Fuying Feng

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Significance Photosynthesis is one of the most fundamental biological processes on Earth. To date, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in six bacterial phyla. Here we report a phototrophic bacterium belonging to the rare and understudied phylum Gemmatimonadetes. This strain, isolated from a freshwater lake in the Gobi Desert, contains fully functional photosynthetic reaction centers. Its photosynthesis genes appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. Our findings not only demonstrate that Gemmatimonadetes represents a new phototrophic bacterial phylum, but also present, to our knowledge, the first evidence that genes for (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla. Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb–long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.

Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca

A red-pigmented, bacteriochlorophyll (BChl) a-producing strain, AP64T, was isolated previously from the freshwater Swan Lake located in the western Gobi Desert. Based on its 16S rRNA gene sequence identity (96.1%) to the type strain Gemmatimonas aurantiaca T-27T, the new isolate was tentatively classified as a member of the bacterial phylum Gemmatimonadetes. Here, we report its formal description and polyphasic characterization. Strain AP64T grew best on agar media under 9.8-15.2% atmospheric oxygen. The cells were rods, dividing by symmetrical or asymmetrical binary fission. Budding structures were also observed. Its genomic DNA G+C content was 64.4% (from the draft genome sequence). Phylogenetic analysis based on the 16S rRNA gene sequence clearly separated AP64T from related species. Its genotypic differentiation from phylogenetically close relatives was further supported by performing in silico DNA-DNA hybridization and calculating average nucleotide identity, whereas the high percentage (67.3%) of shared conserved proteins between strain AP64T and Gemmatimonas aurantiaca T-27T supports the classification of the two strains into the same genus. Strain AP64T contained C16 : 1, C14 : 1 and C18 : 1ω9c as predominant fatty acids. The main respiratory quinone was menaquinone 8 (MK-8). The most distinctive feature of strain AP64T was the presence of fully functional purple bacterial photosynthetic reaction centres. The main CO2-fixation pathways were absent. Strain AP64T was capable of growth and BChl production in constant darkness. Thus, strain AP64T is a facultatively photoheterotrophic organism. It represents a novel species of the genus Gemmatimonas, for which the name Gemmatimonasphototrophica sp. nov. is proposed. The type strain is AP64T ( = DSM 29774T = MCCC 1K00454T). Emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca are also provided.

Spirosoma soli sp. nov., isolated from biological soil crusts

A Gram-negative, aerobic, short rod-shaped, non-motile, pale-yellow bacterial strain was isolated from biological soil crusts collected in the desert of Kubuqi, Inner Mongolia of China, designated MIMBbqt12T. The G+C content of the genomic DNA of strain MIMBbqt12T was 49.5 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MIMBbqt12T belongs to the genus Spirosoma with the highest sequence similarity of 93.5 % to Spirosoma arcticum R2-35T. The major fatty acids of strain MIMBbqt12T were C16 : 0, iso-C15 : 0, iso-C17 : 03-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The results of phenotypic properties and phylogenetic distinctiveness supported that strain MIMBbqt12T represents a novel species of the genus Spirosoma, for which the name Spirosoma soli sp. nov. is proposed. The type strain is MIMBbqt12T (=MCCC 1K01308T=KCTC 42805T).

Mongoliitalea lutea gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a haloalkaline lake.

Two bacterial isolates from the surface water of a haloalkaline lake on the Mongolia Plateau, strains MIM18(T) and MIM19, were characterized; their morphological, physiological and chemotaxonomic characters, and phylogenetic position based on 16S rRNA gene sequences, were determined. The two strains were alkaliphilic, halotolerant, non-motile, aerobic, Gram-negative, orange-red, rod-shaped and oxidase-positive. Growth was observed in 0-5.5% (w/v) NaCl, with optimum growth at 1%. The temperature range for growth was 0-41 °C, with good growth at 28-37 °C and optimum growth at 30-33 °C. The DNA G+C content was 39.8-41.2 mol%. The strains contained menaquinone MK-7 as the major respiratory quinone and phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Predominant cellular fatty acids were iso-C(15:0) (28.1-29.3%), iso-C(17:0) 3-OH (14.6-18.8%), C(15:1)ω6c (5.3-8.6%), C(14:0) 2-OH and/or iso-C(15:0) 2-OH (5.4-6.1%), and iso-C(17:1)ω9c and/or C(16:0) 10-methyl (5.0-6.8%). 16S rRNA gene sequence analysis showed that Belliella and Nitritalea of the family Cyclobacteriaceae were the closest related species with sequence similarities of 91.7-92.3% and 88.2%, respectively, with strains of these genera; other members of the Cyclobacteriaceae had sequence similarities lower than 88%. Phylogenetic analysis indicated that the strains formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Nitritalea, Indibacter, Aquiflexum, Echinicola, Litoribacter, Cyclobacterium and Algoriphagus. Based on the phenotypic and phylogenetic characteristics mentioned above, the two strains are representatives of a single novel species in a new genus; the name Mongoliitalea lutea gen. nov., sp. nov. is proposed, with MIM18(T) (=ACCC 05421(T)=KCTC 23224(T)) as the type strain.

Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China

ABSTRACT Blastomonas is a strictly aerobic bacteriochlorophyll a-producing genus within the alpha-4 Proteobacteria. Here we report the first genome sequence from this genus. The draft genome of Blastomonas sp. strain AAP53 contains a split photosynthesis gene cluster and two gene clusters encoding a flagellar system. Genes for the autotrophic CO2 fixation pathway are absent.

Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase

ABSTRACT Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in Inner Mongolia, North China, has a high capability for producing cold-active cellulase at low temperatures. Here, we report the draft genome sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49 RNA-coding sequences.

Genome Sequences and Photosynthesis Gene Cluster Composition of a Freshwater Aerobic Anoxygenic Phototroph, Sandarakinorhabdus sp. Strain AAP62, Isolated from the Shahu Lake in Ningxia, China

ABSTRACT We report the first genome sequence from the recently established alpha-4 proteobacterial genus Sandarakinorhabdus. The genome of the Sandarakinorhabdus sp. strain AAP62 contains a photosynthesis gene cluster carrying major genes for bacterial reaction centers. The presence of genes related to aerobic respiratory electron transport confirms the lifestyle of this organism as an aerobic anoxygenic photoheterotroph.

Whole-genome sequence of a freshwater aerobic anoxygenic phototroph, Porphyrobacter sp. strain AAP82, isolated from the Huguangyan Maar Lake in Southern China.

ABSTRACT The Porphyrobacter genus (of the class Alphaproteobacteria) contains aerobic anoxygenic phototrophic species. Here we report a draft genome sequence of a freshwater bacterium, Porphyrobacter sp. strain AAP82. It contains a 38-kb-long photosynthesis gene cluster, but carbon-fixation genes are absent. The presence of respiratory enzymes, tricarboxylic acid (TCA) cycle, and the Entner-Doudoroff pathway demonstrates its aerobic photoorganotrophic character.

Mongoliimonas terrestris gen. nov., sp. nov., isolated from desert soil

A Gram-stain-negative, non-motile, aerobic, non-spore-forming, spherical bacterium (strain MIMtkB18T) was isolated from desert soil collected from part of a Mongolian Plateau, territory of Inner Mongolia, PR China. Cell growth could be observed at 20-45 °C (optimum at 40 °C), at a pH of 6-9 (optimum at pH 8.6) and in the presence of 0-1 % (w/v) NaCl (optimum 0 %). The genomic DNA G+C content was 69.6 mol%. 16S rRNA gene sequence analysis showed that strain MIMtkB18T was most closely related to Methylobrevis pamukkalensis PK2T (94.1 %), species of the genus Pleomorphomonas(93.4-94.0 %), and Hartmannibacter diazotrophicus E19T (93.9 %). The sole respiratory quinone was Q-10. The major fatty acids (>5 %) were C18 : 0 (5.7 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (81.6 %). Polar lipids were mainly composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and unidentified phospholipids. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain MIMtkB18T represents a novel genus and species, for which the name Mongoliimonas terrestris sp. nov. is proposed. The type strain is MIMtkB18T (=KCTC 42635T=MCCC 1K00571T).

Sphingomonas crusticola sp. nov., isolated from biological soil crusts

A yellow-pigmented, Gram-stain-negative, short-rod-shaped bacterial strain, MIMD3T, was isolated from biological soil crusts collected in Liangcheng, north-western China. Cell growth could be observed at 10-37 °C (optimum 25 °C), at pH 5-8 (optimum 6.6) and in the presence of 1 % (w/v) NaCl (optimum 0 %). The genomic DNA G+C content was 65.0 mol%. Analysis of 16S rRNA gene sequences showed that strain MIMD3T shared the highest similarity with Sphingomonas vulcanisoli KCTC 42454T (95.1 %), Sphingomonas oligophenolica JCM 12082T (94.8 %), Sphingomonas mali IFO 15500T (94.5 %), Sphingomonas. leidyi ATCC 15260T (94.4 %) and Sphingomonas formosensis CC-Nfb-2T (94.3 %). The strain had Q-10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. The major fatty acids of the strain were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 0 cyclo ω8c, C14 : 0 2-OH and C16 : 0. The main polar lipids of strain MIMD3T were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain MIMD3T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas crusticola sp. nov. is proposed. The type strain is MIMD3T (=KCTC 42801T=MCCC 1K01310T).