Severe lung infection and septicemia caused by Paludibacterium purpuratum---a case report and evaluation of bacterial traits

Paludibacterium species are gram-stain negative rods, facultatively anaerobic, and have been isolated from wetland soil. Clinical infection caused by this genus is rarely reported. We reported an 84-year-old woman with chronic renal disease and hypertension acquired P. purpuratum lung infection and septicemia in southern Taiwan.

Genomic insights into the ecological role and evolution of a novel Thermoplasmata order, “ Candidatus Sysuiplasmatales”

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation and evolution of novel archaeal lineages from a variety of extreme environments. We have utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (“ Candidatus Sysuiplasmatales”) within Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene based analyses revealed a narrow habitat range for these uncultured archaea limiting to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea which typically show obligately anaerobic metabolisms. Notably, “ Ca. Sysuiplasmatales” could conserve energy through degradation of fatty acids, amino acid metabolism and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike its closely related Methanomassiliicoccales and “ Ca. Gimiplasmatales”, “ Ca. Sysuiplasmatales” lack the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that “ Ca. Sysuiplasmatales” and its closely related Methanomassiliicoccales, “ Ca. Gimiplasmatales”, and the SG8-5 and the RBG-16-68-12 orders originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H 4 F Wood–Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. Importance A wide array of archaea populate Earth’s extreme environments thereby they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited considering the uncultured majority of archaeal diversity. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, namely “ Ca . Sysuiplasmatales”, within Thermoplasmata in the extremely acidic mine environments. “ Ca . Sysuiplasmatales” are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between “ Ca . Sysuiplasmatales” and its closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.

Pontibacillus sp. ALD_SL1 and Psychroflexus sp. ALD_RP9, two novel moderately halophilic bacteria isolated from sediment and water from the Aldabra Atoll, Seychelles

Pontibacillus sp. ALD_SL1 and Psychroflexus sp. ALD_RP9 are two novel bacterial isolates from mangrove sediment and a moderately hypersaline pool on the Aldabra Atoll, Seychelles. The isolates represent two novel species were characterised physiologically and genomically. Pontibacillus sp. ALD_SL1 is a facultatively anaerobic yellow, motile, rod-shaped Gram-positive, which grows optimally at a NaCl concentration of 11%, pH 7 and 28°C. It is the third facultatively anaerobic member of the genus Pontibacillus. The organism gains energy through the fermentation of pyruvate to acetate and ethanol under anaerobic conditions. The genome is the first among Pontibacillus that harbours a megaplasmid. Psychroflexus sp. ALD_RP9 is an aerobic heterotroph, which can generate energy by employing bacteriorhodopsins. It forms Gram-negative, orange, non-motile rods. The strain grows optimally at NaCl concentrations of 10%, pH 6.5–8 and 20°C. The Psychroflexus isolate tolerated pH conditions up to 10.5, which is the highest pH tolerance currently recorded for the genus. Psychroflexus sp. ALD_RP9 taxonomically belongs to the clade with the smallest genomes. Both isolates show extensive adaptations to their saline environments yet utilise different mechanisms to ensure survival.

Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology

Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.

Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota

ABSTRACT Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects. IMPORTANCE In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. The candidate phylum Sumerlaeota is widely distributed in various harsh environments. However, their physiology, adaptation mechanisms, and evolution remain elusive due to a lack of pure cultures and limited available genomes. Here, we used genomes from uncultivated members of Sumerlaeota to disclose why these taxa can thrive under diverse harsh conditions and how they evolved from a chemotrophic and facultatively anaerobic common ancestor. This study deeply explored the biology of Sumerlaeota and provided novel insights into their possible roles in global biogeochemical cycles, adaptation mechanisms, ecological significance, and evolutionary history.

Ferrimonas lipolytica sp. nov., a facultatively anaerobic bacterium isolated from seawater

A Gram-stain-negative, motile, facultatively anaerobic rod-shaped bacterium with a polar flagellum, designated strain S7T was isolated from seawater sample collected at Uljin marina, in the East Sea of the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain S7T was affiliated with members of genus Ferrimonas, showing the highest sequence similarities to the type strains Ferrimonas senticii P2S11T (95.7 %), Ferrimonas balearica PATT (95.7 %) and Ferrimonas pelagia CBA4601T (95.1 %). The genome was 4.13 Mbp with a DNA G+C content of 49.4 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between S7T and F. senticii P2S11T and F. balearica PATT yielded ANI values of 71.9 and 70.7 %, and dDDH values of 15.1 and 13.9 %, respectively. The genome of S7T was predicted to encode triacylglycerol lipase, phospholipase A1/A2 and lysophospholipase as well as esterase involved in lipolytic processes. Growth was observed at 8–31 °C (optimum 27 °C), at pH 7–9 (optimum pH 7), and with 1–6 % NaCl (optimum 2 %). The respiratory quinones were MK-7 and Q-7 and the major fatty acids (>10 %) were C16 : 0, C16 : 1ω9c, C17 : 1ω8c, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, and three unidentified lipids. On the basis of the results of this polyphasic analysis, it was determined that the strain represents a novel species of the genus Ferrimonas , for which the name Ferrimonas lipolytica sp. nov. is proposed. The type strain is S7T (=KCTC 72490T=JCM 33793T).

Complete Genome Sequence of Paludibaculum fermentans P105T, a Facultatively Anaerobic Acidobacterium Capable of Dissimilatory Fe(III) Reduction

ABSTRACT Paludibaculum fermentans P105T is a facultatively anaerobic heterotroph of the phylum Acidobacteria which is capable of dissimilatory Fe(III) reduction. This bacterium is a common inhabitant of wetlands and groundwater bodies. The finished genome of strain P105T is 9.53 Mb in size and contains multiple genes coding for membrane-bound multiheme cytochromes.

Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5–10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22T reduced nitrate to nitrite. Major cellular fatty acids were C15 : 1 ω6c (13.6 %), C17 : 0 (11.9 %), anteiso-C15 : 0 (10.6 %) and iso-C15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes . The closest relative of strain MeG22T was Sunxiuqinia faeciviva strain JAM-BA0302T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22T (=NBRC 112896T=DSM 106262T).

Microbiota and Its Antibiotic Susceptibility in Diabetic Foot Infections: Observations From Polish Nonmetropolitan Hospital, 2015-2016

In current clinical practice, in case of symptoms-based suspicion of diabetic foot infection, immediate empiric antibiotic therapy is recommended. Prevailing guidelines do not provide region-specific therapy schemes. To validate existing recommendations, there is an urgent need for a report on diabetic foot infection microbiota patterns in Central Europe. This study aimed to describe diabetic foot infections microbiota and its antibiotic susceptibility in Poland. We conducted a single-center descriptive study at the General Surgery Department, Siedlce Hospital, Poland. Data for all patients diagnosed with diabetic foot infection between January 1, 2015, and December 31, 2016, and corresponding antimicrobial susceptibility tests were extracted. A total of 54 patients were included in the study, with a total of 102 microbiological samples. Among 81 positive samples, 77.1% of the isolated bacteria were Gram-negative. A total of 93.4% of the isolates were facultatively anaerobic bacteria. No obligatory anaerobic bacteria and no yeasts were isolated. Facultatively anaerobic, Gram-negative bacteria, mainly Proteus spp and Escherichia coli, were the most common organisms cultured in diabetic foot infections. This study suggests that the currently implemented treatment recommendations might not be adequate in Poland.