Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used

Strategies for describing myxozoan pathogens, dreadful fish diseases in aquaculture

Myxozoans are obligate endoparasites, cosmopolitan in distribution with both vertebrate and invertebrate hosts. Their myxospores consist of shell valves, polar capsules with coiled polar tubules that are extrudible, and infective amoeboid germs. Myxozoan parasites are most abundant, and due to their increasing number in recent years, they can pose an emerging threat to the fish industry worldwide. Hence, the immediate need is to devise a strategy to understand and detect parasites and parasitism. They may proliferate to different organs with the advancement of infection. This all warrants the development/devising of strategies and results of integrative studies in order to identify these dreadful parasites and resolve taxonomic issues. Different methods whether classical methods including gross morphology or advanced methods such as electron microscopy (SEM, TEM, STEM), Confocal laser scanning microscopy (CLSM), histopathological studies, site preference, host and tissue specificity, a molecular approach using new markers can be clubbed for identification because these parasites are hidden and are difficult to recognize. This group was earlier classified only on the basis of myxospores morphology, but due to the high structural variability of this group advanced methods and approaches have to be implied which can minimize the problems in assigning new species.

Single nucleotide polymorphisms within exon four of the prolactin gene and their effect on milk traits in cattle populations of Ethiopia

Bovine prolactin (PRL) gene is essential for the initiation and maintenance of lactation and exerts multiple effects on mammary alveoli to promote the synthesis and secretion of major components of milk. The objectives of this study were to identify mutations in PRL gene and to evaluate the mutations as potential markers of milk performance traits in cattle populations of Ethiopia. For this purpose, genomic DNA from whole blood was extracted through salting out procedure from 87 animals of five cattle populations of Ethiopia. Accordingly, three single nucleotide polymorphisms (SNPs) were identified of which one SNP g.8323T > A showed missense mutation while the other two SNPs revealed silent mutations. FST values showed statistically significant genetic differentiation among the studied populations. Intermediate polymorphic information content was noted for most SNPs, which indicates the presence of sufficient genetic variation at this locus. Two SNPs showed heterozygote deficiency as a result of positive FIS values. Only g.8398A > G SNP have statistically significant (p < 0.05) effect on average daily milk yield, fat and solid not fat percentage in all studied cattle populations. Therefore, g.8398A > G SNP identified in this study influences cattle milk production and may be used as possible candidate SNP for marker-assisted selection programs in cattle populations of Ethiopia.

Monitoring the Spread of Grapevine Viruses in Vineyards of Contrasting Agronomic Practices: A Metagenomic Investigation

This study investigated the transmission of grapevine viruses, specifically grapevine red blotch virus (GRBV) and grapevine Pinot gris virus (GPGV), in vineyards in Niagara Region, Ontario, Canada. Forty sentinel vines that were confirmed free of GRBV and GPGV by both high-throughput sequencing (HTS) and endpoint polymerase chain reaction (PCR) were introduced to two vineyards (one organic and one conventional) that were heavily infected with both GRBV and GPGV. Four months post-introduction, the sentinel vines were relocated to a phytotron. The HTS results from 15 months post-introduction revealed a widespread infection of GPGV among the sentinel vines but did not detect any GRBV. The GPGV infection rate of sentinel vines in the organic vineyard (13/18) was higher than in the conventional vineyard (1/19). The possibility of an alternative viral reservoir was assessed by testing the most abundant plants in between rows (Medicago sativa, Trifolium repens, Cirsium arvense and Taraxacum officinale), perennial plants in border areas (Fraxinus americana, Ulmus americana, Rhamnus cathartica) and wild grape (unknown Vitis sp.). The HTS result showed that cover crops and perennial plants did not harbor any grapevine viruses, while 4/5 wild grapes tested positive for GPGV but not GRBV. A pairwise sequence identity analysis revealed high similarities between the GPGV isolates found in the established vines on the vineyard and the newly contracted GPGV isolates in the sentinel vines, implicating a recent transmission event. This work provides novel insights into the spread of grapevine viruses in Niagara Region and is also the first direct proof of the spread of GPGV in natural vineyard conditions in North America.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance

Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.

Cryobacterium zhongshanensis sp. nov., an actinobacterium isolated from Antarctic soil

A Gram-staining-positive, heterotrophic, non-spore-forming, non-motile, rod-shaped, strain ZS14-85^T belonging to the genus Cryobacterium was isolated from soil in Antarctica. Growth was observed in the presence of 0-2% (w/v) NaCl, at pH 7.0-9.0 (optimum, pH 7.0) and 4-30 ℃ (optimum, 20 ℃). Phylogenetic analysis showed that strain ZS14-85^T formed a lineage in the genus Cryobacterium. The digital DNA-DNA hybridization (dDDH) values between strain ZS14-85^T and its close relatives Cryobacterium psychrotolerans CGMCC 1.5382^T, Cryobacterium soli MCCC 1K03549^T and Cryobacterium breve NBRC 113800^T were 22.5, 22.3 and 22.2%, respectively. Orthologous Average Nucleotide Identity (OrthoANI) scores between strain ZS14-85^T and C. psychrotolerans CGMCC 1.5382^T, C. breve NBRC 113800^T and C. soli MCCC 1K03549^T were 78.7, 78.1 and 77.7%, respectively. The polar lipids of strain ZS14-85^T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unidentified glycolipid (GL) and two unidentified lipids (L). The major fatty acids were anteiso-C_15:0 (60.7%), iso-C_16:0 (17.0%) and anteiso-C_17:0 (15.2%). MK-10, MK-11 and MK-9 were the predominant respiratory menaquinones. Based on phenotypic, phylogenetic and genotypic data, a novel species, Cryobacterium zhongshanensis sp. nov. is proposed. The type strain is ZS14-85^T (= CCTCC AB 2019396^T = KCTC 49384^T).

Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment

A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

MOTIVATION

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the coronavirus disease 2019 (COVID-19) pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic.

RESULTS

Here, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. matOptimize is currently helping refine on a daily basis possibly the largest-ever phylogenetic tree, containing millions of SARS-CoV-2 sequences.

AVAILABILITY AND IMPLEMENTATION

The matOptimize code is freely available as part of the UShER package (https://github.com/yatisht/usher) and can also be installed via bioconda (https://bioconda.github.io/recipes/usher/README.html). All scripts we used to perform the experiments in this manuscript are available at https://github.com/yceh/matOptimize-experiments.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Characterization of the rare microbiome of rice paddy soil from arsenic contaminated hotspot of West Bengal and their interrelation with arsenic and other geochemical parameters

Rare microbial taxa [bacterial and archaeal operational taxonomic units (OTUs) with mean relative abundance ≤ 0.001%] were critical for ecosystem function, yet, their identity and function remained incompletely understood, particularly in arsenic (As) contaminated rice soils. In the present study we have characterized the rare populations of the As-contaminated rice soil microbiomes from West Bengal (India) in terms of their identity, interaction and potential function. Major proportion of the OTUs (73% of total 38,289 OTUs) was represented by rare microbial taxa (henceforth mentioned as rare taxa), which covered 4.5-15.7% of the different communities. Taxonomic assignment of the rare taxa showed their affiliation to members of Gamma-, Alpha-, Delta- Proteobacteria, Actinobacteria, and Acidobacteria. SO₄^2-, NO₃^-, NH₄⁺and pH significantly impacted the distribution of rare taxa. Rare taxa positively correlated with As were found to be more frequent in relatively high As soil while the rare taxa negatively correlated with As were found to be more frequent in relatively low As soil. Co-occurrence-network analysis indicated that rare taxa whose abundance were correlated strongly (R > 0.8) with As also had strong association (R > 0.8) with PO₄^2-, NO₃^-, and NH₄⁺. Correlation analysis indicated that the rare taxa were likely to involved in two major guilds one, involved in N-metabolism and the second involved in As/Fe as well as other metabolisms. Role of the rare taxa in denitrification and dissimilatory NO₃^- reduction (DNRA), As biotransformation, S-, H-, C- and Fe-, metabolism was highlighted from 16S rRNA gene-based predictive analysis. Phylogenetic analysis of rare taxa indicated signatures of inhabitant rice soil microorganisms having significant roles in nitrogen (N) cycle and As-Fe metabolism. This study provided critical insights into the taxonomic identity, metabolic potentials and importance of the rare taxa in As biotransformation and biogeochemical cycling of essential nutrients in As-impacted rice soils.

Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support

Confidence measures of branch reliability play an important role in phylogenetics as these measures allow to identify trees or parts of a tree that are well supported by the data and thus adequate to serve as basis for evolutionary inference of biological systems. Unreliable branch relationships in phylogenetic analyses are of concern because of their potential to represent incorrect relationships of interest among more reliable branch relationships. The site-concordance factor implemented in the IQ-TREE package is a recently introduced heuristic solution to the problem of identifying unreliable branch relationships on the basis of quartets. We test the performance of the site-concordance measure with simple examples based on simulated data and designed to study its behaviour in branch support estimates related to different degrees of branch length heterogeneities among a ten sequence tree. Our results show that in particular in cases of relationships with heterogeneous branch lengths site-concordance measures may be misleading. We therefore argue that the maximum parsimony optimality criterion currently used by the site-concordance measure may sometimes be poorly suited to evaluate branch support and that the scores reported by the site-concordance factor should not be considered as reliable.

Alteromonas oceanisediminis sp. nov., isolated from deep-sea sediment

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated strain SM 2104^T, was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM 2104^T grew at 10-37 °C (optimum at 25 °C), and with 1.0-9.0% (w/v, optimum with 2-4%) NaCl. It hydrolyzed starch, tween 80 and gelatin but did not reduced nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM 2104^T was affiliated with the genus Alteromonas, sharing the highest 16S rRNA gene sequence similarities with type strains of Alteromonas flava (97.5%) and Alteromonas facilis (97.4%) and forming a distinct clade together with the two Alteromonas species. The digital DNA-DNA hybridization and average nucleotide identity values between strain SM 2104 ^T and type strains of Alteromonas flava and Alteromonas facilis were below 14.5%, and 71.0%, respectively. The major fatty acids of strain SM 2104^T were summed feature 3 (C_16:1ω6c/C_16:1ω7c), C_16:0 and summed feature 8 (C_18:1ω7c/C_18:1ω6c). The major polar lipids of strain SM 2104^T were phosphatidylethanolamine and phosphatidylglycerol and the only respiratory quinone of strain SM 2104^T was ubiquinone-8. The genomic DNA G + C content of strain SM 2104^T was 48.0%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic analyses presented in this study, strain SM 2104^T is considered to represent a novel species within the genus Alteromonas, for which the name Alteromonas oceansediminis sp. nov. is proposed. The type strain is SM 2104^T (= CCTCC AB 2021121^T = KCTC 82867^T).

Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation

The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.

Kangiella shandongensis sp. nov., a novel species isolated from saltern in Yantai, China

A Gram-stain-negative, wheat, rod-shaped, non-motile, non-spore forming, and facultatively anaerobic bacterium strain, designated as PI^T, was isolated from saline silt samples collected in saltern in Yantai, Shandong, China. Growth was observed within the ranges 4-45 °C (optimally at 33 °C), pH 6.0-9.0 (optimally at pH 7.0) and 1.0-11.0% NaCl (optimally at 3.0%, w/v). Strain PI^T showed highest 16S rRNA gene sequence similarity to Kangiella sediminilitoris BB-Mw22^T (98.3%) and Kangiella taiwanensis KT1^T (98.3%). The major cellular fatty acids (> 10% of the total fatty acids) were iso-C_15:0 (52.7%) and summed featured 9 (iso-C_17:1ω9c/C_16:0 10-methyl, 11.8%). The major polar lipids identified were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylglycerol. The major respiratory isoprenoid quinone was Q-8. The G + C content of the genomic DNA was 45.8%. Average Nucleotide Identity values between whole genome sequences of strain PI^T and next related type strains supported the novel species status. Based on physiological, biochemical, chemotaxonomic characteristics and genomic analysis, strain PI^T is considered to represent a novel species within the genus Kangiella, for which the name Kangiella shandongensis sp. nov. is proposed. The type strain is PI^T (= KCTC 82509 ^T = MCCC 1K04352^T).

Lacisediminihabitans changchengi sp. nov., an actinobacterium isolated from Antarctic swamplands mud

A Gram-staining-positive, heterotrophic, non-spore-forming, non-motile, short rod-shaped, strain G11-30^T belonging to the genus Lacisediminihabitans was isolated from a swampland mud in Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on R2A agar media and formed no aerial mycelia and no diffusible pigments on any media tested. The chemotaxonomic results showed 2, 4-diaminobutyric acid (DAB) is the diagnostic diamino acid of the peptidoglycan. MK-10 was the predominant respiratory menaquinone. The major phospholipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentified lipid (L) and unidentified glycolipid (GL). The major fatty acids were anteiso-C15:0 (64.5%) and iso-C15:0 (18.7%). A phylogenetic tree based on 16S rRNA gene sequences showed that strain G11-30^T formed a lineage in the genus Lacisediminihabitans with the closest phylogenetic Lacisediminihabitans profunda CHu50b-6-2^T and Glaciihabitans tibetensis MP203^T (97.9%, 97.5% 16S rRNA gene sequence similarity). A phylogenomic tree based on genome sequence of G11-30^T, conferred by Type Strain Genome Server (TYGS), separated it from L. profunda CHu50b-6-2^T. Strain G11-30^T has a complete genome size of 2.59 Mb, with a G + C content of 66.2 mol%. The digital DNA-DNA hybridization (dDDH) score between strain G11-30^T and reference strains L. profunda CHu50b-6-2^T and G. tibetensis MP203^T were 20.1 and 20.3%, respectively. Concurrently, Average Nucleotide Identity (ANI) score between strain G11-30 ^T against. profunda CHu50b-6-2^T and G. tibetensis MP203^T were 76.2 and72.5%, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, Lacisediminihabitans changchengi sp. nov. is proposed. The type strain is G11-30^T (= CCTCC AA 2019080^T = KCTC49359^T).

Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle

A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PT^T, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PT^T were C_14 : 0, C_16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO₂ and H₂ also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PT^T (=CCUG 74180^T=ATCC TSD-219^T).

Isolation, fermentation, and formulation of entomopathogenic fungi virulent against adults of Diaphorina citri

BACKGROUND

Mycopesticides are important for integrated management of the Asian citrus psyllid, Diaphorina citri. However, there are few reports on the fermentation and formulation for mycopesticides with high virulence against D. citri.

RESULTS

From four different locations in South China, 12 fungal strains were isolated and classified into Beauveria bassiana (two isolates), Fusarium fujikuroi (five isolates), and Cordyceps javanica (five isolates) based on the phylogenetic analysis of ITS1-5.8S rDNA-ITS4 and morphology of colonies and conidia. Based on the highest initial virulence (86.52 ± 2.35%) and best growth characteristics, F-HY002-ACPHali was further optimized for biphasic fermentation (7.85 ± 2.62 × 10⁹  g^-1  dry substrate) with soybean meal + cottonseed flour (1:1) as the solid substrate and full light as the light/dark cycle. Furthermore, the oil-based conidial formulation was optimized with sesame oil as an effective carrier, which significantly enhanced conidial shelf life up to 16 weeks at 26 °C and 4 °C, thermo-stress (50 °C) and UV-B stress resistance, and virulence against adults of D. citri with increased mortalities and decreased LT₅₀ in comparison to that of unformulated conidia.

CONCLUSION

Our results not only provide a valuable native strain with high virulence against adults of D. citri, but also imply the soybean meal + cottonseed flour as valuable solid substrate, full-light exposure as environmental stimuli for solid-state fermentation, and the sesame oil as an effective carrier for the formulation of the C. javanica. These findings will facilitate the development of a potential mycopesticide for the biological control of Asian citrus psyllid.

Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra

Members within the family Rhodbacteraceae are morphologically and genetically highly diverse, and originate mostly from coastal marine environments. In this study, a novel species of this family, designated M0103^T, was isolated from the surface of a sea snail Littorina scabra. Strain M0103^T is Gram-stain-negative, halophilic, non-motile and non-Bacteriochlorophyll a-producing bacterium. Several phenotypic characteristics of the isolate were similar to other species within this family, such as the sole respiratory quinone Q-10 and major fatty acid components C_18 : 1  ω7c, C_18 : 0 and C_16 : 0. Strain M0103^T contains a diphosphatidylglycerol, a phosphatidylglycerol, a phosphatidylcholine, a phosphatidy ethanolamine, a phosphatidylinositol, five unidentified phospholipids and four unidentified polar lipids. Based on the 16S rRNA gene sequence analysis, this isolate showed the closest phylogenetic relationship with 'Palleronia pontilimi' GH1-23^T (95.1 %). Values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of genome sequences were of 70.1-76.4 % and 18.3-20.9 % between the isolate and 24 closely related type strains. Analysis the 4.0 Mb genome of strain M0103^T revealed several putative genes associated with cellular stress resistance, which may play protective roles for the isolate in the adaptation to a marine environment. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain M0103^T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Mesobaculum littorinae gen. nov., sp. nov. is proposed. The type strain is M0103^T (=MCCC 1K03619^T=KCTC 62358^T).

Ecology and population structure of some indigenous geese breeds and the impact of four GH and Pit-1 SNPs on their body weights

This study aims to determine the genetic correlation using nine microsatellite markers to reconstruct the history of some indigenous geese populations, along with the use of four single nucleotides polymorphisms (SNPs) to investigate their correlation with the geese body weight. Microsatellite markers are mainly used to provide updated information on changes in the population structure of geese breeds. The eight goose populations reported 24% private alleles specific for each population. Expected heterozygosity (He) ranged from 0.46 to 0.70. Three breeds were reported highly polymorphic. Inbreeding coefficient (Fis) revealed that three breeds were in a minimum level of extinction danger, while one breed was in a potential endangered situation. Phylogenetic tree, principal component analysis (PCA), and self-organizing map (SOM) were constructed using MATLAB to study the population distribution and relationship among these breeds. Four SNPs were detected, two SNPs at GH gene exon (C123T and C158T), and two SNPs at Pit-1 gene exons (G161A and T282G). Four SNP loci were reported to have a significant effect on geese body weight. They were CT genotype for C123T locus, TT genotype for C158T locus, GG genotype for G161A locus, and GG genotype for T282G locus.

Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar

A Gram-stain-positive, non-pigmented, coccus-shaped, facultatively anaerobic and α-hemolytic bacterium designated as INB8^T was isolated from a hypersaline marine water sample collected at the Inland Sea of Qatar. The isolate was able to grow at 25-40 °C (optimum, 30 °C), at pH 5-11 and with 2-8% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain INB8^T was placed within the family Aerococcaceae with the highest sequence similarity to Facklamia tabacinasalis CCUG 30090^T (99.5%), followed by Facklamia hominis CCUG 36813^T (93.9%), Facklamia sourekii Y17312^T (93.8%), Facklamia ignava CCUG 37419^T (93.6%), Facklamia miroungae CCUG 42728^T (93.5%), Suicoccus acidiformans ZY16052^T (93.5%), Facklamia languida CCUG 37842^T (93.2%), Ignavigranum ruoffiae (93.1%), and Dolosicoccus paucivorans DSM 15742^T (90.8%). Average nucleotide identity and digital DNA-DNA hybridization values between strain INB8^T and F. tabacinasalis CCUG 30090^T were determined to be 94.5% and 58.9% respectively, confirming strain INB8^T represents a novel species. The major fatty acids were C_14:0, C_16:0, C_18:0 and C_18:1 ω9c_. The G + C content of strain INB8^T determined from the genome was 36.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic information, it is proposed that Facklamia tabacinasalis should be reclassified as Ruoffia tabacinasalis, Facklamia ignava be reclassified as Falseniella ignava, and Facklamia sourekii be reclassified Hutsoniella sourekii. It is further proposed that strain INB8^T should be classified as a species of the genus Ruoffia for which the name Ruoffia halotolerans sp. nov. is proposed. The type strain is INB8^T (= LMG 30291^T = CCUG 70701^T = QCC/B60/17^T).

Elizabethkingia argenteiflava sp. nov., isolated from the pod of soybean, Glycine max

Soybean pods, separated and enclosed from the outside environment, are considered a suitable place to find new microbes. A Gram-stain-negative, aerobic bacterium, bacterial strain (YB22T) was isolated from the pod of Glycine max (soybean) collected from a rural area in Republic of Korea and characterized by using polyphasic taxonomy. Cells of the strain were rod-shaped (approximately 0.4-0.6 µm wide and 4.0-5.0 µm long), non-flagellated and formed silver-yellow colonies. Cells grew at 25-35 °C (optimum, 28-30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-2.0% NaCl (optimum, 0 % NaCl). 16S rRNA gene sequencing showed that strain YB22T was phylogenetically closest to the genus Elizabethkingia, and showed highest similarities to Elizabethkingia occulta G4070T (96.7 %), Elizabethkingia meningoseptica ATCC 13253T (96.7 %), Elizabethkingia miricola DSM 14571T (96.6 %), Elizabethkingia bruuniana G0146T (96.5 %), Elizabethkingia ursingii G4122T (96.4 %) and Elizabethkingia anophelis R26T (96.2 %). Average amino acid identity values between strain YB22T and other taxa in the genus Elizabethkingia were all above the threshold range of genus determination. Average nucleotide identity and digital DNA-DNA hybridization values between strain YB22T and other phylogenetic relatives were all found to be below the threshold range for species determination. The respiratory quinone of strain YB22T was menaquinone 6 (MK-6) and the predominant cellular fatty acids were iso-C15 : 0 (47.8 %) and iso-C17 : 0 3-OH (18.5 %). The major polar lipids were phosphatidylethanolamine, four unidentified aminolipids and three unidentified polar lipids. The phylogenetic analysis and physiological and biochemical data showed that strain YB22T should represent a novel species in the genus Elizabethkingia, for which the name Elizabethkingia argenteiflava sp. nov. is proposed. The type strain for this novel species is YB22T (=KCCM 43263T=JCM 32097T).

Natronorubrum halalkaliphilum sp. nov., a haloalkaliphilic archaeon isolated from soda lake in Inner Mongolia Autonomous Region, China

A haloalkaliphilic strain JWXQ-INN-674^T was isolated from the water sample of a soda lake in Inner Mongolia Autonomous Region, China. Cells of the strain were coccoid, motile, and strictly aerobic. The strain was able to grow in presence of 2.6-5.4 M NaCl (optimum concentration is 3.4 M) at 30-50 °C (optimum temperature is 42 °C) and pH 7-9.5 (optimum pH is 9.0). The 16S rRNA gene sequence of strain JWXQ-INN-674^T showed 95.3-96.6% similarity to members of the genus Natronorubrum of the family Natrialbaceae. The whole genome sequencing of strain JWXQ-INN-674^T revealed a genome size of 4.56 M bp and a DNA G + C content of 62.5 mol%. Genome relatedness of strain JWXQ-INN-674^T and other species in the genus Natronorubrum was analyzed by average nucleotide identity and digital DNA-DNA hybridization with the values of 76.8-90.6 and 23.1-39.3%, respectively. The strain possessed the polar lipids phosphatidylglycerol and methylated phosphatidylglycerol phosphate lipid. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of genus Natronorubrum, Natronorubrum halalkaliphilum sp. nov. (type strain JWXQ-INN-674^T = CGMCC 1.17283^T = JCM 34245^T).

Biodegradation of Unpretreated Low-Density Polyethylene (LDPE) by Stenotrophomonas sp. and Achromobacter sp., Isolated From Waste Dumpsite and Drilling Fluid

Exploring the catabolic repertoire of natural bacteria for biodegradation of plastics is one of the priority areas of biotechnology research. Low Density Polyethylene (LDPE) is recalcitrant and poses serious threats to our environment. The present study explored the LDPE biodegradation potential of aerobic bacteria enriched from municipal waste dumpsite and bentonite based drilling fluids from a deep subsurface drilling operation. Considerable bacterial growth coupled with significant weight loss of the LDPE beads (∼8%), change in pH to acidic condition and biofilm cell growth around the beads (CFU count 10⁵-10⁶/cm²) were noted for two samples (P and DF2). The enriched microbial consortia thus obtained displayed high (65-90%) cell surface hydrophobicity, confirming their potential toward LDPE adhesion as well as biofilm formation. Two LDPE degrading bacterial strains affiliated to Stenotrophomonas sp. and Achromobacter sp. were isolated as pure culture from P and DF2 enrichments. 16S rRNA gene sequences of these isolates indicated their taxonomic novelty. Further biodegradation studies provided strong evidence toward the LDPE metabolizing ability of these two organisms. Atomic Fore Microscopy (AFM) and Scanning Electron Microscopy (SEM) revealed considerable damage (in terms of formation of cracks, grooves, etc.) on the micrometric surface of the LDPE film. Analysis of the average roughness (Ra), root mean square roughness (Rq), average height (Rz), maximum peak height (Rp), and maximum valley depth (Rv) (nano-roughness parameters) through AFM indicated 2-3 fold increase in nano-roughness of the LDPE film. FTIR analysis suggested incorporation of alkoxy (1000-1090 cm^-1), acyl (1220 cm^-1), nitro (1500-1600 cm^-1), carbonyl (1720 cm^-1) groups into the carbon backbone, formation of N-O stretching (1360 cm^-1) and chain scission (905 cm^-1) in the microbially treated LDPEs. Increase in carbonyl index (15-20 fold), double bond index (1.5-2 fold) and terminal double bond index (30-40 fold) confirmed that biodegraded LDPEs had undergone oxidation, vinylene formation and chain scission. The data suggested that oxidation and dehydrogenation could be the key steps allowing formation of low molecular weight products suitable for their further mineralization by the test bacteria. The study highlighted LDPE degrading ability of natural bacteria and provided the opportunity for their development in plastic remediation process.

Genetic characterization of a Marek's disease virus strain isolated in Japan

Background

Marek’s disease virus (MDV) causes malignant lymphomas in chickens (Marek’s disease, MD). MD is currently controlled by vaccination; however, MDV strains have a tendency to develop increased virulence. Distinct diversity and point mutations are present in the Meq proteins, the oncoproteins of MDV, suggesting that changes in protein function induced by amino acid substitutions might affect MDV virulence. We previously reported that recent MDV isolates in Japan display distinct mutations in Meq proteins from those observed in traditional MDV isolates in Japan, but similar to those in MDV strains isolated from other countries.

Methods

To further investigate the genetic characteristics in Japanese field strains, we sequenced the whole genome of an MDV strain that was successfully isolated from a chicken with MD in Japan. A phylogenetic analysis of the meq gene was also performed.

Results

Phylogenetic analysis revealed that the Meq proteins in most of the Japanese isolates were similar to those of Chinese and European strains, and the genomic sequence of the Japanese strain was classified into the Eurasian cluster. Comparison of coding region sequences among the Japanese strain and MDV strains from other countries revealed that the genetic characteristics of the Japanese strain were similar to those of Chinese and European strains.

Conclusions

The MDV strains distributed in Asian and European countries including Japan seem to be genetically closer to each other than to MDV strains from North America. These findings indicate that the genetic diversities of MDV strains that emerged may have been dependent on the different vaccination-based control approaches.

On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.

Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis

We investigated the taxonomic relationships among Streptomyces diastaticus subsp. ardesiacus, Streptomyces diastaticus subsp. diastaticus, Streptomyces gougerotii and Streptomyces rutgersensis. The 16S rRNA gene sequence similarity between S. diastaticus subsp. ardesiacus and S. diastaticus subsp. diastaticus was 97.7 %, whereas S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis showed 100 % nucleotide sequence identity. In addition, S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis formed a single clade in the phylogenetic tree. Digital DNA-DNA relatedness between S. diastaticus subsp. diastaticus and S. diastaticus subsp. ardesiacus was only 22.8%, indicative of different species. In comparison, DNA-DNA relatedness values for S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that S. diastaticus subsp. ardesiacus should be classified as an independent species, Streptomyces ardesiacus sp. nov. The type strain is NBRC 13412^T (=ATCC 3315^T=CBS 713.72^T=DSM 40496^T=ISP 5496^T=JCM 4745^T=NBRC 3714^T=NRRL B-1241^T=RIA 1373^T). Our data also suggests that S. rutgersensis and S. gougerotii should be reclassified as later heterotypic synonyms of S. diastaticus.

Molecular and taxonomic characterization of arsenic (As) transforming Bacillus sp. strain IIIJ3-1 isolated from As-contaminated groundwater of Brahmaputra river basin, India

Background

Microbe-mediated redox transformation of arsenic (As) leading to its mobilization has become a serious environmental concern in various subsurface ecosystems especially within the alluvial aquifers. However, detailed taxonomic and eco-physiological attributes of indigenous bacteria from As impacted aquifer of Brahmaputra river basin has remained under-studied.

Results

A newly isolated As-resistant and -transforming facultative anaerobic bacterium IIIJ3–1 from As-contaminated groundwater of Jorhat, Assam was characterized. Near complete 16S rRNA gene sequence affiliated the strain IIIJ3–1 to the genus Bacillus and phylogenetically placed within members of B. cereus sensu lato group with B. cereus ATCC 14579(T) as its closest relative with a low DNA-DNA relatedness (49.9%). Presence of iC17:0, iC15:0 fatty acids and menaquinone 7 corroborated its affiliation with B. cereus group, but differential hydroxy-fatty acids, C18:2 and menaquinones 5 & 6 marked its distinctiveness. High As resistance [Maximum Tolerable Concentration = 10 mM As³⁺, 350 mM As⁵⁺], aerobic As³⁺ (5 mM) oxidation, and near complete dissimilatory reduction of As ⁵⁺ (1 mM) within 15 h of growth designated its physiological novelty. Besides O₂, cells were found to reduce As⁵⁺, Fe³⁺, SO₄²⁻, NO₃⁻, and Se⁶⁺ as alternate terminal electron acceptors (TEAs), sustaining its anaerobic growth. Lactate was the preferred carbon source for anaerobic growth of the bacterium with As⁵⁺ as TEA. Genes encoding As⁵⁺ respiratory reductase (arr A), As³⁺ oxidase (aioB), and As³⁺ efflux systems (ars B, acr3) were detected. All these As homeostasis genes showed their close phylogenetic lineages to Bacillus spp. Reduction in cell size following As exposure exhibited the strain’s morphological response to toxic As, while the formation of As-rich electron opaque dots as evident from SEM-EDX possibly indicated a sequestration based As resistance strategy of strain IIIJ3–1.

Conclusion

This is the first report on molecular, taxonomic, and ecophysiological characterization of a highly As resistant, As³⁺ oxidizing, and dissimilatory As⁵⁺ reducing Bacillus sp. IIIJ3–1 from As contaminated sites of Brahmaputra river basin. The strain’s ability to resist and transform As along with its capability to sequester As within the cells demonstrate its potential in designing bioremediation strategies for As contaminated groundwater and other ecosystems.

Francisella salimarina sp. nov., isolated from coastal seawater

Four strains (SYSU SYW-1^T, SYW-2, SYW-3 and XLW-1) were isolated from seawater near the shore in Guangdong Province, China. Cells were Gram-stain-negative, aerobic, non-motile and non-spore-forming. Growth was observed at a temperature range of 16-40 °C (optimum, 32 °C), a pH range of 4-8 (optimum, pH 7) and in the presence of up to 10 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified phospholipid. The respiratory quinone was ubiquinone 8 (UQ-8), and the predominant fatty acids were C_18 : 0 3-OH, C_10 : 0, C_14 : 0 and C_18 : 1ω9c. Comparison of 16S rRNA gene and genome sequences confirmed that these strains represented a novel member of the genus Francisella, with less than 98.8 % 16S rRNA gene sequence similarity and less than 95 % genomic average nucleotide identity to recognized Francisella species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree based on a concatenation of 28 protein marker sequences both indicated that the strains clustered with 'Francisella salina' TX07-7308 and 'Francisella marina' E95-16, but formed a distinct lineage group among the other members of the genus Francisella. The DNA G+C contents of the four strains were determined to be 32.9, 32.7, 32.9 and 32.9 %, respectively (genome). On the basis of phenotypic and genotypic features, the strains are considered to represent a novel species of the genus Francisella, for which the name Francisella salimarina sp. nov. is proposed. The type strain is SYSU SYW-1^T (=CGMCC 1.17031^T=NBRC 113781^T).

Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf

Strain B66^T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66^T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66^T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C_16 : 0, summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c/iso-C_15 : 0 2-OH and iso-C_15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66^T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66^T (=QCC B003/17^T=LMG 30288 ^T=CCUG 70703^T).

Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis

We investigated the taxonomic relationships among Streptomyces hygroscopicus subsp. glebosus , Streptomyces libani subsp. rufus and Streptomyces platensis . The three species formed a single clade in the phylogenetic trees based on 16S rRNA gene sequence and multilocus sequence analyses. Digital DNA–DNA hybridization using whole genome sequences suggested that S. hygroscopicus subsp. glebosus , S. libani subsp. rufus and S. platensis belong to the same genomospecies. Previously reported phenotypic data also supported this synonymy. Therefore, S. hygroscopicus subsp. glebosus and S. libani subsp. rufus should be reclassified as later heterotypic synonyms of S. platensis .

Transmission of Koala Retrovirus from Parent Koalas to a Joey in a Japanese Zoo

KoRV is unique among retroviruses in that one strain (KoRV-A) is undergoing endogenization, whereas the other main subtype (KoRV-B) and another subtype (KoRV-C) are reportedly exogenous strains. Its transmission and pathogenesis are of interest in the study of retroviruses and are crucial for any conservation strategy geared toward koala health. This study provides new evidence on the modes of KoRV transmission from parent koalas to their joey. We found vertical transmission of KoRV-A, confirming its endogenization, but with closer conservation between the joey and its sire than its dam (previous reports on joeys are rare but have postulated dam-to-joey vertical transmission). This is also the first report of a KoRV-B-negative joey from KoRV-B-positive parents, contrasting with the few previous reports of 100% transmission of KoRV-B from dams to joeys. Thus, the results in this study give some novel insights for the transmission mode of KoRV.

Koala retrovirus (KoRV) is of an interest to virologists due to its currently active endogenization into the koala (Phascolarctos cinereus) genome. Although KoRV has frequently been isolated in wild and captive koala populations, its pathogenesis and transmission remain to be fully characterized, and most previous research has concentrated on adult koalas rather than on joeys. Here, we characterized KoRV isolates obtained from a deceased male joey and its parents (animals reared in a Japanese zoo) to investigate KoRV transmission mode and pathogenesis. We sequenced the KoRV long terminal repeat (LTR) and envelope genes isolated from the joey and its parents and found KoRV-A and KoRV-C in genomic DNA from both the parents and the joey. Notably, both parents were also positive for KoRV-B, whereas the joey was KoRV-B negative, further confirming that KoRV-B is an exogenous strain. The KoRV LTR sequence of the joey was considerably closer to that of its sire than its dam. For further characterization, total KoRV, KoRV-A, KoRV-B, and KoRV-C proviral loads were quantified in peripheral blood mononuclear cells from the parents and in blood samples from the joey. Total KoRV, KoRV-A, and KoRV-C proviral loads were also quantified for different tissues (bone, liver, kidney, lung, spleen, heart, and muscle) from the joey, revealing differences suggestive of a distinct tissue tropism (highest total KoRV proviral load in the spleen and lowest in bone). The amount of KoRV-C in the parents was less than that in the joey. Our findings contribute to an improved understanding of KoRV pathogenesis and transmission mode and highlight useful areas for future research.

IMPORTANCE KoRV is unique among retroviruses in that one strain (KoRV-A) is undergoing endogenization, whereas the other main subtype (KoRV-B) and another subtype (KoRV-C) are reportedly exogenous strains. Its transmission and pathogenesis are of interest in the study of retroviruses and are crucial for any conservation strategy geared toward koala health. This study provides new evidence on the modes of KoRV transmission from parent koalas to their joey. We found vertical transmission of KoRV-A, confirming its endogenization, but with closer conservation between the joey and its sire than its dam (previous reports on joeys are rare but have postulated dam-to-joey vertical transmission). This is also the first report of a KoRV-B-negative joey from KoRV-B-positive parents, contrasting with the few previous reports of 100% transmission of KoRV-B from dams to joeys. Thus, the results in this study give some novel insights for the transmission mode of KoRV.

Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment

Three novel actinobacterial strains, designated as TPS16^T, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0-8 % (w/v) NaCl. Cell-wall hydrolysis showed the presence of meso-diaminopimelic acid. The strains were closely related to Marinactinospora thermotolerans SCSIO 00652^T (97.60 %) and Marinactinospora endophytica YIM 690053^T (96.87 %) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including gyrB, recA and rpoB genes further confirmed that strain TPS16^T represented a distinct branch within the family Nocardiopsaceae. The predominant menaquinones were MK-11(H₂), MK-10(H₂), MK-11(H₄) and MK-10(H₄), while the major fatty acids were found to be iso-C_16 : 0, anteiso-C_17 : 0, iso-C_15 : 0 and C_18 : 1ω9c. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, Marinitenerispora gen. nov., is proposed within the family Nocardiopsaceae based on polyphasic data and the type species is Marinitenerispora sediminis gen. nov., sp. nov. The type strain is TPS16^T (=DSM 46825^T=TBRC 5138^T).

Cellulomonas algicola sp. nov., an actinobacterium isolated from a freshwater alga

An actinomycete strain, TKZ-21^T, was isolated from a freshwater alga (Chetophoraceae) collected from the Takizawa River, Yamanashi, Japan, and examined using a polyphasic taxonomic approach. Cells were Gram-stain positive, aerobic, non-sporulating, motile, and coccoid or short rod-shaped. The strain grew in the presence of 0-4 % (w/v) NaCl, between pH 6-9.4, and over a temperature range of 15-40 °C, with optimum growth at 30 °C. The peptidoglycan type of strain TKZ-21^T was A4β, containing l-ornithine as diagnostic diamino acid and d-glutamic acid as the interpeptide bridge. The predominant menaquinone was MK-9(H₄). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, ninhydrin-positive glycolipid, and unidentified phospholipids. The major cellular fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0, and the DNA G+C content was 75.6 mol%. On the basis of 16S rRNA gene sequence analysis, strain TKZ-21^T was closely related to Cellulomonas fimi (98.5 % sequence similarity) and Cellulomonas biazotea (98.3 %). The genome orthoANI value between strain TKZ-21^T and C. biazotea and C. fimi were 84.7 and 84.2 %, respectively. On the basis of fatty acid and MALDI-TOF MS profile analysis, phylogenetic analyses, genomic analysis, and phenotypic data, it is proposed that the isolate be classified as a representative of a novel species of the genus Cellulomonas, with the name Cellulomonas algicola sp. nov. The type strain is TKZ-21^T (=NBRC 112905^T=TBRC 8129^T).

Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013

Enteroviruses (EVs) are among the most common viruses infecting humans worldwide but only a few Non-Polio Enterovirus (NPEV) isolates have been characterized in the Democratic Republic of Congo (DR Congo). Moreover, circulating vaccine-derived polioviruses (PVs) [cVDPVs] isolated during multiple outbreaks in DR Congo from 2004 to 2018 have been characterized so far only by the sequences of their VP1 capsid coding gene. This study was carried to i) investigate the circulation and genetic diversity of NPEV and polio vaccine isolates recovered from healthy children and Acute Flaccid Paralysis (AFP) patients, ii) evaluate the occurrence of genetic recombination among EVs belonging to the Enterovirus C species (including PVs) and iii) identify the virological factors favoring multiple emergences of cVDPVs in DR Congo. The biological material considered in this study included i) a collection of 91 Sabin-like PVs, 54 cVDPVs and 150 NPEVs isolated from AFP patients between 2008 and 2012 in DR Congo and iii) a collection of 330 stool specimens collected from healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. Studied virus isolates were sequenced in four distinct sub-genomic regions 5’-UTR, VP1, 2C^ATPase and 3D^pol. Resulting sequences were compared through comparative phylogenetic analyses. Virus isolation showed that 19.1% (63/330) healthy children were infected by EVs including 17.9% (59/330) of NPEVs and 1.2% (4/330) of type 3 Sabin-like PVs. Only one EV-C type, EV-C99 was identified among the NPEV collection from AFP patients whereas 27.5% of the 69 NPEV isolates typed in healthy children belonged to the EV-C species: CV-A13 (13/69), A20 (5/69) and A17 (1/69). Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences in at least one of the targeted non-structural regions of their genomes: 5’UTR, 2C^ATPase and 3D^pol. Some of these non-vaccine sequences of the recombinant cVDPVs were strikingly related to homologous sequences from co-circulating CV-A17 and A20 in the 2C^ATPase region as well as to those from co-circulating CV-A13, A17 and A20 in the 3D^pol region. This study provided the first evidence uncovering CV-A20 strains as major recombination partners of PVs. High quality AFP surveillance, sensitive environmental surveillance and efficient vaccination activities remain essential to ensure timely detection and efficient response to recombinant cVDPVs outbreaks in DR Congo. Such needs are valid for any epidemiological setting where high frequency and genetic diversity of Coxsackieviruses A13, A17 and A20 provide a conducive viral ecosystem for the emergence of virulent recombinant cVDPVs.

The strategy of the Global Polio Eradication Initiative is based on the surveillance of patients suffering from Acute Flaccid Paralysis (AFP) and mass vaccination with live-attenuated vaccine strains of polioviruses (PVs) in endemic areas. However, vaccine strains of PVs can circulate and replicate for a long time when the vaccine coverage of the population is low. Such prolonged circulation and replication of vaccine strains of PVs can result to the emergence of circulating vaccine-derived polioviruses [cVDPVs] that are as virulent as wild PVs. In this study, we performed the molecular characterization of a large collection of 377 virus isolates recovered from paralyzed patients between 2008 and 2012 in DR Congo and healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. We found that the genetic diversity of enteroviruses of the species Enterovirus C is more important than previously reported. Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences of the 2C ATPase and/or 3D polymerase coding genes acquired from co-circulating Coxsackieviruses A13, A17 and A20. Coxsackieviruses A20 strains were identified for the first time as major partners of genetic recombination with co-circulating live-attenuated polio vaccine strains.

Our findings highlight the need to reinforce and maintain high quality surveillance of PVs and efficient immunization activities in order to ensure early detection and control of emerging cVDPVs in all settings where high frequency and diversity of Coxsackieviruses A13, A17 and A20 have been documented.

Environmental variation shapes genetic variation in Bouteloua gracilis: Implications for restoration management of natural populations and cultivated varieties in the southwestern United States

With the increasing frequency of large-scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind-dispersed, perennial grass consisting of several cytotypes (2n = 2×-6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species' environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety-four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as "outliers," consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long-term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.

Phosphodiesterase EdpX1 Promotes Xanthomonas oryzae pv. oryzae Virulence, Exopolysaccharide Production, and Biofilm Formation

In Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, there are over 20 genes encoding GGDEF, EAL, and HD-GYP domains, which are potentially involved in the metabolism of second messenger c-di-GMP. In this study, we focused on the characterization of an EAL domain protein, EdpX1. Deletion of the edpX1 gene resulted in a 2-fold increase in the intracellular c-di-GMP levels, which were restored to the wild-type levels in the complemented ΔedpX1(pB-edpX1) strain, demonstrating that EdpX1 is an active phosphodiesterase (PDE) in X. oryzae pv. oryzae. In addition, colorimetric assays further confirmed the PDE activity of EdpX1 by showing that the E153A mutation at the EAL motif strongly reduced its activity. Virulence assays on the leaves of susceptible rice showed that the ΔedpX1 mutant was severely impaired in causing disease symptoms. In trans expression of wild-type edpX1, but not edpX1 ^E153A, was able to complement the weakened virulence phenotype. These results indicated that an active EAL domain is required for EdpX1 to regulate the virulence of X. oryzae pv. oryzae. We then demonstrated that the ΔedpX1 mutant was defective in secreting exopolysaccharide (EPS) and forming biofilms. The expression of edpX1 in the ΔedpX1 mutant, but not edpX1 ^E153A, restored the defective phenotypes to near-wild-type levels. In addition, we observed that EdpX1-green fluorescent protein (EdpX1-GFP) exhibited multiple subcellular localization foci, and this pattern was dependent on its transmembrane (TM) region, which did not seem to directly contribute to the regulatory function of EdpX1. Thus, we concluded that EdpX1 exhibits PDE activity to control c-di-GMP levels, and its EAL domain is necessary and sufficient for its regulation of virulence in X. oryzae pv. oryzae.IMPORTANCE Bacteria utilize c-di-GMP as a second messenger to regulate various biological functions. The synthesis and degradation of c-di-GMP are catalyzed by GGDEF domains and an EAL or HD-GYP domain, respectively. Multiple genes encoding these domains are often found in one bacterial strain. For example, in the genome of X. oryzae pv. oryzae PXO99^A, 26 genes encoding proteins containing these domains were identified. Therefore, to fully appreciate the complexity and specificity of c-di-GMP signaling in X. oryzae pv. oryzae, the enzymatic activities and regulatory functions of each GGDEF, EAL, and HD-GYP domain protein need to be elucidated. In this study, we showed that the EAL domain protein EdpX1 is a major PDE to regulate diverse virulence phenotypes through the c-di-GMP signaling pathway.

Big data analysis of human mitochondrial DNA substitution models: a regression approach

BACKGROUND

We study Phylotree, a comprehensive representation of the phylogeny of global human mitochondrial DNA (mtDNA) variations, to better understand the mtDNA substitution mechanism and its most influential factors. We consider a substitution model, where a set of genetic features may predict the rate at which mtDNA substitutions occur. To find an appropriate model, an exhaustive analysis on the effect of multiple factors on the substitution rate is performed through Negative Binomial and Poisson regressions. We examine three different inclusion options for each categorical factor: omission, inclusion as an explanatory variable, and by-value partitioning. The examined factors include genes, codon position, a CpG indicator, directionality, nucleotide, amino acid, codon, and context (neighboring nucleotides), in addition to other site based factors. Partitioning a model by a factor's value results in several sub-models (one for each value), where the likelihoods of the sub-models can be combined to form a score for the entire model. Eventually, the leading models are considered as viable candidates for explaining mtDNA substitution rates.

RESULTS

Initially, we introduce a novel clustering technique on genes, based on three similarity tests between pairs of genes, supporting previous results regarding gene functionalities in the mtDNA. These clusters are then used as a factor in our models. We present leading models for the protein coding genes, rRNA and tRNA genes and the control region, showing it is disadvantageous to separate the models of transitions/transversions, or synonymous/non-synonymous substitutions. We identify a context effect that cannot be attributed solely to protein level constraints or CpG pairs. For protein-coding genes, we show that the substitution model should be partitioned into sub-models according to the codon position and input codon; additionally we confirm that gene identity and cluster have no significant effect once the above factors are accounted for.

CONCLUSIONS

We leverage the large, high-confidence Phylotree mtDNA phylogeny to develop a new statistical approach. We model the substitution rates using regressions, allowing consideration of many factors simultaneously. This admits the use of model selection tools helping to identify the set of factors best explaining the mutational dynamics when considered in tandem.

PQ, a new program for phylogeny reconstruction

BACKGROUND

Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood.

RESULTS

We developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle. Being tested on natural sequences PQ improves upon the results of maximum parsimony and maximum likelihood. Working with alignments of 10 and 15 sequences, it also outperforms the FastME program, which is based on one of the distance-based principles. Among all tested programs PQ is proved to be the least susceptible to long branch attraction. FastME outperforms PQ when processing alignments of 45 sequences, however. We confirm a recent result that on natural sequences FastME outperforms maximum parsimony and maximum likelihood. At the same time, both PQ and FastME are inferior to maximum parsimony and maximum likelihood on simulated sequences. PQ is open source and available to the public via an online interface.

CONCLUSIONS

The software we developed offers an open-source alternative for phylogenetic reconstruction for relatively small sets of proteins and nucleic acids, with up to a few tens of sequences.

Molecular and eco-physiological characterization of arsenic (As)-transforming Achromobacter sp. KAs 3-5T from As-contaminated groundwater of West Bengal, India

Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3-5^T has been investigated in order to gain an insight into As-geomicrobiology in the contaminated groundwater. The bacterium is isolated from As-rich groundwater of West Bengal, India. Comparative 16S rRNA gene sequence phylogenetic analysis confirmed that the strain KAs 3-5^T is closely related to Achromobacter mucicolens LMG 26685^T (99.17%) and Achromobacter animicus LMG 26690^T (99.17%), thus affiliated to the genus Achromobacter. Strain KAs 3-5^T is nonflagellated, mesophilic, facultative anaerobe, having a broad metabolic repertoire of using various sugars, sugar-/fatty acids, hydrocarbons as principal carbon substrates, and O₂, NO₃^-, NO₂^-, and Fe³⁺ as terminal electron acceptors. Growth with hydrocarbons led to cellular aggregation and adherence of the cells to the hydrocarbon particles confirmed through electron microscopic observations. The strain KAs 3-5^T showed high As resistance (MIC of 5 mM for As³⁺, 25 mM for As⁵⁺) and reductive transformation of As⁵⁺ under aerobic conditions while utilizing both sugars and hydrocarbons. Molecular taxonomy specified a high genomic GC content (65.5 mol %), ubiquinone 8 (UQ-8) as respiratory quinone, spermidine as predominant polyamine in the bacterium. The differential presence of C_12:0, C_14:0 2-OH, C_18:1 ω7c, and C _14:0 iso 3-OH/ C_16:1 iso fatty acids, phosphatidylglycerol (PG), phosphatidylcholine (PC), two unknown phospholipid (PL1, PL2) as polar lipids, low DNA-DNA relatedness (33.0-41.0%) with the Achromobacter members, and unique metabolic capacities clearly indicated the distinct genomic and physiological properties of strain KAs 3-5^T among known species of the genus Achromobacter. These findings lead to improve our understanding on metabolic flexibility of bacteria residing in As-contaminated groundwater and As-bacteria interactions within oligotrophic aquifer system.

Taxonomy and physiology of Pseudoxanthomonas arseniciresistens sp. nov., an arsenate and nitrate-reducing novel gammaproteobacterium from arsenic contaminated groundwater, India

Reductive transformation of toxic arsenic (As) species by As reducing bacteria (AsRB) is a key process in As-biogeochemical-cycling within the subsurface aquifer environment. In this study, we have characterized a Gram-stain-negative, non-spore-forming, rod-shaped As reducing bacterium designated KAs 5-3^T, isolated from highly As-contaminated groundwater of India. Strain KAs 5-3^T displayed high 16S rRNA gene sequence similarity to the members of the genus Pseudoxanthomonas, with P. mexicana AMX 26B^T (99.25% similarity), P. japonensis 12-3^T (98.9 0%), P. putridarboris WD-12^T (98.02%), and P. indica P15^T (97.27%) as closest phylogenetic neighbours. DNA-DNA hybridization study unambiguously indicated that strain KAs 5-3^T represented a novel species that was separate from reference strains of P. mexicana AMX 26B^T (35.7%), P. japonensis 12-3^T (35.5%), P. suwonensis 4M1^T (35.5%), P. wuyuanensis XC21-2^T (35.0%), P. indica P15^T (32.5%), P. daejeonensis TR6-08^T (32.0%), and P. putridarboris WD12^T (22.1%). The DNA G+C content of strain KAs 5-3^T was 64.9 mol %. The predominant fatty acids were C_15:0 (37.4%), C_16:0 iso (12.6%), C_17:1 iso ω9c (10.5%), C_15:0 anteiso (9.5%), C_11:0 iso 3-OH (8.5%), and C_16:1 ω7c/ C_16:1 ω6c (7.5%). The major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, and two unknown phospholipids (PL1, PL2). Ubiquinone 8 (Q8) was the predominant respiratory quinone and spermidine was the major polyamine of the strain KAs 5-3^T. Cells of strain KAs 5-3^T showed the ability to use O₂, As⁵⁺, NO₃^-, NO₂^-, and Fe³⁺ as terminal electron acceptors as well as to reduce As⁵⁺ through the cytosolic process under aerobic incubations. Genes encoding arsenate reductase (arsC) for As-detoxification, nitrate- and nitrite reductase (narG and nirS) for denitrification were detected in the strain KAs 5-3^T. Based on taxonomic and physiological data, strain KAs 5-3^T is described as a new representative member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas arseniciresistens sp. nov. is proposed. The type strain is KAs 5-3^T (= LMG 29169^T = MTCC 12116^T = MCC 3121^T).

Streptosporangium minutum sp. nov., isolated from garden soil exposed to microwave radiation

The actinobacterium, strain M26^T, was isolated from garden soil that was pre-treated with microwave radiation. The soil sample was collected in Roodepoort, Gauteng Province, South Africa as part of an antibiotic-screening programme. The isolate produced branched vegetative mycelium with sporangiophores bearing small sporangia ranging from 3 to 6 μm in diameter. Rapid genus identification revealed that the isolate belongs to the genus Streptosporangium. To confirm this result, the strain was subjected to polyphasic taxonomic characterisation. Chemotaxonomic characteristics were as follows: meso-DAP in the peptidoglycan, the whole-cell hydrolysate yielded madurose, predominant menaquinones were MK9 (21%), MK9(H₂) (40%), MK9(H₄) (31%) and MK9(H₆) (3%); the polar lipid profile included an aminolipid, phosphoglycolipids, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine. In addition, the fatty acid profile showed the presence of C_16:0 (12.8%), C_17:1ω8c (14.2%), and 10-methyl-C_17:0 (15.8%). Furthermore, 16S rRNA gene sequence phylogenetic analysis showed that the strain is closely related to members of the genus Streptosporangium, which supports its classification within the family Streptosporangiaceae. Strain M26^T exhibited antibiosis against a range of pathogenic bacteria, including, but not limited to Acinetobacter baumannii ATCC 19606^T, Enterobacter cloacae subsp. cloacae ATCC BAA-1143, Enterococcus faecalis ATCC 51299 (vancomycin resistant), Escherichia coli ATCC 25922, Listeria monocytogenes ATCC 19111, Mycobacterium tuberculosis H37Rv^T, Pseudomonas aeruginosa ATCC 27853, Salmonella enterica subsp. arizonae ATCC 13314^T, and the methicillin-resistant Staphylococcus aureus subsp. aureus ATCC 33591 (MRSA). The name Streptosporangium minutum is proposed with the type strain M26^T (=LMG 28850^T =NRRL B-65295^T).

Morphological and Molecular Identification of the Causal Agent of Anthracnose Disease of Avocado in Kenya

Anthracnose disease of avocado contributes to a huge loss of avocado fruits due to postharvest rot in Kenya. The causal agent of this disease has not been clear but presumed to be Colletotrichum gloeosporioides as reported in other regions where avocado is grown. The fungus mainly infects fruits causing symptoms such as small blackish spots, "pepper spots," and black spots with raised margin which coalesce as infection progresses. Due to economic losses associated with the disease and emerging information of other species of fungi as causal agents of the disease, this study was aimed at identifying causal agent(s) of the disease. A total of 80 fungal isolates were collected from diseased avocado fruits in Murang'a County, the main avocado growing region in Kenya. Forty-six isolates were morphologically identified as Colletotrichum spp. based on their cultural characteristics, mainly whitish, greyish, and creamish colour and cottony/velvety mycelia on the top side of the culture and greyish cream with concentric zonation on the reverse side. Their spores were straight with rounded end and nonseptate. Thirty-four isolates were identified as Pestalotiopsis spp. based on their cultural characteristics: whitish grey mycelium with black fruiting structure on the upper side and greyish black one on the lower side and septate spores with 3-4 septa and 2 or 3 appendages at one end. Further molecular studies using ITS indicated Colletotrichum gloeosporioides, Colletotrichum boninense, and Pestalotiopsis microspora as the causal agents of anthracnose disease in avocado. However, with this being the first report, there is a need to conduct further studies to establish whether there is coinfection or any interaction thereof.

Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis

An antibiotic producing novel Planctomycete strain, designated JC280^T, was isolated from the surface of the plant Hydrilla verticillata collected from an alkaline lake (Buffalo lake), University of Hyderabad, Hyderabad, India. The morphological and chemotaxonomic properties of strain JC280^T were in agreement with the characteristics of the genus Planctopirus. The cell shape was spherical to ovoid and some were tear drop shaped. The cells were Gram-stain-negative divided by budding presenting stalks and rosette formation and were non-sporulating. Crateriform structures with a sub-polar flagellum were observed. Characteristic polyamines were putrescine and spermidine. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid (PL1), unidentified glycolipids (GL1-2), an unidentified aminophospholipid (APL), and an unidentified lipid (L3). Major (>10%) fatty acids were C_16:0, C_17:1ω8c, C_18:1ω9c, and summed feature-3. Major (88%) respiratory quinone was MK-6 with minor amount (12%) of MK-7. Strain JC280^T showed 99.7% 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776^T. To resolve their full taxonomic position, the genome sequence was obtained and compared with the available P. limnophila DSM 3776^T genome. The genome sequence of strain JC280^T was 5,750,243 bp in size with a total of 4490 protein-coding genes, 66 RNA genes, and 2 CRISPR repeats. Based on whole-genome statistics, ANI value, in silico DDH, diversity of secondary metabolite biosynthetic gene clusters, distinct physiological, biochemical and chemotaxonomic differences, strain JC280^T represents a new species in the genus Planctopirus, for which the name Planctopirus hydrillae sp. nov. is proposed. The type strain is JC280^T (=KCTC 42880^T = LMG 29153^T).

Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances

I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a cherry is a pair of adjacent leaves descending from the most recent common ancestor), and the other with two. When genetic distances are underestimated, the 3-cherry tree shape is favored with either the ME or FM criterion. When the genetic distances are overestimated, the ME criterion favors the 2-cherry tree, but the direction of bias with the FM criterion depends on whether negative branches are allowed, i.e. allowing negative branches favors the 3-cherry tree shape but disallowing negative branches favors the 2-cherry tree shape. The extent of the bias is explored by computer simulation of sequence evolution.

MySSP: Non-stationary evolutionary sequence simulation, including indels

MySSP is a new program for the simulation of DNA sequence evolution across a phylogenetic tree. Although many programs are available for sequence simulation, MySSP is unique in its inclusion of indels, flexibility in allowing for non-stationary patterns, and output of ancestral sequences. Some of these features can individually be found in existing programs, but have not all have been previously available in a single package.

Evolution of Proteins and Proteomes: A Phylogenetics Approach

The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics in particular has been gaining ground in the study of protein and proteome evolution. Nowadays, the use of phylogenetics is instrumental not only to infer the evolutionary relationships among species and their genome sequences, but also to reconstruct ancestral states of proteins and proteomes and hence trace the paths followed by evolution. Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role.

Streptomyces swartbergensis sp. nov., a novel tyrosinase and antibiotic producing actinobacterium

As part of an antibiotic screening program, an actinobacterium, strain HMC13^T, was isolated from soil collected from the banks of the Gamka River, Western Cape Province, South Africa. The isolate was found to produce branched mycelia that differentiated into spiral spore chains with spiny spores. 16S rRNA gene sequence analysis showed the strain to be closely related to Streptomyces caelestis NRRL 2418^T (99.72%) and Streptomyces azureus NBRC 12744^T (99.51%). Chemotaxonomic analyses confirmed the classification of the strain as a member of the genus Streptomyces: LL-DAP in the peptidoglycan, no diagnostic sugars in the whole cell sugar pattern, dominant menaquinones including MK9(H₈), MK9(H₆), and the polar lipids detected included phosphatidylethanolamine. The fatty acid profile revealed the presence of mostly branched, saturated fatty acids: iso-C_15:0 (14.4%), anteiso-C_15:0 (21.1%), iso-C_16:0 (16.8%), C_16:1ω7c/2-OH iso-C_15:0 (5.8%), C_16:0 (6.2%), iso-C_17:1ω9c (5.8%), iso-C_17:0 (5.9%), and anteiso-C_17:0 (9.6%). Strain HMC13^T is a tyrosinase producer and exhibits very strong antibiosis against Mycobacterium aurum A+ and Staphylococcus aureus subsp. aureus ATCC 33591 (methicillin resistant), while only weak activity was observed against Bacillus cereus ATCC 10876, Enterococcus faecium VanA (vancomycin resistant), Enterococcus faecalis ATCC 51299 (vancomycin resistant) and Candida tropicalis ATCC 750^T. Strain HMC13^T (= LMG 28849^T = NRRL B-65294^T) is proposed as the type strain of a new species, to be named Streptomyces swartbergensis sp. nov.

Structural characterization of a putative chitin synthase gene in Phytophthora spp. and analysis of its transcriptional activity during pathogenesis on potato and soybean plants

Although chitin is a major component of the fungal cell wall, in oomycetes (fungal-like organisms), this compound has only been found in very little amounts, mostly in the cell wall of members of the genera Achlya and Saprolegnia. In the oomycetes Phytophthora infestans and P. sojae the presence of chitin has not been demonstrated; however, the gene putatively encoding chitin synthase (CHS), the enzyme that synthesizes chitin, is present in their genomes. The evolutionary significance of the CHS gene in P. infestans and P. sojae genomes is not fully understood and, therefore, further studies are warranted. We have cloned and characterized the putative CHS genes from two Phytophthora spp. and multiple isolates of P. infestans and P. sojae and analyzed their phylogenetic relationships. We also conducted CHS inhibition assays and measured CHS transcriptional activity in Phytophthora spp. during infection of susceptible plants. Results of our investigations suggest that CHS contains all the motifs that are typical in CHS genes of fungal origin and is expressed, at least at the mRNA level, during in vitro and in planta growth. In infected tissues, the highest levels of expression occurred in the first 12 h post inoculation. In addition, results from our inhibition experiments appear to suggest that CHS activity is important for P. infestans normal vegetative growth. Because of the considerable variation in expression during infection when compared to basal expression observed in in vitro cultures of non-sporulating mycelium, we hypothesize that CHS may have a meaningful role in Phytophthora pathogenicity.

Herpetosiphon gulosus sp. nov., a filamentous predatory bacterium isolated from sandy soil and Herpetosiphon giganteus sp. nov., nom. rev

Three filamentous gliding bacteria from the German Collection of Microorganisms and Cell Cultures, Hp g11, Hp g471 and Hp g472, were subjected to a phylogenetic analysis. These organisms had previously been classified as members of the genus Herpetosiphon based on their growth physiology and morphology. However, a taxonomic assignment at the species level had not been carried out. Analysis of 16S rRNA sequences now confirmed the close relationship of strain Hp g472 to Herpetosiphon aurantiacus DSM 785T (98.6 % nucleotide identity) and Herpetosiphon geysericola DSM 7119T (97.7 %). The results of DNA-DNA hybridization experiments further implied that strain Hp g472 should be classified as a distinct species. The DNA G+C content of strain Hp g472 was 49.9 mol%. The major quinone was MK-10 and the predominant cellular fatty acids were C18 : 1, C16 : 1 and C16 : 0. Based on phenotypic, chemotaxonomic and phylogenetic data it was concluded that strain Hp g472 represents a novel species of the genus Herpetosiphon, for which the name Herpetosiphon gulosus sp. nov. is proposed. The type strain is Hp g472T (=DSM 52871T=NBRC 112829T). In contrast to Hp g472T, the strains Hp g11 and Hp g471 exhibited closest 16S rRNA gene sequence similarity (>99 %) with 'Herpetosiphon giganteus' Hp a2. The distinctive genotypic and phenotypic properties of the latter supported the revival of the name as Herpetosiphon giganteus (ex Reichenbach & Golecki, 1975) sp. nov., nom. rev. We propose the previously deposited reference strain DSM 589T=NBRC 112828T as the type strain.

Virgisporangium myanmarense sp. nov., a novel motile actinomycete isolated from an anthill soil in Myanmar

An actinomycete strain, designated MM04-1133^T, was isolated from an anthill soil sample collected in Bagan, Myanmar. To establish the taxonomic status of this strain, the isolate was subjected to a polyphasic approach. Strain MM04-1133^T was Gram-staining positive, aerobic, motile and formed long and narrow sporangia directly above the surface of the substrate mycelium. Whole-cell hydrolysates of the strain contained 3-OH-diaminopimelic acid, arabinose, glucose, galactose, mannose, rhamnose and xylose. The predominant menaquinones were MK-10(H₆) and MK-10(H₈). The major cellular fatty acids were iso-C_16:0 and anteiso-C_17:0. The diagnostic phospholipid was phosphatidylethanolamine. The G+C content of the DNA was 69.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MM04-1133^T clustered within the genus Virgisporangium, with the sequence exhibiting highest similarity (98.5% identity) with Virgisporangium ochraceum NBRC 16418^T. The strain grew in the presence of 0-1% (w/v) NaCl, at pH 5-8 and at 20-40 °C, with optimal growth at 30-37 °C. Based on phylogenetic analysis and chemotaxonomic and phenotypic data, we propose classifying this isolate as a novel species of the genus Virgisporangium, to be designated as Virgisporangium myanmarense sp. nov. The type strain is MM04-1133^T (=NBRC 112733^T=VTCC 910008^T).