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The question of whether there is or was life on Mars has been one of the most pivotal since Schiaparellis' telescopic observations of the red planet. With the advent of the space age, this question can be addressed directly by exploring the surface of Mars and by bringing samples to Earth for analysis. The latter, however, is not free of problems. Life can be found virtually everywhere on Earth. Hence the potential for contaminating the Mars samples and compromising their scientific integrity is not negligible. Conversely, if life is present in samples from Mars, this may represent a potential source of extraterrestrial biological contamination for Earth. A range of measures and policies, collectively termed 'planetary protection', are employed to minimise risks and thereby prevent undesirable consequences for the terrestrial biosphere. This report documents discussions and conclusions from a workshop held in 2012, which followed a public conference focused on current capabilities for performing life-detection studies on Mars samples. The workshop focused on the evaluation of Mars samples that would maximise scientific productivity and inform decision making in the context of planetary protection. Workshop participants developed a strong consensus that the same measurements could be employed to effectively inform both science and planetary protection, when applied in the context of two competing hypotheses: 1) that there is no detectable life in the samples; or 2) that there is martian life in the samples. Participants then outlined a sequence for sample processing and defined analytical methods that would test these hypotheses. They also identified critical developments to enable the analysis of samples from Mars. © 2014 The Committee on Space Research (COSPAR).

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. © 2009 Macmillan Publishers Limited. All rights reserved.

The application of PCR primers specific for the plasmid DNA sequences of incompatibility (Inc) groups shows that IncQ and IncP DNA sequences are present in soil and manure slurry while IncN and IncW sequences are present mainly in manure samples. The method offers a good technique for identifying Inc-containing plasmids in nonculturable and culturable bacteria. However, the primers identify only those sequences that are highly similar to their reference sequences. The DNA of plasmids classified on the basis on conventional methods may differ from that of the reference sequences.

K. Althoff and colleagues' study of the phylogenetic position of prokaryotic associates of the marine sponge Halichondria panicea isolated from different marine sites by comparing sequences of PCR fragments with published 16S rDNA entries by the search programs BLAST, FASTA and RDP is interesting. This is because 16S rDNA sequences may offer important insights into the natural relationships among prokaryotic species. The highly conservative primary structure and the rich secondary structure permit unambiguous alignment and fast determination of misidentified nucleotides.

Reviews the report by Althoff in 1998 that analyzed the phylogenetic position of prokaryotic associates of the marine sponge Halichondria panicea. Details on the result of the study conducted by Althoff; Inapplicability of the clone sequences for quantification and qualification of prokaryotic taxa.

We present a full genome sequence for the thermophilic denitrifier Geobacillus thermodenitrificans subsp. calidus DSM 22629 T (3,408,575 bp, 48.94% GC). This genome includes 3,615 predicted genes, including those needed to reduce nitrate to nitrogen gas. This organism and genome sequence provide valuable resources for future phylogenetic, genomic, and biotechnological research., Competing Interests: The authors declare no conflict of interest.

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences., Competing Interests: The authors declare no competing financial interests., (© 2022 The Authors.)

Four aerobic bacteria with bacteriolytic capabilities were isolated from the brackish water site Strait Uzynaral of Lake Balkhash in Kazakhstan. The morphology and physiology of the bacterial isolates have subsequently been analyzed. Using matrix assisted laser desorption ionization-time of flight mass spectrum and partial 16S rRNA gene sequence analyses, three of the isolates have been identified as Pseudomonas veronii and one as Paenibacillus apiarius . We determined the capability of both species to lyse pre-grown cells of the Gram-negative strains Pseudomonas putida SBUG 24 and Escherichia coli SBUG 13 as well as the Gram-positive strains Micrococcus luteus SBUG 16 and Arthrobacter citreus SBUG 321 on solid media. The bacteriolysis process was analyzed by creating growth curves and electron micrographs of co-cultures with the bacteriolytic isolates and the lysis sensitive strain Arthrobacter citreus SBUG 321 in nutrient-poor liquid media. One metabolite of Paenibacillus apiarius was isolated and structurally characterized by various chemical structure determination methods. It is a novel antibiotic substance.

A bacterial strain, Gram staining negative, aerobic, long rod, motile bacterium with flagellum, designated strain YIM 98829 T , was isolated from the Aiding Lake in Xinjiang province, North-West China. The isolate produced oval subterminal endospores in swollen sporangia. The predominant menaquinone was MK-7. The cell wall peptidoglycan contained ornithine, serine, aspartic acid, glutamic acid, and alanine, while diaminopimelic acid could not be detected. The major whole-cell sugars contained xylose, glucose, galactose, and mannose. Diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid, and two unidentified aminophospholipids were part of the polar lipid profile. Iso-C 15:0 and anteiso-C 15:0 were the major fatty acids. The DNA G + C content of the type strain was 38.0 mol%. Phylogenetic analysis indicated that the isolate belongs to the genus Alkalibacillus. However, it differed from its closest relatives, A. haloalkaliphilus DSM 5271 T (97.04%), A. filiformis 4AG T (96.99%), and A. silvisoli BM2 T (96.95%) in some physiological characteristics. DNA-DNA hybridization result indicated low levels of relatedness between strain YIM 98829 T and A. haloalkaliphilus JCM 12303 T (16.9%). On the basis of physiological, phenotypic, and chemotaxonomic data, strain YIM 98829 T represents a novel species of genus Alkalibacillus, for which the name Alkalibacillus aidingensis sp. nov. is proposed. The type strain is YIM 98829 T (= NBRC 114103 T  = CGMCC 1.17260 T  = DSM 112470 T )., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300 T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7-8 and with 0.5-2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys-l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H 4 ) and contained minor amounts of MK-8(H 2 ), MK-8(H 6 ) and MK-9(H 4 ). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C 15 : 0 , iso-C 14 : 0 ) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae , order Micrococcales ) as a sister taxon to the previously described species Haloactinobacterium glacieicola , sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300 T (=DSM 108350 T =CIP 111667 T ) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae , i.e. the genera Haloactinobacterium and Ruania . Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12 T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12 T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12 T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12 T was anteiso C 15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C 20 : 4 ω6,9,12,16c) was present in strain B12 T and Kineococcus glutinatus YIM 75677 T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12 T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae , including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12 T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12 T . Multi-locus sequence and whole genome sequence analyses confirmed that B12 T clades with other Kineococcus species. Average nucleotide identity of strain B12 T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae . Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12 T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12 T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12 T in order Kineosporiales , confirming that strain B12 T is a novel member of family Kineosporiaceae . Based on these analyses and other genome characteristics, strain B12 T is assigned to a novel species within the genus Kineococcus , and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12 T (=FJII-L1-CM-PAB2 T ; NRRL B-65556 T , DSM 110506 T )., (Copyright © 2020 Mhatre, Singh, Wood, Parker, Pukall, Verbarg, Tindall, Neumann-Schaal and Venkateswaran.)