the mesophilic strains KIBI-1(T) and YMTK-2(T) occurred at pH 6.0-7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25-50 degrees C with optimal growth at around 37 degrees C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G + C contents of the DNA of strains IMO-1(T), KIBI-1(T) and YMTK-2(T) were respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1(T) were anteiso-C(17 : 0), iso-C(15 : 0), C(16 : 0) and anteiso-C(15 : 0), whereas those for mesophilic strains KIBI-1(T) and YMTK-2(T) were branched C(14 : 0), iso-C(15 : 0), C(16 : 0) and branched C(17 : 0), and branched C(17 : 0), C(16 : 0), C(14 : 0) and C(17 : 0), respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon 'Anaerolineae' of the bacterial phylum Chloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylum Chloroflexi. Here, Anaerolinea thermolimosa sp. nov. (type strain IMO-1(T) = CM 12577(T) = DSM 16554(T)), Levilinea saccharolytica gen. nov., sp. nov. (type strain KIBI-1(T) = JCM 12578(T) = DSM 16555(T)) and Leptolinea tardivitalis gen. nov., sp. nov. (type strain YMTK-2(T) = JCM 12579(T) = DSM 16556(T)) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon 'Anaerolineae' into Anaerolineae classis nov. and Caldilineae classis nov. We also propose the subordinate taxa Anaerolineales ord. nov., Caldilineales ord. nov., Anaerolineaceae fam. nov. and Caldilineaceae fam. nov.
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Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp nov., a thermophilic anaerobic bacterium pertaining to the phylum "Chloroflexi", isolated from a deep hot aquifer in the Aquitaine Basin
Article
  • May 2011
A new strictly anaerobic thermophilic multicellular filamentous bacterium (0.2-0.3μm×>100μm), designated GNS-1(T), was isolated from a deep hot aquifer in France. It was non-motile, and stained Gram-negative. Optimal growth was observed at 65°C, pH 7.0, and 2gL(-1) of NaCl. Strain GNS-1(T) was chemoorganotrophic fermenting ribose, glucose, galactose, arabinose, fructose, mannose, maltose, sucrose, xylose, raffinose, pyruvate, and xylan. Yeast extract was required for growth. The end products of glucose fermentation were lactate, acetate, CO(2), and H(2). The G+C content of the DNA was 57.6mol%. Its closest phylogenetic relative was Bellilinea caldifistulae with 92.5% similarity. Based on phylogenetic, genotypic and phenotypic characteristics, strain GNS-1(T) (DSM 23592(T), JCM 16980(T)) is proposed to be assigned to a novel species of a novel genus within the class Anaerolineae (subphylum I), phylum "Chloroflexi", Thermanaerothrix daxensis gen. nov., sp. nov. The GenBank accession number is HM596746.
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Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance
Article
  • Sep 2009
Cultivation-independent molecular surveys have shown members of the bacterial phylum Chloroflexi to be ubiquitous in various natural and artificial ecosystems. Among the subphylum-level taxa of the Chloroflexi known to date, the formerly uncultured 'subphylum I' had well been recognized as a typical group that contains a number of environmental gene clones with no culture representatives. In order to reveal their ecophysiology, attempts were made over the past decade to domesticate them into laboratory cultures, and significant advances have been made in cultivating strains belonging to the group. The microorganisms characterized so far include seven species in six genera, i.e., Anaerolinea, Levilinea, Leptolinea, Bellilinea, Longilinea, and Caldilinea, and were proposed to represent two classes, Anaerolineae and Caldilineae, providing solid insights into the phenotypic and genetic properties common to the group. Another subphylum-level uncultured group of the Chloroflexi, i.e., the class Ktedonobacteria, has also been represented recently by a cultured strain. In addition to the results from these tangible cultures, data obtained from functional analyses of uncultured Chloroflexi populations by assessing substrate uptake patterns are accumulating at an encouraging rate. In this review, recent findings on the ecological significance and possible ecophysiological roles of 'Chloroflexi subphylum I' are discussed based on findings from both the characteristics of the cultured Chloroflexi and molecular-based analyses.
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