Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil

Abstract

A non-motile, rod-shaped, red-pigmented bacterium, designated strain BZ33r T , was isolated from soil of an industrial site. Cells stained Gram-negative and were aerobic and psychrophilic, showing good growth at 1-20 6C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ33rT was related to members of the genus Hymenobacter and had highest sequence similarity with Hymenobacter aerophilus DSM 13606 T (97.5 %). The predominant cellular fatty acids were anteiso-C 15 : 0 (20.3 %), summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH; 20.2 %), iso-C 15 : 0 (20.0 %), summed feature 4 (iso-C 17 : 1 I and/or anteiso-C 17 : 1 B; 8.2 %) and C 16 : 1 v5c (7.9 %). Strain BZ33r T had MK-7 as the major menaquinone. The polyamine pattern contained sym-homospermidine as the major compound with moderate amounts of spermidine. Phosphatidylethanolamine, three unknown aminophospholipids, two unknown aminolipids, two unknown glycolipids and five unknown polar lipids were present in the polar lipid profile. The G+C content of the DNA was 61.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain BZ33r T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter psychrophilus sp. nov. is proposed. The type strain is BZ33r T (5DSM 22290The genus Hymenobacter, which belongs to the phylum Bacteroidetes, order Sphingobacteriales, family Cytophagaceae, was proposed by Hirsch et al. (1998) et al., 2009). In this study, we report the characterization of a novel bacterium of the genus Hymenobacter isolated from an industrial site. Strain BZ33rT was isolated from soil containing high levels of heavy oil and heavy metals at an industrial site in Bozen, South Tyrol (Italy). Soil was collected under sterile conditions in spring 2008. A sample of 10 g was shaken (150 r.p.m.) with 90 ml sterile 1 % sodium pyrophosphate for 20 min. Appropriate dilutions, prepared with sterile saline solution (0.9 % NaCl), were plated (0.1 ml) on R2AThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain BZ33rT is GQ131579.A supplementary figure and a supplementary table are available with the online version of this paper. T was routinely grown on nutrient agar (0.5 % peptone, 0.3 % beef extract and 1.5 % agar, pH 7.0) at 20 u C and used as a reference strain.DNA was extracted and purified as described by Sambrook et al. (1989). The gene encoding 16S rRNA was amplified by PCR with two universal primers (Zhang et al., 2006). PCR products were cloned in pGEM-T vectors by using the pGEM-T easy vector systems (Promega) according to the manufacturer's instructions. Sequencing reactions were performed as described by Zhang et al. (2006). The nearly complete 16S rRNA gene sequence (1511 bp) of strain BZ33rT was analysed by using the FASTA algorithm. Phylogenetic analysis with the program MEGA version 3.0 (Kumar et al., 2004) showed that strain BZ33rT grouped with members of the genus Hymenobacter and formed a distinct clust...

Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans gen. nov., and Parahymenobacter gen. nov

“…Seven species of Clade1, H. arizonensis [12], H. glaciei and H. antarcticus [13], H. soli [62], H. metalli, H. flocculans [63] and H. ginsengisoli [11] T =LMG 24240 T =KCTC 12607 T was designated as the type species of the genus, first described species among Clade1. Clade2 contains 17 species; H. actinosclerus [64], H. aerophilus [65], H. algoricola, H. elongatus and H. fastidiosus [13], H. chitinivorans, H. gelipurpurascens and H. norwichensis [10], H. daecheongensis [66], H. roseosalivarius [9], H. rigui [67], H. psychrophilus [68], H. psychrotolerans [69], H. perfusus [63], H. tibetensis [70], H. xinjiangensis [71] and H.…”

Hymenobacter mucosus sp. nov., isolated from a karst cave soil sample

“…The genus is well-known for its high DNA G+C contents (54–72 mol%) compared with other members of the family Cytophagaceae . Members of the genus Hymenobacter have been isolated from various environments, including deserts (Zhang et al , 2007, 2009), vegetated soils (Hoang et al , 2013; Jin et al , 2014; Kim et al , 2008; Su et al , 2014; Zhang et al , 2011), sandstones (Han et al , 2014; Hirsch et al , 1998) and wetland (Baik et al , 2006). At the time of writing, the genus comprised 37 species (http://www.bacterio.net/hymenobacter.html; Parte, 2014), including the recently described species ‘ Hymenobacter swuensis ’ (Lee et al , 2014), ‘ Hymenobacter humi ’ (Srinivasan et al , 2015), Hymenobacter latericoloratus and Hymenobacter luteus (Liu et al , 2015).…”

Hymenobacter terrenus sp. nov., isolated from biological soil crusts

“…Their representatives inhabit various environments, such as soil, glacier, marine, freshwater and air (Han et al , 2014). Soil is the habitat origin for 17 species of the genus, including Hymenobacter arizonensis (Reddy & Garcia-Pichel, 2013), H. daecheongensis (Xu et al , 2009), H. deserti (Zhang et al , 2009), H. ginsengisoli (Hoang et al , 2013), ‘ H. humi ’(Srinivasan et al , 2015a), H. kanuolensis (Su et al , 2014), H. latericoloratus , H. luteus (Liu et al , 2015), H. psychrophilus (Zhang et al , 2011), H. qilianensis (Han et al , 2014), H. roseus (Subhash et al , 2014), H. roseosalivarius (Hirsch et al , 1998), H. ruber (Jin et al , 2014), H. soli (Kim et al , 2008), ‘ H. swuensis ’ (Lee et al , 2014), ‘ H. terrae ’ (Srinivasan et al , 2015b) and H. xinjiangensis (Zhang et al , 2007).…”