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Systematic and Applied Microbiology

Dimitry Y Sorokin, Alexander G Elcheninov, Stepan V Toshchakov, Nicole J Bale, Jaap S Sinninghe Damsté, Tatiana V Khijniak, Ilya V Kublanov
No abstract text is available yet for this article.
August 1, 2019: Systematic and Applied Microbiology
Fei-Na Li, Qinpei Lu, Shui-Lin Liao, Tao Jin, Wenjun Li, Cheng-Hang Sun
Two novel strains, designated 11W25H-1T and 8H24J-4-2T , were isolated from surface-sterilized plant tissues collected from the Taklamakan Desert in the Xinjiang Uygur Autonomous Region, China. The strains were characterized by a polyphasic approach in order to clarify their taxonomic positions. They were Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped. The 16S rRNA gene sequences of the strains showed highest similarities with Labedella gwakjiensis KCTC 19176T (99.2% and 98.9%, respectively) and Labedella endophytica CPCC 203961T (98...
July 30, 2019: Systematic and Applied Microbiology
Yong Hua Li, Rui Wang, Xin Hua Sui, En Tao Wang, Xiao Xia Zhang, Chang Fu Tian, Wen Feng Chen, Wen Xin Chen
Nine slow-growing rhizobia isolated from effective nodules on peanut (Arachis hypogaea) were characterized to clarify the taxonomic status using a polyphasic approach. They were assigned to the genus Bradyrhizobium on the basis of 16S rRNA sequences. MLSA of concatenated glnII-recA-dnaK genes classified them into three species represented by CCBAU 53390T , CCBAU 51670T and CCBAU 51778T , which presented the closest similarity to B. guangxiense CCBAU 53363T , B. guangdongense CCBAU 51649T and B. manausense BR 3351T , B...
July 19, 2019: Systematic and Applied Microbiology
Omar Bouhnik, Salma ElFaik, Soufiane Alami, Chouhra Talbi, Hanane Lamin, Hanaa Abdelmoumen, Germán Tortosa Muñoz, Eulogio J Bedmar, Mustapha Missbah El Idrissi
The purpose of this work was to study the genetic diversity of the nodule-forming bacteria associated with native populations of Vachellia gummifera growing wild in Morocco. The nearly complete 16S rRNA gene sequences from three selected strains, following ARDRA and REP-PCR results, revealed they were members of the genus Ensifer and the sequencing of the housekeeping genes recA, gyrB, dnaK and rpoB, and their concatenated phylogenetic analysis, showed that the 3 strains belong to the species E. fredii. Based on the nodC and nodA phylogenies, the 3 strains clearly diverged from the type and other reference strains of E...
July 17, 2019: Systematic and Applied Microbiology
Xiaoman Xie, Nicolai Müller
Desulfatiglans anilini is a sulfate-reducing bacterium (SRB) capable of oxidizing aniline, although growth and aniline turnover rates are slow, making it difficult to analyze the metabolism of the strain. Therefore, this study was designed to investigate the effect of sulfide on growth of D. anilini cultures, in order to improve its growth and aniline turnover rates, and study the biochemical mechanisms of sulfide inhibition. Hydrogen sulfide was found to inhibit growth of D. anilini, regardless of whether the strain was grown with aniline or phenol, and complete inhibition was observed at 20mM hydrogen sulfide...
July 17, 2019: Systematic and Applied Microbiology
C Coimbra, R Branco, P V Morais
Tungsten (W) is a valuable element with considerable industrial and economic importance that belongs to the European Union list of critical metals with a high supply risk. Therefore, the development of effective and new methods for W recovery is essential to ensure a sustainable supply. In the present study, the Sulfitobacter dubius W transport system TupABC was explored in order to demonstrate both its functionality in Escherichia coli cells and to construct a bioaccumulator (EcotupW). The complete gene cluster tupBCA or partial gene cluster tupBC were cloned in an expression vector and transformed into E...
July 15, 2019: Systematic and Applied Microbiology
Insa Bakenhus, Bernd Wemheuer, Pinar Akyol, Helge-Ansgar Giebel, Leon Dlugosch, Rolf Daniel, Meinhard Simon
Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and amplicon sequencing of the total (16S rRNA gene) and potentially active (16S rRNA transcripts), community are the major state of the art approaches for assessing the composition of bacterial communities in marine pelagic and other ecosystems. However, CARD-FISH and amplicon sequencing methods have not yet been directly compared to assess the composition of bacterioplankton communities. Therefore, these approaches were used to study the composition of bacterial communities in two North Sea seawater mesocosm experiments supplemented with diatom-derived organic matter (OM)...
July 4, 2019: Systematic and Applied Microbiology
K Laroucau, F Vorimore, R Aaziz, L Solmonson, R C Hsia, P M Bavoil, P Fach, M Hölzer, A Wuenschmann, K Sachse
Chlamydiaceae are obligate intracellular bacterial pathogens for humans and animals. A recent study highlighted that a Chlamydiaceae intermediary between C. psittaci and C. abortus can infect hawks. Here, an isolate was obtained upon passage of cloacal and conjunctival sac material collected from a female hatch-year red-shouldered hawk (Buteo lineatus) in cultured cells. The diseased bird, one of 12 birds housed in a rehabilitation center, developed conjunctivitis and later died. Swabs from both sites tested positive for Chlamydia using the QuickVue Chlamydia test...
June 19, 2019: Systematic and Applied Microbiology
Jun-Lian Gao, Jing Xue, Hui Yan, Shuai Tong, Mohammad Sayyar Khan, Li-Wei Wang, Xiao-Jie Mao, Xiuhai Zhang, Jian-Guang Sun
Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273T and Pantoea rwandensis LMG 26275T , but on a separate branch...
June 7, 2019: Systematic and Applied Microbiology
Regina Rettenmaier, Carina Duerr, Klaus Neuhaus, Wolfgang Liebl, Vladimir V Zverlov
Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biological triplicates, revealed an average richness of 48 different OTU's with an average evenness of 0...
May 23, 2019: Systematic and Applied Microbiology
Lorena Jacqueline Gómez-Godínez, Selene Lizbeth Fernandez-Valverde, Julio Cesar Martinez Romero, Esperanza Martínez-Romero
Plant roots are inhabited by a large diversity of microbes, some of which are beneficial for the growth of plants and known as plant growth promoting rhizobacteria (PGPR). In this work, we designed a multispecies inoculum of PGPRs containing Rhizobium phaseoli, Sinorhizobium americanum and Azospirillum brasilense nitrogen-fixing strains and other plant-growth promoting bacteria such as Bacillus amyloliquefaciens and Methylobacterium extorquens. We evaluated the effect of this group of bacteria on the growth of one-month-old maize plants...
May 22, 2019: Systematic and Applied Microbiology
Vanesa Natalin Rocha Martin, Christophe Lacroix, Jiri Killer, Vera Bunesova, Evelyn Voney, Christian Braegger, Clarissa Schwab
The infant gut harbors a diverse microbial community consisting of several taxa whose persistence depends on adaptation to the ecosystem. In healthy breast-fed infants, the gut microbiota is dominated by Bifidobacterium spp.. Cutibacterium avidum is among the initial colonizers, however, the phylogenetic relationship of infant fecal isolates to isolates from other body sites, and C. avidum carbon utilization related to the infant gut ecosystem have been little investigated. In this study, we investigated the phylogenetic and phenotypic diversity of 28 C...
May 16, 2019: Systematic and Applied Microbiology
Despina Tsementzi, Luis M Rodriguez-R, Carlos A Ruiz-Perez, Alexandra Meziti, Janet K Hatt, Konstantinos Konstantinidis
The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis"...
May 6, 2019: Systematic and Applied Microbiology
Vahid Keshavarz-Tohid, Jordan Vacheron, Audrey Dubost, Claire Prigent-Combaret, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Yvan Moënne-Loccoz, Daniel Muller
Bacteria of the Pseudomonas putida group are studied for a large panel of properties ranging from plant growth promotion and bioremediation to pathogenicity. To date, most of the classification of individual pseudomonads from this group relies on 16S RNA gene analysis, which is insufficient for accurate taxonomic characterization within bacterial species complexes of the Pseudomonas putida group. Here, a collection of 20 of these bacteria, isolated from various soils, was assessed via multi-locus sequence analysis of rpoD, gyrB and rrs genes...
May 2, 2019: Systematic and Applied Microbiology
Soumaya Tounsi-Hammami, Christine Le Roux, Sana Dhane-Fitouri, Philippe De Lajudie, Robin Duponnois, Faysal Ben Jeddi
With a view to introducing white lupin (Lupinus albus L.) for cultivation in Tunisian calcareous soils, compatible indigenous rhizobia for nitrogen-fixing symbiosis were investigated and characterized. Two L. albus varieties, Mekna and Lumen, were used to trap rhizobia in soil samples collected from 56 sites with high active lime contents (0-49%). Nodulation occurred in only 15 soils. The local variety, Mekna, developed significantly more root nodules and had a trapping capacity in more soils than the imported variety Lumen...
April 13, 2019: Systematic and Applied Microbiology
Ana S Ramírez, Orestes M Vega-Orellana, Tomeu Viver, José B Poveda, Rubén S Rosales, Carlos G Poveda, Joachim Spergser, Michael P Szostak, Mª José Caballero, Lorenzo Ressel, Janet M Bradbury, Mª Mar Tavío, Smruthi Karthikeyan, Rudolf Amann, Konstantinos T Konstantinidis, Ramon Rossello-Mora
Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 °C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated...
April 12, 2019: Systematic and Applied Microbiology
Juanita R Avontuur, Marike Palmer, Chrizelle W Beukes, Wai Y Chan, Martin P A Coetzee, Jochen Blom, Tomasz Stępkowski, Nikos C Kyrpides, Tanja Woyke, Nicole Shapiro, William B Whitman, Stephanus N Venter, Emma T Steenkamp
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium...
April 4, 2019: Systematic and Applied Microbiology
Soufiane Alami, Hanane Lamin, Omar Bouhnik, Salma El Faik, Abdelkarim Filali-Maltouf, Hanaa Abdelmoumen, Eulogio J Bedmar, Mustapha Missbah El Idrissi
Astragalus algarbiensis is a wild herbaceous legume growing in Maamora, the most important cork oak forest in northern Africa. It is a plant of great importance as fodder in silvopastoral systems, and in the restoration of poor and degraded soils. The purpose of this study was to describe the biodiversity of rhizobia nodulating this plant and determine their identity. Out of 80 bacterial isolates, 56 strains isolated from root nodules of A. algarbiensis were characterized. ERIC-PCR fingerprinting grouped the strains in two main clusters containing 29 and 27 isolates, respectively, and the amplified ribosomal DNA restriction analysis (ARDRA) generated two different ribotypes...
March 25, 2019: Systematic and Applied Microbiology
María Camacho, Carlos Medina, Dulce Nombre Rodríguez-Navarro, Francisco Temprano Vera
Biodiversity studies of native Mesorhizobium spp. strains able to nodulate the annual herbaceous legume Biserrula pelecinus L. in soils from Southwest Spain have been carried out. One or two isolates per plant, 30 in total, were randomly selected for further characterization. There was no association between the presence of mesorhizobia nodulating-B. pelecinus and the chemical or textural properties of the soils. The isolates were tested for their symbiotic effectiveness on this forage legume under greenhouse conditions and characterized on the basis of physiological parameters: carbon source utilisation (API 50CH), 16S rRNA sequencing and ERIC-PCR, lipopolysaccharide, protein and plasmid profiles...
March 25, 2019: Systematic and Applied Microbiology
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