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11 pages, 1805 KiB

Open AccessArticle

Isolation, Genomic and Metabolomic Characterization of Streptomyces tendae VITAKN with Quorum Sensing Inhibitory Activity from Southern India

by Nabila Mohammed Ishaque, Ilia Burgsdorf, Jessie James Limlingan Malit, Subhasish Saha, Roberta Teta, Daniela Ewe, Krishnan Kannabiran, Pavel Hrouzek, Laura Steindler, Valeria Costantino and Kumar Saurav

Microorganisms 2020, 8(1), 121; https://doi.org/10.3390/microorganisms8010121 - 16 Jan 2020

Cited by 16 | Viewed by 5555

Abstract

Streptomyces are among the most promising genera in terms of production ability to biosynthesize a variety of bioactive secondary metabolites with pharmaceutical interest. Coinciding with the increase in genomic sequencing of these bacteria, mining of their genomes for biosynthetic gene clusters (BGCs) has [...] Read more.

Streptomyces are among the most promising genera in terms of production ability to biosynthesize a variety of bioactive secondary metabolites with pharmaceutical interest. Coinciding with the increase in genomic sequencing of these bacteria, mining of their genomes for biosynthetic gene clusters (BGCs) has become a routine component of natural product discovery. Herein, we describe the isolation and characterization of a Streptomyces tendae VITAKN with quorum sensing inhibitory (QSI) activity that was isolated from southern coastal part of India. The nearly complete genome consists of 8,621,231bp with a GC content of 72.2%. Sequence similarity networks of the BGCs detected from this strain against the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) database and 3365 BGCs predicted by antiSMASH analysis of publicly available complete Streptomyces genomes were generated through the BiG-SCAPE-CORASON platform to evaluate its biosynthetic novelty. Crude extract analysis using high-performance liquid chromatography connected to high resolution tandem mass spectrometry (HPLC-HRMS/MS) and dereplication through the Global Natural Product Social Molecular Networking (GNPS) online workflow resulted in the identification of cyclic dipeptides (2, 5-diketopiperazines, DKPs) in the extract, which are known to possess QSI activity. Our results highlight the potential of genome mining coupled with LC-HRMS/MS and in silico tools (GNPS) as a valid approach for the discovery of novel QSI lead compounds. This study also provides the biosynthetic diversity of BGCs and an assessment of the predicted chemical space yet to be discovered. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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17 pages, 6090 KiB

Open AccessArticle

Microbial Community Analyses Associated with Nine Varieties of Wine Grape Carposphere Based on High-Throughput Sequencing

by Shiwei Zhang, Xi Chen, Qiding Zhong, Xuliang Zhuang and Zhihui Bai

Microorganisms 2019, 7(12), 668; https://doi.org/10.3390/microorganisms7120668 - 9 Dec 2019

Cited by 41 | Viewed by 5848

Abstract

Understanding the composition of microbials on the grape carposphere may provide direct guidance for the wine brewing. In this work, 16S rRNA and ITS (Internal Transcribed Spacer) fungal amplicon sequencing were performed to investigate the differences of epiphytic microbial communities inhabiting different varieties [...] Read more.

Understanding the composition of microbials on the grape carposphere may provide direct guidance for the wine brewing. In this work, 16S rRNA and ITS (Internal Transcribed Spacer) fungal amplicon sequencing were performed to investigate the differences of epiphytic microbial communities inhabiting different varieties of wine grape berries. The results showed that the dominated phylum of different wine grape carpospheres were Proteobacteria, Actinomycetes, Firmicutes, Gemmatimonadete, and Bacteroidetes. The dominant bacterial genera of different wine grape varieties were Pseudomonas, Arthrobacter, Bacillus, Pantoea, Planomicrobium, Massilia, Curtobacterium, Corynebacterium, Cellulomonas, Sphingomonas, and Microvirga. The fungal communities of the grapes were dominated by Ascomycota for all nine wine varieties. The dominant fungal genera on grape carposphere were Alternaria, Cladosporium, unclassified Capnodiales, Phoma, Rhodotorula, Cryptococcus, Aureobasidium, and Epicoccum. Community structure exerts a significant impact on bacterial Bray-Curtis dissimilarity on six red grapes and also a significant bacterial impact on three white grapes. Community structure exerts a significant impact on fungal Bray-Curtis dissimilarity on six red grapes but weak or no fungal impact on three white grapes. The results revealed that grape variety plays a significant role in shaping bacterial and fungal community, varieties can be distinguished based on the abundance of several key bacterial and fungal taxa. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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26 pages, 7899 KiB

Open AccessArticle

Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation

by Fedia Ben Mefteh, Ali Chenari Bouket, Amal Daoud, Lenka Luptakova, Faizah N. Alenezi, Neji Gharsallah and Lassaad Belbahri

Microorganisms 2019, 7(10), 382; https://doi.org/10.3390/microorganisms7100382 - 23 Sep 2019

Cited by 14 | Viewed by 4070

Abstract

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. [...] Read more.

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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15 pages, 1232 KiB

Open AccessArticle

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment

by Alessia Bani, Luigimaria Borruso, Kirsty J. Matthews Nicholass, Tommaso Bardelli, Andrea Polo, Silvia Pioli, María Gómez-Brandón, Heribert Insam, Alex J. Dumbrell and Lorenzo Brusetti

Microorganisms 2019, 7(9), 349; https://doi.org/10.3390/microorganisms7090349 - 12 Sep 2019

Cited by 16 | Viewed by 5329

Abstract

Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a [...] Read more.

Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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15 pages, 2703 KiB

Open AccessArticle

Different Secondary Metabolite Profiles of Phylogenetically almost Identical Streptomyces griseus Strains Originating from Geographically Remote Locations

by Ignacio Sottorff, Jutta Wiese, Matthias Lipfert, Nils Preußke, Frank D. Sönnichsen and Johannes F. Imhoff

Microorganisms 2019, 7(6), 166; https://doi.org/10.3390/microorganisms7060166 - 6 Jun 2019

Cited by 29 | Viewed by 6492

Abstract

As Streptomyces have shown an outstanding capacity for drug production, different campaigns in geographically distant locations currently aim to isolate new antibiotic producers. However, many of these newly isolated Streptomyces strains are classified as identical to already described species. Nevertheless, as discrepancies in [...] Read more.

As Streptomyces have shown an outstanding capacity for drug production, different campaigns in geographically distant locations currently aim to isolate new antibiotic producers. However, many of these newly isolated Streptomyces strains are classified as identical to already described species. Nevertheless, as discrepancies in terms of secondary metabolites and morphology are possible, we compared two Streptomyces strains with identical 16S rRNA gene sequences but geographically distant origins. Chosen were an Easter Island Streptomyces isolate (Streptomyces sp. SN25_8.1) and the next related type strain, which is Streptomyces griseus subsp. griseus DSM 40236^T isolated from Russian garden soil. Compared traits included phylogenetic relatedness based on 16S rRNA gene sequences, macro and microscopic morphology, antibiotic activity and secondary metabolite profiles. Both Streptomyces strains shared several common features, such as morphology and core secondary metabolite production. They revealed differences in pigmentation and in the production of accessory secondary metabolites which appear to be strain-specific. In conclusion, despite identical 16S rRNA classification Streptomyces strains can present different secondary metabolite profiles and may well be valuable for consideration in processes for drug discovery. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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23 pages, 7750 KiB

Open AccessArticle

Phenotypic and Molecular Analyses of Rhizoctonia spp. Associated with Rice and Other Hosts

by Regina Faye C. Sandoval and Christian Joseph R. Cumagun

Microorganisms 2019, 7(3), 88; https://doi.org/10.3390/microorganisms7030088 - 19 Mar 2019

Cited by 11 | Viewed by 9209

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

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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17 pages, 2857 KiB

Open AccessArticle

Phylogenomic Analyses of Bradyrhizobium Reveal Uneven Distribution of the Lateral and Subpolar Flagellar Systems, Which Extends to Rhizobiales

by Daniel Garrido-Sanz, Miguel Redondo-Nieto, Elías Mongiardini, Esther Blanco-Romero, David Durán, Juan I. Quelas, Marta Martin, Rafael Rivilla, Aníbal R. Lodeiro and M. Julia Althabegoiti

Microorganisms 2019, 7(2), 50; https://doi.org/10.3390/microorganisms7020050 - 13 Feb 2019

Cited by 9 | Viewed by 5026

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 110^T 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 110^T 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

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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15 pages, 826 KiB

Open AccessReview

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

by Olawale Israel Omomowo and Olubukola Oluranti Babalola

Microorganisms 2019, 7(11), 481; https://doi.org/10.3390/microorganisms7110481 - 23 Oct 2019

Cited by 117 | Viewed by 10358

Abstract

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will [...] Read more.

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner. Full article

(This article belongs to the Special Issue Feature Papers in Environmental Microbiology)

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