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17 pages, 2578 KiB

Open AccessArticle

Screening of GABA-Producing Lactic Acid Bacteria from Thai Fermented Foods and Probiotic Potential of Levilactobacillus brevis F064A for GABA-Fermented Mulberry Juice Production

by Jirapat Kanklai, Tasneem Chemama Somwong, Patthanasak Rungsirivanich and Narumol Thongwai

Microorganisms 2021, 9(1), 33; https://doi.org/10.3390/microorganisms9010033 - 24 Dec 2020

Cited by 43 | Viewed by 6494

Abstract

Gamma-aminobutyric acid (GABA), the inhibitory neurotransmitter, can be naturally synthesized by a group of lactic acid bacteria (LAB) which is commonly found in rich carbohydrate materials such as fruits and fermented foods. Thirty-six isolates of GABA-producing LAB were obtained from Thai fermented foods. [...] Read more.

Gamma-aminobutyric acid (GABA), the inhibitory neurotransmitter, can be naturally synthesized by a group of lactic acid bacteria (LAB) which is commonly found in rich carbohydrate materials such as fruits and fermented foods. Thirty-six isolates of GABA-producing LAB were obtained from Thai fermented foods. Among these, Levilactobacillus brevis F064A isolated from Thai fermented sausage displayed high GABA content, 2.85 ± 0.10 mg/mL and could tolerate acidic pH and bile salts indicating a promising probiotic. Mulberry (Morus sp.) is widely grown in Thailand. Many mulberry fruits are left to deteriorate during the high season. To increase its value, mulberry juice was prepared and added to monosodium glutamate (MSG), 2% (w/v) prior to inoculation with 5% (v/v) of L. brevis F064A and incubated at 37 °C for 48 h to obtain the GABA-fermented mulberry juice (GABA-FMJ). The GABA-FMJ obtained had 3.31 ± 0.06 mg/mL of GABA content, 5.58 ± 0.52 mg gallic acid equivalent/mL of antioxidant activity, 234.68 ± 15.53 mg cyanidin-3-glucoside/mL of anthocyanin, an ability to inhibit growth of Bacillus cereus TISTR 687, Salmonella Typhi DMST 22842 and Shigella dysenteriae DMST 1511, and 10.54 ± 0.5 log₁₀ colony-forming units (CFU)/mL of viable L. brevis F064A cell count. This GABA-FMJ was considered as a potential naturally functional food for human of all ages. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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11 pages, 1787 KiB

Open AccessArticle

Apophysomyces jiangsuensis sp. nov., a Salt Tolerant and Phosphate-Solubilizing Fungus from the Tidelands of Jiangsu Province of China

by Siyu Li, Ruiming Han, Huanshi Zhang, Yongchun Song, Fugeng Zhao and Pei Qin

Microorganisms 2020, 8(12), 1868; https://doi.org/10.3390/microorganisms8121868 - 26 Nov 2020

Cited by 4 | Viewed by 2256

Abstract

A newly isolated phosphate-solubilizing fungus from the topsoil of Spartina alterniflora habitats in Yancheng coastal salt marsh was cultivated. Scanning electron microscopy observation revealed that the sporangia are nearly spherical, peach-shaped, and the spores formed on the top of sporangia. The spores are [...] Read more.

A newly isolated phosphate-solubilizing fungus from the topsoil of Spartina alterniflora habitats in Yancheng coastal salt marsh was cultivated. Scanning electron microscopy observation revealed that the sporangia are nearly spherical, peach-shaped, and the spores formed on the top of sporangia. The spores are ellipsoidal with raised white nubbins on the surface. Based on a polyphasic study and the genetic distance analysis referring to the sequence analysis of ITS (ITS1 + 5.8S + ITS2) and 28S rDNA (D1/D2 domains) genes, the novel species belongs to the genus Apophysomyces and is named as A. jiangsuensis. The optimum growth temperature and salinity of the new species were 28 °C and 1.15% NaCl, respectively. A study of its phosphate-solubilizing ability revealed that the fungus had an obvious decomposition effect on lecithin, Ca₃(PO₄)₂, and AlPO₃, respectively. The pH of the fermented liquid progressively decreased from 6.85 to 2.27 after 7 days of incubation, indicating that the low molecular weight organic acids excreted into the culture liquor were oxalic, succinic, and malic acids and a trace amount of citric acid. Among these, oxalic acid was the major organic acid, and its amount reached 652.5 mg/L. These results indicated that the main mechanism underlying the dissolved phosphorus was related to the secretion of large amounts of organic acids. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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17 pages, 2966 KiB

Open AccessArticle

Culturable Bacterial Community on Leaves of Assam Tea (Camellia sinensis var. assamica) in Thailand and Human Probiotic Potential of Isolated Bacillus spp.

by Patthanasak Rungsirivanich, Witsanu Supandee, Wirapong Futui, Vipanee Chumsai-Na-Ayudhya, Chaowarin Yodsombat and Narumol Thongwai

Microorganisms 2020, 8(10), 1585; https://doi.org/10.3390/microorganisms8101585 - 14 Oct 2020

Cited by 12 | Viewed by 4711

Abstract

Assam tea plants (Camellia sinensis var. assamica) or Miang are found in plantations and forests of Northern Thailand. Leaf fermentation has been performed for centuries, but little information is available about their associated microbial community. One hundred and fifty-seven bacterial isolates [...] Read more.

Assam tea plants (Camellia sinensis var. assamica) or Miang are found in plantations and forests of Northern Thailand. Leaf fermentation has been performed for centuries, but little information is available about their associated microbial community. One hundred and fifty-seven bacterial isolates were isolated from 62 Assam tea leaf samples collected from 6 provinces of Northern Thailand and classified within the phyla of Firmicutes, Actinobacteria, and Proteobacteria. Phayao and Phrae provinces exhibited the highest and the lowest bacterial diversities, respectively. The bacterial community structural pattern demonstrated significant differences between the west and the east sides. Since some Bacillus spp. have been reported to be involved in fermented Miang, Bacillus spp. isolated in this study were chosen for further elucidation. Bacillus siamensis ML122-2 exhibited a growth inhibitory effect against Staphylococcus aureus ATCC 25923 and MRSA DMST 20625, and the highest survival ability in simulated gastric and intestinal fluids (32.3 and 99.7%, respectively), autoaggregation (93.2%), cell surface hydrophobicity (50.0%), and bacterial adherence with Vero cells (75.8% of the control Lactiplantibacillusplantarum FM03-1). This B. siamensis ML122-2 is a promising probiotic to be used in the food industry and seems to have potential antibacterial properties relevant for the treatment of antibiotic-resistant infections. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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11 pages, 1647 KiB

Open AccessArticle

Larvae of the Clothing Moth Tineola bisselliella Maintain Gut Bacteria that Secrete Enzyme Cocktails to Facilitate the Digestion of Keratin

by Andreas Vilcinskas, Michael Schwabe, Karina Brinkrolf, Rudy Plarre, Natalie Wielsch and Heiko Vogel

Microorganisms 2020, 8(9), 1415; https://doi.org/10.3390/microorganisms8091415 - 14 Sep 2020

Cited by 8 | Viewed by 4392

Abstract

The evolutionary success of insects is promoted by their association with beneficial microbes that enable the utilization of unusual diets. The synanthropic clothing moth Tineola bisselliella provides an intriguing example of this phenomenon. The caterpillars of this species have adapted to feed on [...] Read more.

The evolutionary success of insects is promoted by their association with beneficial microbes that enable the utilization of unusual diets. The synanthropic clothing moth Tineola bisselliella provides an intriguing example of this phenomenon. The caterpillars of this species have adapted to feed on keratin-rich diets such as feathers and wool, which cannot be digested by most other animals and are resistant to common digestive enzymes. Inspired by the hypothesis that this ability may be conferred by symbiotic microbes, we utilized a simple assay to detect keratinase activity and a method to screen gut bacteria for candidate enzymes, which were isolated from feather-fed larvae. The isolation of DNA from keratin-degrading bacterial strains followed by de novo genome sequencing resulted in the identification of a novel bacterial strain related to Bacillus sp. FDAARGOS_235. Genome annotation identified 20 genes with keratinase domains. Proteomic analysis of the culture supernatant from this gut bacterium grown in non-nutrient buffer supplemented with feathers revealed several candidate enzymes potentially responsible for keratin degradation, including a thiol-disulfide oxidoreductase and multiple proteases. Our results suggest that the unusual diet of T. bisselliella larvae promotes their association with keratinolytic microorganisms and that the ability of larvae to feed on keratin can at least partially be attributed to bacteria that produce a cocktail of keratin-degrading enzymes. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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21 pages, 1978 KiB

Open AccessArticle

Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

by Ivete Sandra Maquia, Paula Fareleira, Isabel Videira e Castro, Denise R. A. Brito, Ricardo Soares, Aniceto Chaúque, M. Manuela Ferreira-Pinto, Erica Lumini, Andrea Berruti, Natasha S. Ribeiro, Isabel Marques and Ana I. Ribeiro-Barros

Microorganisms 2020, 8(9), 1291; https://doi.org/10.3390/microorganisms8091291 - 24 Aug 2020

Cited by 11 | Viewed by 4526

Abstract

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina [...] Read more.

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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15 pages, 1760 KiB

Open AccessArticle

Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar

by Leon Marič, Ilse Cleenwerck, Tomaž Accetto, Peter Vandamme and Janja Trček

Microorganisms 2020, 8(8), 1178; https://doi.org/10.3390/microorganisms8081178 - 3 Aug 2020

Cited by 30 | Viewed by 6131

Abstract

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S–23S rRNA gene internal transcribed [...] Read more.

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S–23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S–23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206^T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515^T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C_19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C_18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382^T and AV436^T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382^T (= ZIM B1054^T = LMG 31303^T = CCM 8958^T) and of Komagataeibacter melomenusus AV436^T (= ZIM B1056^T = LMG 31304^T = CCM 8959^T). Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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13 pages, 14943 KiB

Open AccessArticle

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

by Léa Girard, Cédric Lood, Hassan Rokni-Zadeh, Vera van Noort, Rob Lavigne and René De Mot

Microorganisms 2020, 8(8), 1166; https://doi.org/10.3390/microorganisms8081166 - 31 Jul 2020

Cited by 20 | Viewed by 5196

Abstract

The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or [...] Read more.

The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or engaging in more laborious and costly approaches. The rpoD gene, like the 16S rRNA gene, is included in most MLSA procedures and has already been suggested for the rapid identification of certain groups of Pseudomonas. However, a comprehensive overview of the rpoD-based phylogenetic relationships within the Pseudomonas genus is lacking. In this study, we present the rpoD-based phylogeny of 217 type strains of Pseudomonas and defined a cutoff value of 98% nucleotide identity to differentiate strains at the species level. To validate this approach, we sequenced the rpoD of 145 environmental isolates and complemented this analysis with whole genome sequencing. The rpoD sequence allowed us to accurately assign Pseudomonas isolates to 20 known species and represents an excellent first diagnostic tool to identify new Pseudomonas species. Finally, rpoD amplicon sequencing appears as a reliable and low-cost alternative, particularly in the case of large environmental studies with hundreds or thousands of isolates. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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24 pages, 3210 KiB

Open AccessArticle

Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh

by Otun Saha, M. Nazmul Hoque, Ovinu Kibria Islam, Md. Mizanur Rahaman, Munawar Sultana and M. Anwar Hossain

Microorganisms 2020, 8(8), 1135; https://doi.org/10.3390/microorganisms8081135 - 27 Jul 2020

Cited by 39 | Viewed by 6268

Abstract

The avian pathogenic Escherichia coli (APEC) strains are the chief etiology of colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs), and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using [...] Read more.

The avian pathogenic Escherichia coli (APEC) strains are the chief etiology of colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs), and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into ten, nine, and eight distinct genotypes by RAPD assay (discriminatory index, DI = 0.8707), BOX-PCR (DI = 0.8591) and ERIC-PCR (DI = 0.8371), respectively. The combination of three phylogenetic markers (chuA, yjaA and DNA fragment TspE4.C2) classified APEC isolates into B2₃ (37.36%), A1 (33.91%), D2 (11.49%), B2₂ (9.20%), and B1 (8.05%) phylotypes. Majority of the APEC isolates (75–100%) harbored VGs (ial, fimH, crl, papC, and cjrC). These VGs (papC and cjrC) and phylotypes (D2 and B2) of APEC had significant (p = 0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (clade A and clade B) of APEC, where clade A had 98–100% similarity with E. coli APEC O78 and E. coli EHEC strains, and clade B had closest relationship with E. coli O169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades, while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers, and possessed plasmids of varying ranges (1.0 to 54 kb). In vitro antibiogram profiling revealed that 100% isolates were resistant to ≥3 antibiotics, of which 61.96%, 55.24%, 53.85%, 51.16% and 45.58% isolates in phylotypes B1, D2, B2₂, B2₃, and A1, respectively, were resistant to these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B2₂, showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%), and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation among phylotypes with CRB (p = 0.008), biofilm formation (p = 0.02), drug resistance (p = 0.03), and VGs (p = 0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic-resistant APEC strains from different phylotypes suggest the use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in poultry farms in Bangladesh. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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11 pages, 916 KiB

Open AccessArticle

Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies

by Lucilla Iacumin, Francesca Cecchini, Marco Vendrame and Giuseppe Comi

Microorganisms 2020, 8(8), 1099; https://doi.org/10.3390/microorganisms8081099 - 23 Jul 2020

Cited by 6 | Viewed by 2959

Abstract

To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial [...] Read more.

To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial population studies was tested. Our results indicated that ePCR results in uniform amplification of several DNA molecules, overcoming the major limitations of conventional PCR, such as preferential amplification and DNA concentration dependence. Moreover, ePCR-DGGE resulted in higher sensitivity when compared to conventional PCR-DGGE methods used for studying microbial populations in a complex matrix. In fact, compared to conventional PCR, the DGGE profiles of ePCR products permitted the detection of a higher number of the species that were present in the tested sample. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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22 pages, 2805 KiB

Open AccessArticle

Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes

by Daniel Vieira, Soraia Esteves, Carolina Santiago, Eduardo Conde-Sousa, Ticiana Fernandes, Célia Pais, Pedro Soares and Ricardo Franco-Duarte

Microorganisms 2020, 8(7), 1001; https://doi.org/10.3390/microorganisms8071001 - 4 Jul 2020

Cited by 1 | Viewed by 3969

Abstract

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between [...] Read more.

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains’ technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains’ technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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23 pages, 5376 KiB

Open AccessArticle

Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae—Phylogeny, Phenotypes, Ecology and Domestication

by Ana Pontes, Mathias Hutzler, Patrícia H. Brito and José Paulo Sampaio

Microorganisms 2020, 8(6), 903; https://doi.org/10.3390/microorganisms8060903 - 15 Jun 2020

Cited by 34 | Viewed by 7651

Abstract

Saccharomyces cerevisiae—the most emblematic and industrially relevant yeast—has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially [...] Read more.

Saccharomyces cerevisiae—the most emblematic and industrially relevant yeast—has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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20 pages, 5604 KiB

Open AccessArticle

Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics

by Eiko E. Kuramae, Stan Derksen, Thiago R. Schlemper, Maurício R. Dimitrov, Ohana Y. A. Costa and Adriana P. D. da Silveira

Microorganisms 2020, 8(5), 725; https://doi.org/10.3390/microorganisms8050725 - 13 May 2020

Cited by 38 | Viewed by 5537

Abstract

Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum [...] Read more.

Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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11 pages, 861 KiB

Open AccessArticle

Bacillus telluris sp. nov. Isolated from Greenhouse Soil in Beijing, China

by He-Bao Guo, Shan-Wen He, Xing Wang, Kyu-Kyu Thin, Hai-Lei Wei and Xiao-Xia Zhang

Microorganisms 2020, 8(5), 702; https://doi.org/10.3390/microorganisms8050702 - 10 May 2020

Cited by 7 | Viewed by 3579

Abstract

A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium, which we designated as strain 03113^T, was isolated from greenhouse soil in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 03113^T is in the genus Bacillus and had the highest [...] Read more.

A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium, which we designated as strain 03113^T, was isolated from greenhouse soil in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 03113^T is in the genus Bacillus and had the highest similarity to Bacillus solani CCTCC AB 2014277^T (98.14%). The strain grew at 4 °C–50 °C (optimum 37 °C), with 0–10% (w/v) NaCl (optimum 5%), and in the range of pH 3.0–12.0 (optimum pH 8.0). Menaquinone was identified as MK-7, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main major cellular fatty acids detected were anteiso-C_15:0 (51.35%) and iso-C_15:0 (11.06%), which are the predominant cellular fatty acids found in all recognized members of the genus Bacillus. The 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANI), and in silico DNA—DNA hybridization (DDH) value between strain 03113^T and the most closely related species were 70.5% and 22.6%, respectively, which supported our conclusion that 03113^T represented a novel species in the genus Bacillus. We demonstrated that type strain 03113^T (=ACCC 03113^T=JCM 33017^T) was a novel species in the genus Bacillus, and the name Bacillus telluris sp. nov. was proposed. Strain 03113^T secreted auxin IAA and carried the nitrogenase iron protein (nifH) gene, which indicated that strain 03113^T has the potential to fix nitrogen and promote plant growth. Bacillus telluris sp. nov. 03113^T is a potential candidate for the biofertilizers of organic agriculture areas. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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12 pages, 3418 KiB

Open AccessArticle

Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture

by Juanjuan Zhao, Xia Zhao, Junru Wang, Qi Gong, Xiaoxia Zhang and Guishan Zhang

Microorganisms 2020, 8(4), 608; https://doi.org/10.3390/microorganisms8040608 - 22 Apr 2020

Cited by 16 | Viewed by 5446

Abstract

A flagellate, rod–shaped bacterium designated strain M15^T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity [...] Read more.

A flagellate, rod–shaped bacterium designated strain M15^T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140^T (99.64%) and Rhizobium pusense NRCPB10^T (99.36%), respectively. The complete genome of the strain M15^T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140^T (88.11%, 54.80%), R. pusense NRCPB10^T (86.00%, 53.00%) and R. nepotum 39/7^T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15^T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15^T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15^T (=JCM 32903^T = ACCC 60121^T), and the strain M15^T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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15 pages, 4052 KiB

Open AccessArticle

Characterization of a Versatile Plant Growth-Promoting Rhizobacterium Pseudomonas mediterranea Strain S58

by Yilin Gu, Jing Wang, Zhenyuan Xia and Hai-Lei Wei

Microorganisms 2020, 8(3), 334; https://doi.org/10.3390/microorganisms8030334 - 27 Feb 2020

Cited by 19 | Viewed by 4661

Abstract

Plant growth-promoting rhizobacterial strain S58 was isolated from the tobacco rhizosphere. It showed strong antagonism against a battery of plant pathogenic fungi and bacteria, and controlled wheat sharp eyespot and tobacco wildfire diseases efficiently. Further tests showed that strain S58 solubilized organic phosphate [...] Read more.

Plant growth-promoting rhizobacterial strain S58 was isolated from the tobacco rhizosphere. It showed strong antagonism against a battery of plant pathogenic fungi and bacteria, and controlled wheat sharp eyespot and tobacco wildfire diseases efficiently. Further tests showed that strain S58 solubilized organic phosphate and produced siderophore, protease, ammonia, and indole-3-acetic acid. In Arabidopsis thaliana, it promoted plant growth and changed root system architecture by restricting the growth of primary roots and increasing lateral root numbers. We relied on morphological, biochemical, physiological characteristics, and molecular phylogenic analysis to identify strain S58 as Pseudomonas mediterranea. The complete genome of strain S58 has a single circular chromosome of 6,150,838 bp with a 61.06% G+C content. The bacterial genome contained 5,312 predicted genes with an average length of 992.90 bp. A genome analysis suggested that P. mediterranea S58 was a rich cyclic lipopeptide (CLP)-producing strain that possessed seven non-ribosomal peptide gene clusters for CLP synthesis. Leaf inoculation of the bacterial culture and supernatants triggered cell death-like immunity in tobacco. Quantitative real-time PCR assays showed that the strain S58 induced the expression of pattern-triggered immunity and cell death marker genes, but not jasmonic acid marker genes. The results suggested that P. mediterranea S58 is a novel, versatile plant growth-promoting agent with multiple beneficial traits for plants. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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17 pages, 3428 KiB

Open AccessArticle

Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov.

by Chun-Zhi Jin, Ye Zhuo, Xuewen Wu, So-Ra Ko, Taihua Li, Feng-Jie Jin, Chi-Yong Ahn, Hee-Mock Oh, Hyung-Gwan Lee and Long Jin

Microorganisms 2020, 8(2), 262; https://doi.org/10.3390/microorganisms8020262 - 15 Feb 2020

Cited by 23 | Viewed by 5481

Abstract

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5^T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5^T has 64.4% G+C content and contains 4240 [...] Read more.

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5^T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5^T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5^T, except for N₂O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5^T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5^T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5^T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5^T. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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14 pages, 2175 KiB

Open AccessArticle

Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species

by Jiang Li, Ruyu Gao, Yun Chen, Dong Xue, Jiahui Han, Jin Wang, Qilin Dai, Min Lin, Xiubin Ke and Wei Zhang

Microorganisms 2020, 8(1), 101; https://doi.org/10.3390/microorganisms8010101 - 10 Jan 2020

Cited by 19 | Viewed by 4400

Abstract

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based [...] Read more.

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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15 pages, 3180 KiB

Open AccessArticle

Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain

by Miguel Rodríguez, José Carlos Reina, Victoria Béjar and Inmaculada Llamas

Microorganisms 2019, 7(12), 637; https://doi.org/10.3390/microorganisms7120637 - 2 Dec 2019

Cited by 2 | Viewed by 4348

Abstract

A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10^T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 [...] Read more.

A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10^T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10^T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047^T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C_15:0, C_16:0, and iso-C_15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10^T (= CECT 9541^T =LMG 30535^T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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Review

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29 pages, 1138 KiB

Open AccessReview

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

by Davide Francioli, Guillaume Lentendu, Simon Lewin and Steffen Kolb

Microorganisms 2021, 9(2), 361; https://doi.org/10.3390/microorganisms9020361 - 12 Feb 2021

Cited by 51 | Viewed by 11161

Abstract

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have [...] Read more.

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies. Full article

(This article belongs to the Special Issue Microbial Isolation and Characterization)

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