ABSTRACT
The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as
Alcaligenes faecalis
,
Comamonas terrigena
, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection,
Alkanindiges illinoisensis
, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.
The taxonomic positions of members within the family
Pseudonocardiaceae
were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family
Pseudonocardiaceae
were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values. The family
Pseudonocardiaceae
consists of the type genus
Pseudonocardia
, as well as the genera
Actinoalloteichus
,
Actinocrispum
,
Actinokineospora
,
Actinomycetospora
,
Actinophytocola
,
Actinopolyspora
,
Actinorectispora
,
Actinosynnema
,
Allokutzneria
, Allosaccharopolyspora gen. nov.,
Amycolatopsis
,
Bounagaea
,
Crossiella
,
Gandjariella
,
Goodfellowiella
,
Haloactinomyces
,
Haloechinothrix
,
Halopolyspora
, Halosaccharopolyspora gen. nov.,
Herbihabitans
,
Kibdelosporangium
,
Kutzneria
,
Labedaea
,
Lentzea
,
Longimycelium
,
Prauserella
,
Saccharomonospora
,
Saccharopolyspora
,
Saccharothrix
,
Salinifilum
,
Sciscionella
,
Streptoalloteichus
,
Tamaricihabitans
,
Thermocrispum
,
Thermotunica
and
Umezawaea
. The G+C contents of the
Pseudonocardiaceae
genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that
Actinokineospora mzabensis
is a heterotypic synonym of
Actinokineospora spheciospongiae
,
Lentzea deserti
is a heterotypic synonym of
Lentzea atacamensis
,
Prauserella endophytica
is a heterotypic synonym of
Prauserella coralliicola
, and
Prauserella flava
and
Prauserella sediminis
are heterotypic synonyms of
Prauserella salsuginis
. This study addresses the nomenclature conundrums of
Actinoalloteichus cyanogriseus
and
Streptomyces caeruleus
as well as
Micropolyspora internatus
and
Saccharomonospora viridis
.
AbstractCable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the “saltwater” Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.
SummaryPhototrophic members of the Chloroflexota phylum are enigmas in the evolution of phototrophy. Although all previously characterized phototrophic Chloroflexota members use a Type II reaction center (RCII) to perform light energy conversion1,2, many members host chlorosomes, a light-harvesting apparatus only otherwise reported among Type I reaction center (RCI)-containing phototrophs3. Here we report the discovery and cultivation of “Candidatus Chlorohelix allophototropha”, the first known member of the Chloroflexota to use RCI, rather than RCII, for phototrophy. Cultivated from an iron-rich Boreal Shield lake, “Ca. Chx. allophototropha” cells contain chlorosomes and encode a novel fifth clade of RCI protein. Phylogenomic data demonstrate that “Ca. Chx. allophototropha” shares closest ancestry to RCII-utilizing relatives for multiple photosynthesis accessory genes, including chlorosomes. Thus, we propose that the enigmatic distribution of chlorosomes in the Chloroflexota phylum resulted from genetic interaction of RCI- and RCII-utilizing Chloroflexota members. Although undetected previously, metatranscriptome data demonstrate that RCI-utilizing Chloroflexota members can be among the most active populations in illuminated anoxic waters of Boreal Shield lakes, which number in the millions globally4. Our results establish the Chloroflexota as the only bacterial phylum containing RCI- and RCII-utilizing anoxygenic phototrophs, providing new context for understanding the origins of phototrophic life on Earth.
Rickettsiales (Rickettsia spp., Ehrlichia spp., and Anaplasma spp., etc.) are generally recognized as potentially emerging tick-borne pathogens. However, some bacteria and areas in China remain uninvestigated. In this study, we collected 113 ticks from mammals in Guizhou Province, Southwest China, and screened for the Rickettsiales bacteria. Subsequently, two spotted fever group Rickettsia species and one Candidatus Lariskella sp. were detected and characterized. “Candidatus Rickettsia jingxinensis” was detected in Rhipicephalus microplus (1/1), Haemaphysalis flava (1/3, 33.33%), Haemaphysalis kitaokai (1/3), and Ixodes sinensis (4/101, 3.96%), whereas Rickettsia monacensis was positive in H. flava (1/3), H. kitaokai (2/3), and I. sinensis ticks (74/101, 73.27%). At least two variants/sub-genotypes were identified in the R. monacensis isolates, and the strikingly high prevalence of R. monacensis may suggest a risk of human infection. Unexpectedly, a Candidatus Lariskella sp. belonging to the family Candidatus Midichloriaceae was detected from Ixodes ovatus (1/4) and I. sinensis (10/101, 9.90%). The gltA and groEL gene sequences were successfully obtained, and they show the highest (74.63–74.89% and 73.31%) similarities to “Candidatus Midichloria mitochondrii”, respectively. Herein, we name the species “Candidatus Lariskella guizhouensis”. These may be the first recovered gltA and groEL sequences of the genus Candidatus Lariskella.
ABSTRACT
In the past 10 years, the number of endosymbionts described within the bacterial order
Rickettsiales
has constantly grown. Since 2006, 18 novel
Rickettsiales
genera inhabiting protists, such as ciliates and amoebae, have been described. In this work, we characterize two novel bacterial endosymbionts from
Paramecium
collected near Bloomington, IN. Both endosymbiotic species inhabit the cytoplasm of the same host. The Gram-negative bacterium “
Candidatus
Bealeia paramacronuclearis” occurs in clumps and is frequently associated with the host macronucleus. With its electron-dense cytoplasm and a distinct halo surrounding the cell, it is easily distinguishable from the second smaller symbiont, “
Candidatus
Fokinia cryptica,” whose cytoplasm is electron lucid, lacks a halo, and is always surrounded by a symbiontophorous vacuole. For molecular characterization, the small-subunit rRNA genes were sequenced and used for taxonomic assignment as well as the design of species-specific oligonucleotide probes. Phylogenetic analyses revealed that “
Candidatus
Bealeia paramacronuclearis” clusters with the so-called “basal”
Rickettsiales
, and “
Candidatus
Fokinia cryptica” belongs to “
Candidatus
Midichloriaceae.” We obtained tree topologies showing a separation of
Rickettsiales
into at least two groups: one represented by the families
Rickettsiaceae
,
Anaplasmataceae
, and “
Candidatus
Midichloriaceae” (RAM clade), and the other represented by “basal
Rickettsiales
,” including “
Candidatus
Bealeia paramacronuclearis.” Therefore, and in accordance with recent publications, we propose to limit the order
Rickettsiales
to the RAM clade and to raise “basal
Rickettsiales
” to an independent order,
Holosporales
ord. nov., inside
Alphaproteobacteria
, which presently includes four family-level clades. Additionally, we define the family “
Candidatus
Hepatincolaceae” and redefine the family
Holosporaceae
.
IMPORTANCE
In this paper, we provide the characterization of two novel bacterial symbionts inhabiting the same
Paramecium
host (Ciliophora, Alveolata). Both symbionts belong to “traditional”
Rickettsiales
, one representing a new species of the genus “
Candidatus
Fokinia” (“
Candidatus
Midichloriaceae”), and the other representing a new genus of a “basal”
Rickettsiales
. According to newly characterized sequences and to a critical revision of recent literature, we propose a taxonomic reorganization of “traditional”
Rickettsiales
that we split into two orders:
Rickettsiales sensu stricto
and
Holosporales
ord. nov. This work represents a critical revision, including new records of a group of symbionts frequently occurring in protists and whose biodiversity is still largely underestimated.