Topical Collection "Feature Papers in Environmental Microbiology"

A topical collection in Microorganisms (ISSN 2076-2607). This collection belongs to the section "Environmental Microbiology".

Editor

Guest Editor
Dr. Nico Jehmlich

Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
Website | E-Mail
Phone: +493412354767
Interests: Metaproteomics, Protein-Stable Isotope Probing, Microbiome Biology, Environmental Microbiology

Topical Collection Information

Dear Colleagues,

As described in the title, this Topical Collection, Feature Papers in Environmental Microbiology, aims to collect high quality research articles, short communications, and review articles in all the fields of environmental microbiology. As the aim of this Topical Collection is to illustrate, through selected works, the frontier research in environmental microbiology, we encourage the editorial board members of the Environmental Microbiology Section of Microorganisms to contribute papers reflecting the latest progress in their research field, or to invite relevant experts and colleagues to do so.

Topics include, but are not limited to, the following:

Structure and function of microbial communities
Microbial community genetics, transcriptomics, proteomics, and metabolomics
Microbial interaction
Microbial communication
Microbial ecology
Microbial population biology
Biogeochemical processes (C-, N-, P-, and S-cycles)
Microbial life in extreme environments
Evolutionary processes of microbial communities
Biofilm formation and surfaces of microbes
Metabolic flux analysis and stable isotope probing (DNA, RNA, and protein)
Microbiome biology of environmental habitats (e.g., soil, rhizosphere, or
aquifer)
Microbial treatment—microbial biodegradation, microbial bioremediation,
microbial and waste recycling, microbial pesticide, microbial
fertilizer, and so on
Microbial pollution—pathogenic microorganisms in the environment
(water, soil, air, and food)—microbial metabolism, and environmental pollution
(e.g., microbial toxin), and so on
Microbiological monitoring—testing methods and monitoring techniques
development

Dr. Nico Jehmlich
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

2019

Open AccessArticle
Phenotypic and Molecular Analyses of Rhizoctonia spp. Associated with Rice and Other Hosts
Microorganisms 2019, 7(3), 88; https://doi.org/10.3390/microorganisms7030088
Received: 20 February 2019 / Revised: 11 March 2019 / Accepted: 15 March 2019 / Published: 19 March 2019
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Abstract
Forty-two Rhizoctonia isolates were collected from rice, mung bean, and grasses from Laguna, Philippines. Sixteen isolates were binucleate Rhizoctonia (BNR), while 26 were multinucleate Rhizoctonia (MNR). BNR isolates produced white to brown, small sclerotia (<1.0 mm) except for mung bean isolates. Twenty MNR [...] Read more.
Forty-two Rhizoctonia isolates were collected from rice, mung bean, and grasses from Laguna, Philippines. Sixteen isolates were binucleate Rhizoctonia (BNR), while 26 were multinucleate Rhizoctonia (MNR). BNR isolates produced white to brown, small sclerotia (<1.0 mm) except for mung bean isolates. Twenty MNR isolates produced big (>1.0 mm), light to dark brown sclerotia, three produced salmon-colored masses in the medium, and three did not produce sclerotia. Twenty-three MNR isolates were identified as R. solani AG1-IA using specific primers. Deduced Internal Transcribed Spacer (ITS) sequences of BNR isolates D1FL, NVL, and ScNL shared 100, 97, and 100% identity with R. oryzae-sativae, respectively, while MNR isolates BMgL, IbMgL, and MaSL that produced salmon-colored masses shared 100, 90, and 100% identity with R. oryzae, respectively. Preliminary analysis of the DNA fingerprint patterns generated by repetitive-element PCR (rep-PCR) clustered the 42 isolates into three: R. solani, R. oryzae-sativae, and R. oryzae, together with Ceratobasidium sp. R. solani isolates were pathogenic on rice (TN1), barnyard grass, mungbean (Pagasa 3), and tomato (Athena), while R. oryzae and R. oryzae-sativae isolates were only pathogenic on rice, Echinochloa crus-galli, and tomato. R. solani and R. oryzae were found to be more virulent than R. oryzae-sativae. Full article
Figures

Figure 1

Open AccessArticle
Phylogenomic Analyses of Bradyrhizobium Reveal Uneven Distribution of the Lateral and Subpolar Flagellar Systems, Which Extends to Rhizobiales
Microorganisms 2019, 7(2), 50; https://doi.org/10.3390/microorganisms7020050
Received: 19 December 2018 / Revised: 10 February 2019 / Accepted: 11 February 2019 / Published: 13 February 2019
PDF Full-text (2857 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no [...] Read more.
Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no obvious role, since its performance is explained by cooperation with the subpolar flagellum. In contrast, the lateral flagellum is the only type of flagella present in the related Rhizobiaceae family. In this work, we have analyzed the phylogeny of the Bradyrhizobium genus by means of Genome-to-Genome Blast Distance Phylogeny (GBDP) and Average Nucleotide Identity (ANI) comparisons of 128 genomes and divided it into 13 phylogenomic groups. While all the Bradyrhizobium genomes encode the subpolar flagellum, none of them encodes only the lateral flagellum. The simultaneous presence of both flagella is exclusive of the B. japonicum phylogenomic group. Additionally, 292 Rhizobiales order genomes were analyzed and both flagellar systems are present together in only nine genera. Phylogenetic analysis of 150 representative Rhizobiales genomes revealed an uneven distribution of these flagellar systems. While genomes within and close to the Rhizobiaceae family only possess the lateral flagellum, the subpolar flagellum is exclusive of more early-diverging families, where certain genera also present both flagella. Full article
Figures

Figure 1

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