Martha E Trujillo

University of Salamanca · Department of Microbiology and Genetics

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and event...

The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has tra...

Two novel Micromonospora strains, STR1-7 T and STR1S-6 T , were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora . They grew from 20 to 37 °C, from pH...

A non-motile, novel actinobacterial strain, Kera-3T, which is a gram-positive, aerobic, rod-shaped bacterium, was isolated from human keratinocytes on 1/10 diluted R2A agar. Whole-cell hydrolysis of amino acids revealed the presence of meso-DAP, alanine, and glutamic acid. The predominant menaquinone was MK-9 (H8), whereas the primary fatty acids w...

Background The misuse of antibiotics in the last decade led to the quick emergence of antibiotic resistance among pathogenic microorganisms. It has become a serious health problem that motivates researchers to explore new antimicrobial compounds. Micromonospora is one of the most important producers of commercially successful secondary bioactive me...

Ca.tel.li.glo'bo.si.spo'ra. L. fem. dim. n. catella , small chain; L. masc. adj. globosus , spherical; Gr. fem. n. spora , a seed and in biology a spore; N.L. fem. n. Catelliglobosispora , small chain and spherical spores (organism forming). Actinomycetota / Actinomycetes / Micromonosporales / Micromonosporaceae / Catelliglobosispora Gram‐stain‐pos...

The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names ‘validly published’ under that code in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Here, it is reiterat...

Six actinobacterial strains isolated from diverse legume tissues collected in various locations in Spain were characterized to determine their taxonomic status. Using 16S rRNA gene sequencing, the strains were primarily identified as members of the genus Micromonospora with more than 99 % similarity. Digital DNA–DNA hybridization values and average...

A non-motile, novel actinobacterial strain, designated Kera-3 T , was isolated on 1/10 diluted R2A agar from human keratinocytes. Strain Kera-3 T was Gram-stain-positive, aerobic and rod-shaped. The whole-cell hydrolysis of amino acids contained meso-DAP, alanine, and glutamic acids. The main menaquinone was MK-9 (H8). The major fatty acids were C...

Five novel species from healthy plants and other substrates are described. These are Paenibacillus glycinicola sp. nov. from Glycine max in Iowa, United States; Paenibacillus triticicola sp. nov. from Triticum aestivum in Australia, Allium cepa in Texas, garden soil in Wisconsin, cow's milk in New York state, Panicum virgatum in Michigan, sweet sor...

The taxonomic status of two Gordonia strains, designated BEN371 and CON9T, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of Gordonia species and three authenticated Gordonia amarae strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences sh...

Klugiella (Klu.gi.el'la. N.L. fem. n. Klugiella named after Michael J. Klug, an American entomologist/microbiologist who, along with S. Kotarski, first described the microbial community of Tipula abdominalis larval gut, from which strain 44C3 T was isolated). Actinomycetota / Actinomycetia / Micrococcales / Microbacteriaceae / Klugiella Gram‐stain...

Understanding plant-microbe interactions with the possibility to modulate the plant’s microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed...

A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus Agromyces. The type strain with the highest pairwise similarity was Agromyces marinus H23-8T (97.3%). The genome...

An alkaliphilic actinobacterium, designated VN6-2 T , was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2 T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2 T exhibited a 16S rRNA gene sequence similarity o...

Two novel Pseudomonas species associated with healthy plants and other habitats are described from the United States. They are Pseudomonas zeiradicis strain PI116 from corn in Missouri, compost from Massachusetts, urban soil from Iowa and water of Lake Erie; and Pseudomonas soyae strain JL117 from soybean in Indiana and Wisconsin, and soil in Wyomi...

Ha.ma.da.e'a. N.L. fem. n. Hamadaea of Hamada, named after Masa Hamada, the Japanese microbiologist who made a tremendous contribution to actinomycete research. Actinobacteria / Actinomycetia / Micromonosporales / Micromonosporaceae / Hamadaea Gram-stain-positive, aerobic, and nonmotile actinobacteria. Vegetative hyphae are produced but not aerial...

Ja.tro.phi.ha'bi.tans. N.L. fem. n. Jatropha scientific name of a botanical genus; L. pres. part. habitans inhabiting; N.L. part. adj. used as a masc. n. Jatrophihabitans inhabitant of Jatropha. Actinobacteria / Actinomycetia / Jatrophihabitantales / Jatrophihabitantaceae / Jatrophihabitans Gram-stain-positive, nonmotile, and nonsporulated rods. Ae...

An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues incl...

There arefewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardised publication, most typically a ‘single strain species descriptio...

Schu.man.nel'la. N.L. fem. dim. n. Schumannella, named after Peter Schumann, a German microbiologist, who contributed to the taxonomy of actinobacteria. Actinobacteria / Actinomycetia / Micrococcales / Microbacteriaceae / Schumannella Aerobic, nonmotile, and non-spore-forming actinobacteria that produce single, straight, and rod-shaped cells that a...

Ad.ler.creut'zi.a. N.L. fem. n. Adlercreutzia, named after H. Adlercreutz (Emeritus Professor, University of Helsinki, Finland), for his contributions to research on the effects of phytoestrogens on human health. Actinobacteria / Coriobacteriia / Eggerthellales / Eggerthellaceae / Adlercreutzia Gram-stain-positive, non-spore-forming, and nonmotile...

Three novel Pseudomonas species associated with healthy plants are described from the United States. They are Pseudomonas arenae sp. nov. from soybean in Missouri and Phragmites sp. in New Jersey; Pseudomonas glycinis sp. nov. from Vaccinium macrocarpon fruit in Massachusetts, groundwater in Tennessee and soybean in Indiana; and Pseudomonas harudin...

Three novel Pseudomonas species associated with healthy plants are described from the United States. They are Pseudomonas arenae sp. nov. from soybean in Missouri and Phragmites sp. in New Jersey; Pseudomonas glycinis sp. nov. from Vaccinium macrocarpon fruit in Massachusetts, groundwater in Tennessee and soybean in Indiana; and Pseudomonas harudin...

Four novel bacterial species collected from healthy tissues of corn, rice and soybean plants in the United States are described. These include Cellulomonas zeae sp. nov. isolated from corn in Indiana; Lelliottia zeae sp. nov. from corn in Indiana and rice in Arkansas; Paraburkholderia zeae sp. nov. isolated from corn in Iowa; and Sphingomonas zeige...

Homoserinimonas (Ho.mo.se.ri.ni.mo'nas. N.L. neut. n. homoserinum, homoserine; L. fem. n. monas, a unit, monad; N.L. fem. n. Homoserinimonas, homoserine monad, referring to the presence of homoserine in the cell wall). Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Homoserinimonas Aerobic and non‐spore‐forming actinobacterium...

The International Journal of Systematic and Evolutionary Microbiology (IJSEM) will move to ‘true continuous publication’ during the first months of 2021 to modernize the workflow and align it with the current online-only nature of the journal. In the new format, articles will be cited using an article number rather than page numbering. The article...

Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and minera...

Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here we used DNA metabarcoding data from litter and mineral...

Two morphologically similar halophilic strains, named USBA 874 and USBA 960T, were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. Both isolates had non-spore-forming, Gram-stain-negative and motile cells that grew aerobically. The strains grew optimally at 30 °C, pH 7.0 and with 25 % NaCl (w/...

Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus Salinispora and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized Salinispora species. Comparative genomic analy...

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code...

Heavy metal pollution in the environment is an increasing problem due to natural and anthropogenic activities. The use of bacteria for bioremediation of soils contaminated with heavy metals has gained a lot of attention as it can be considered effective, economic and environmentally sustainable. In this work, we investigated the capacity of endophy...

The genus Micromonospora has been found in nodules of several legumes and some new species of this genus were isolated from these plant organs. In this study we analysed the taxonomic diversity of Micromonospora strains isolated from alfalfa nodules in Spain and Australia on the basis of three phylogenetic markers, the rrs and gyrB genes and 16S-23...

The accompanying article 'Candidatus List No. 1: Lists of names of prokaryotic Candidatus taxa' can be found here: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003789.

Blas.to.coc'cus. Gr. masc. n. blastos bud, shoot; N.L. masc. n. coccus (from Gr. masc. n. kokkos grain, seed) coccus; N.L. masc. n. Blastococcus budding coccus. Actinobacteria / Actinobacteria / Geodermatophilales / Geodermatophilaceae / Blastococcus Gram‐stain‐positive; coccoid; occurs singly, in pairs, or in tetrads. Often reproducing by budding...

Au.ra.ti.coc'cus. L. masc. adj. auratus golden; N.L. masc. n. coccus (from Gr. masc. n. kokkos a grain, seed) a coccus; N.L. masc. n. Auraticoccus golden coccus. Actinobacteria / Actinobacteria / Propionibacteriales / Propionibacteriaceae / Auraticoccus Strictly aerobic, nonmotile, nonspore forming actinobacterium. Gram‐stain positive. Colonies are...

Spor.ich'thy.a. Gr. fem. n. spora seed (and in biology, a spore); Gr. masc. n. ichthys fish; N.L. fem. n. Sporichthya an organism with fish‐like spores. Actinobacteria / Actinobacteria / Frankiales / Sporichthyaceae / Sporichthya Aerobic or facultatively anaerobic actinobacteria. Cells are Gram‐stain‐variable, with young cells being Gram‐stain‐nega...

Spor.ich.thy.a'les. (N.L. fem. n. Sporichthya, type genus of the order; ‐ales, ending to denote an order; N.L. fem. pl. n. Sporichthyales, the Sporichthya order). Actinobacteria / Actinobacteria / Sporichthyales Soil‐inhabiting actinobacteria with a unique morphology. Short aerial mycelium forms rod‐shaped to coccoid spores that may develop polar f...

Spo.ro.tri.cha.ce'ae. N.L. fem. n. Sporichthya type genus of the family; suff. ‐aceae ending to denote a family; N.L. fem. pl. n. Sporichthyaceae the Sporichthya family. Actinobacteria / Actinobacteria / Frankiales / Sporichthyaceae Group of microorganisms with a unique and complex morphology. Aerobic or facultatively anaerobic. Gram‐stain‐variable...

A consortium of highly degrading microorganisms was used in a an integrated bioaugmentation/electrocoagulation process for treating olive mill wastewater. The system was investigated for treating 1m3 d-1, at a pilot scale, for two years; hydraulic loading rate and organic loading rate was 2880 l m-2 d-1 and 37930 g COD m-2 d-1, respectively. Averag...

Recently a number of queries were received about the ways in which requests for validation of names of taxa effectively published in journals other than the IJSEM are approved or denied and about the criteria used by the List Editors of the journal when deciding whether or not a validation request can be approved. As this process may be unclear to...

During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T, S2903, and...

A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the...

Number of orthologous genes that conform the pan genome, core genome and singletons of Micromonospora saelicesensis (Group 1) and Micromonospora noduli (Group II). In parenthesis, values expressed as percentages based on an average genome of 6531 genes for M. saelicesensis and 6540 genes for M. noduli.

Pair-wise OGRI values for ANI, OrthoANI and dDDH between M. saelicesensis (Group I) and M. noduli (Group II) strains.

List of genes used in core-genome phylogenomic analysis based on UBCG (Na et al., 2018).

(A) Venn diagram showing the number of orthologous genes clusters that integrate the core and disposable genomes, and singletons of all strains in Group I (Micromonospora saelicesensis). (B) Venn diagram showing the number of orthologous gene clusters that integrate the core genome and disposable genomes, and singletons of all strains in Group II (...

Pan- and Core genome development plot of Micromonospora noduli and Micromonospora saelicesensis strains. The orange and blue lines show the progression in the pan- and core genomes as more genomes are added.

Predicted phenotypes vs. experimental phenotypic data based on 19 carbon source substrates. In silico prediction negative, phenotype not expressed (purple); in silico prediction negative (genes not found), phenotype expressed (red); in silico prediction positive, phenotype not expressed (light green) and in silico prediction positive, phenotype exp...

Genome sequence accession numbers of strains used in this work.

BIOLOG phenotypic profiles of M. saelicesensis and M. noduli strains. +, positive; –, negative; c, conflicting.

Differential phenotypic characteristics between M. saelicesensis and M. noduli as reported by Carro and colleagues (Carro et al., 2016). +, Positive; –, Negative; w, Weak.

Carbon source substrates tested at different times using the same laboratory conditions. +, positive; –, negative; w, weak.

Glaciibacter (Gla.ci.i.bac'ter. L. n. glacies ice; N.L. masc. n. bacter rod; N.L. masc. n. Glaciibacter a rod of the ice). Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Glaciibacter Gram stain positive, aerobic, non‐spore‐forming actinobacterium. Motile by a single polar flagellum. Colonies on TSA are white, round, smooth, a...

The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged...

A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broa...

A novel actinobacterial strain, designated EPI-7T, was isolated on R2A agar from human skin (keratinocytes) and subjected to a taxonomic study using a polyphasic approach. Strain EPI-7Tshowed a Gram-positive reaction, was non-motile, non-spore-forming, and cells had a rod-shape. Colonies were round, convex and pale yellow. Phylogenetic analysis bas...

As an addendum to the earlier proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes (Oren et al., Int J Syst Evol Microbiol 2015;65:4284-4287) we propose the suffix -ota to denote phyla, replacing the somewhat awkward -aeota. We therefore present a new draft modified version of Rule 8 of the International C...

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea pr...

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for...

The discovery that the actinobacterium Micromonospora inhabits nitrogen-fixing nodules raised questions as to its potential ecological role. The capacity of two Micromonospora strains to infect legumes other than their original host, Lupinus angustifolius, was investigated using Medicago and Trifolium as test plants. Compatible rhizobial strains we...

Two actinobacterial isolates, strains SG15(T) and SGB14(T), were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consisten...

Eleven actinobacterial strains were isolated from a rock sample collected in the Atacama Desert. Molecular typing by BOX-PCR divided the strains into three clusters and showed that, although very similar, they were not clones. Three strains, ATK01, ATK03T and ATK17, each representing one of the defined BOX clusters, were chosen for further characte...

Gryl.lo.tal.pi'co.la. N.L. n. Gryllotalpa scientific name of a genus of insects; L. suff. ‐ cola (from L. masc. or fem. n. incola ) inhabitant, dweller; N. L. masc. n. Gryllotalpicola Grylllotalpa ‐dweller, referring to the isolation of strains from the gut of the African mole cricket, Gryllotalpa africana . Actinobacteria / Actinobacteria / Microc...

Na.a'si.a. N.L. fem. n. Naasia derived from the abbreviation NAAS, for the National Academy of Agricultural Science, where taxonomic studies of this taxon were conducted. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Naasia Gram‐stain positive, aerobic , and nonsporulating actinobacterium. Colonies on R2A agar are round, opa...

Ho.mo.se.ri.ni.bac'ter. N.L. neut. n. homoserinum homoserine; N.L. masc. n. bacter , a rod; N.L. masc. n. Homoserinibacter [homoserine rod] refers to the presence of Homoserine in the cell wall. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Homoserinibacter Gram‐stain positive, aerobic , and nonsporulating actinobacterium. C...

Ca.ni.bac'ter. L. n. canis dog; N.L. masc. n. bacter rod; N.L. masc. n. Canibacter rod of the dog. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Canibacter Gram‐stain positive, facultatively anaerobic , nonsporulating, and nonmotile actinobacterium . Colonies are circular and grayish‐white. Cells are rod shaped and frequentl...

Di.a.mi.no.bu.ty.ri.ci.bac'ter. N.L. n. acidum diaminobutyricum , DAB; N.L. masc. n. bacter , a rod; N.L. masc. n. Diaminobutyricibacter , a rod with DAB‐containing peptidoglycan. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Diaminobutyricibacter Gram‐stain positive, aerobic , and nonsporulating actinobacterium. Colonies on...

Ru.da.i.bac'ter. N.L. n. RuDA , acronym for Rural Development Administration; N.L. masc. n. bacter , a rod; N.L. masc. n. Rudaibacter , a rod named after RDA. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Rudaibacter Gram‐stain positive, aerobic , and nonsporulating actinobacterium. Colonies are yellow to deep yellow with ag...

Com.pos.ti.mo'nas. N.L. n. compostum compost; L. fem. n. monas a unit, monad; N.L. fem. n. Compostimonas a bacterium isolated from compost. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Compostimonas Gram‐stain positive, aerobic, nonmotile actinobacterium. Colonies are white round and convex. Cells are short rods and nonspor...

Three actinobacterial strains were isolated from roots of the salt-marsh plant Halimione portulacoides collected in Ria de Aveiro, Portugal. Molecular typing using ERIC-PCR fingerprinting showed the strains to be highly similar. Phylogenetic analyses based on the 16S rRNA gene sequence and MLSA using gyrB, rpoB, recA and ppk and 16S rRNA genes sequ...

A diversity study on the presence of Micromonospora strains in Pisum sativum nodules collected from Cañizal (Spain) has put on evidence the high number of isolates that might represent new species. In the present work, we have characterized three of these isolates: GUI23T, GUI43T and GUI63T. Phenotypic and genotypic analyses confirmed that all stra...