Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava

Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs

The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.

Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain

From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100^T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100^T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.

Bacterial dynamics of sugarcane silage in the tropics

The objective of this study was to evaluate changes in the bacterial community in sugarcane silage, in distinct soil types along the storage period. We depicted the bacterial community associated with sugarcane, before and after ensiling, through a massive sequencing of the gene 16S rRNA using MiSeq platform. The ensilage process shifted the composition of the bacterial community from the heterofermentative lactic acid bacteria Leuconostoc to bacteria belonging to the genera Acinetobacter, Ralstonia and Novosphingobium. However, this shift did not convey statically significant differences in alfa diversity metrics. In addition, similarity percentage analysis showed that the bacterial Operational Taxonomic Units that were primarily responsible for the observed differences were Leuconostoc, Pseudomonas, Acinetobacter, Ralstonia, Fructobacillus, Novosphingobium, Lactobacillus, Burkholderia and Clostridium sensu stricto 1. The storage period was the most important factor responsible for changes in the bacterial community of silages. Results confirmed that the type of soil did not influence the dissimilarity found among samples.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium

Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.

Microbial compositions and metabolic interactions in one- and two-phase partitioning airlift bioreactors treating a complex VOC mixture

Engineered microbial ecosystems in bioscrubbers for the treatment of volatile organic compounds (VOCs) have been complicated by complex VOC mixtures from various industrial emissions. Microbial associations with VOC removal performance of the bioscrubbers are still not definitive. Here, one- and two-phase partitioning airlift bioreactors were used for the treatment of a complex VOC mixture. Microbial characteristics in both bioreactors were uncovered by high-throughput metagenomics sequencing. Results showed that dominant species with specialized VOC biodegradability were mainly responsible for high removal efficiency of relative individual VOC. Competitive enzyme inhibitions among the VOC mixture were closely related to the deterioration of removal performance for individual VOC. Relative to the mass transfer resistance, the specialized biodegrading functions of microbial inoculations and enzymatic interactions among individual VOC biodegradation also must be carefully evaluated to optimize the treatment of complex VOC mixtures in bioreactors.

Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.

Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water

A mesophilic bacterium appearing as curved rod-shaped cells was isolated from Lake Michigan water. It exhibited highest similarities with Sediminibacterium ginsengisoli DCY13T (94.4 %); Sediminibacterium salmoneum NJ-44T (93.6 %) and Hydrotalea flava CCUG 51397 T (93.1 %) while similarities with other recognized species were <92.0 %. The primary polar lipid was phosphatidylethanolamine, with moderate amounts of two unidentified glycolipids, three unknown polar lipids, one unknown aminophospholipid and one aminolipid. The primary respiratory quinone was MK-7 and sym-homospermidine was the primary polyamine. The major cellular fatty acids were iso-C15 : 1G, iso-C15 : 0, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, with moderate amounts of iso-C16 : 0. The presence of glycolipids differentiated the novel strains from related genera. The DNA mol% G+C content of the type strain MU-2T was 45.2. Results for other phenotypic and molecular analyses indicated that strain MU-2T is a representative of a novel genus and species for which the name Vibrionimonas magnilacihabitans is proposed. The type strain is MU-2T ( = NRRL B-59231 = DSM 22423).

Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus

A light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 °C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes , exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5T is considered to represent a novel species of a new genus in the family Chitinophagaceae , for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5T ( = CCTCC AB 2013017T = KCTC 32316T). An emended description of Flavihumibacter petaseus is also proposed.

Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae

Two isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family Chitinophagaceae . Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of Filimonas lacunae is provided.

High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods

Two hydrothermal springs (AI: 51 °C, pH 3; AIV: 92 °C, pH 8) were analysed to determine prokaryotic community composition. Using pyrosequencing, 93,576 partial 16S rRNA gene sequences amplified with V2/V3-specific primers for Bacteria and Archaea were investigated and compared to 16S rRNA gene sequences from direct metagenome sequencing without prior amplification. The results were evaluated by fluorescence in situ hybridization (FISH). While in site AIV Bacteria and Archaea were detected in similar relative abundances (Bacteria 40 %, Archaea 35 %), the acidic spring AI was dominated by Bacteria (68 %). In spring AIV the combination of 16S rRNA gene sequence analysis and FISH revealed high abundance (>50 %) of heterotrophic bacterial genera like Caldicellulosiruptor, Dictyoglomus, and Fervidobacterium. In addition, chemolithoautotrophic Aquificales were detected in the bacterial community with Sulfurihydrogenibium being the dominant genus. Regarding Archaea, only Crenarchaeota, were detected, dominated by the family Desulfurococcaceae (>50 %). In addition, Thermoproteaceae made up almost 25 %. In the acidic spring (AI) prokaryotic diversity was lower than in the hot, slightly alkaline spring AIV. The bacterial community of site AI was dominated by organisms related to the chemolithoautotrophic genus Acidithiobacillus (43 %), to the heterotrophic Acidicaldus (38 %) and to Anoxybacillus (7.8 %). This study reveals differences in the relative abundance of heterotrophic versus autotrophic microorganisms as compared to other hydrothermal habitats. Furthermore, it shows how different methods to analyse prokaryotic communities in complex ecosystems can complement each other to obtain an in-depth picture of the taxonomic composition and diversity within these hydrothermal springs.

Cecembia calidifontis sp. nov., isolated from a hot spring runoff, and emended description of the genus Cecembia

Two red-pigmented isolates, designated RQ-33(T) and TU-13, were recovered from hot spring runoffs on the Island of São Miguel in the Azores, Portugal. These organisms have an optimum growth temperature of approximately 45 °C and an optimum pH for growth between 7.5 and 8.5. Based on 16S rRNA gene sequence analysis, the novel isolates were most closely related to the type strain of Cecembia lonarensis at 96.4 % pairwise similarity. Cells of the two isolates were non-motile, rod-shaped, Gram-stain-negative, strictly aerobic, and oxidase- and catalase-positive. The major fatty acids were iso-C15 : 0 and C15 : 0, phosphatidylethanolamine was the major polar lipid, and menaquinone 7 was the major respiratory quinone. Based on phylogenetic analyses, and physiological and biochemical characteristics, these isolates from the Azores represent a novel species of the genus Cecembia for which the name Cecembia calidifontis is proposed with strain RQ-33(T) ( = DSM 21411(T) = LMG 24596(T)) as the type strain. The description of the genus Cecembia is also emended.