Publications by authors named "Tomislav Cernava"

68 Publications

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems - A Selection of Case Studies.

Front Microbiol 2022 4;13:834622. Epub 2022 Jul 4.

School of Life Sciences, Pondicherry University, Puducherry, India.

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2022.834622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9315449PMC
July 2022

Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens.

J Adv Res 2022 07 18;39:49-60. Epub 2021 Oct 18.

College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China. Electronic address:

Introduction: A broad spectrum of rhizosphere bacteria and fungi were shown to play a central role for health, fitness and productivity of their host plants. However, implications of host metabolism on microbiota assembly in the phyllosphere and potential consequences for holobiont functioning were sparsely addressed. Previous observations indicated that tea plants might reduce disease occurrence in various forests located in their proximity; the underlying mechanisms and potential implications of the phyllosphere microbiota remained elusive.

Objectives: This study aimed atdeciphering microbiome assembly in the tea plant phyllosphere throughout shoot development as well as elucidating potential implications of host metabolites in this process. The main focus was to explore hidden interconnections between the homeostasis of the phyllosphere microbiome and resistance to fungal pathogens.

Methods: Profiling of host metabolites and microbiome analyses based on high-throughput sequencing were integrated to identify drivers of microbiome assembly throughout shoot development in the phyllosphere of tea plants. This was complemented by tracking of beneficial microorganisms in all compartments of the plant. Synthetic assemblages (SynAss), bioassays and field surveys were implemented to verify functioning of the phyllosphere microbiota.

Results: Theophylline and epigallocatechin gallate, two prevalent metabolites at the early and late shoot development stage respectively, were identified as the main drivers of microbial community assembly. Flavobacterium and Myriangium were distinct microbial responders at the early stage, while Parabacteroides and Mortierella were more enriched at the late stage. Reconstructed, stage-specific SynAss suppressed various tree phytopathogens by 13.0%-69.3% in vitro and reduced disease incidence by 8.24%-41.3% in vivo.

Conclusion: The findings indicate that a functional phyllosphere microbiota was assembled along with development-specific metabolites in tea plants, which continuously suppressed prevalent fungal pathogens. The insights gained into the temporally resolved metabolite response of the tea plant microbiota could provide novel solutions for disease management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jare.2021.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9263646PMC
July 2022

Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis.

Environ Microbiome 2022 Jun 24;17(1):33. Epub 2022 Jun 24.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Background: Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis.

Results: In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community.

Conclusions: The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40793-022-00425-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233336PMC
June 2022

Di-n-butyl phthalate negatively affects humic acid conversion and microbial enzymatic dynamics during composting.

J Hazard Mater 2022 08 6;436:129306. Epub 2022 Jun 6.

Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China. Electronic address:

To understand the effects of phthalic acid esters (PAEs) on humic acid (HA) conversion, enzymatic and specific metabolic dynamics during composting under di-n-butyl phthalate (DBP) stress were evaluated for the first time. The results indicated that HA conversion was mainly related to bacteria rather than fungi, with positive associations with Actinobacteria, Chloroflexi, and Gemmatimonadota (all P < 0.05), and negative associations with Proteobacteria and Bacteroidota (all P < 0.05), while DBP stress retarded HA formation by altering the core microbes related to HA formation and their metabolic functions. Moreover, typical hydrolase and oxidoreductase activities were altered under DBP stress, proteases and cellulases were hindered, and peroxidases as well as polyphenol oxidases were promoted during composting. Overall, our data shows that DBP stress can retard HA formation and compost maturation by interfering with microbial activity. This study provides potentially useful information for the degradation and reuse of PAE-contaminated waste.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhazmat.2022.129306DOI Listing
August 2022

Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes.

Sci Data 2022 06 1;9(1):254. Epub 2022 Jun 1.

State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.

The plant microbiota plays crucial roles in sustaining plant health and productivity. Advancing plant microbiome research and designing sustainable practices for agriculture requires in-depth assessments of microorganisms associated with different host plants; however, there is little information on functional aspects of many microorganisms of interest. Therefore, we enriched microorganisms from the phyllosphere of 110 rice genotypes and subjected them to shotgun metagenomic sequencing to reconstruct bacterial genomes from the obtained datasets. The approach yielded a total of 1.34 terabases of shotgun-sequenced metagenomic data. By separately recovering bacterial genomes from each of the 110 rice genotypes, we recovered 569 non-redundant metagenome-assembled genomes (MAGs) with a completeness higher than 50% and contaminations less than 10%. The MAGs were primarily assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia. The presented data provides an extended basis for microbiome analyses of plant-associated microorganisms. It is complemented by detailed metadata to facilitate implementations in ecological studies, biotechnological mining approaches, and comparative assessments with genomes or MAGs from other studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41597-022-01320-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160027PMC
June 2022

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts.

Nat Microbiol 2022 06 26;7(6):831-843. Epub 2022 May 26.

State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Department of Plant Protection, Zhejiang University, Hangzhou, China.

Plant-pathogenic fungi form intimate interactions with their associated bacterial microbiota during their entire life cycle. However, little is known about the structure, functions and interaction mechanisms of bacterial communities associated with fungal fruiting bodies (perithecia). Here we examined the bacterial microbiome of perithecia formed by Fusarium graminearum, the major pathogenic fungus causing Fusarium head blight in cereals. A total of 111 shared bacterial taxa were identified in the microbiome of 65 perithecium samples collected from 13 geographic locations. Within a representative culture collection, 113 isolates exhibited antagonistic activity against F. graminearum, with Pantoea agglomerans ZJU23 being the most efficient in reducing fungal growth and infectivity. Herbicolin A was identified as the key antifungal compound secreted by ZJU23. Genetic and chemical approaches led to the discovery of its biosynthetic gene cluster. Herbicolin A showed potent in vitro and in planta efficacy towards various fungal pathogens and fungicide-resistant isolates, and exerted a fungus-specific mode of action by directly binding and disrupting ergosterol-containing lipid rafts. Furthermore, herbicolin A exhibited substantially higher activity (between 5- and 141-fold higher) against the human opportunistic fungal pathogens Aspergillus fumigatus and Candida albicans in comparison with the clinically used fungicides amphotericin B and fluconazole. Its mode of action, which is distinct from that of other antifungal drugs, and its efficacy make herbicolin A a promising antifungal drug to combat devastating fungal pathogens, both in agricultural and clinical settings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41564-022-01131-xDOI Listing
June 2022

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines.

Microb Biotechnol 2022 May 20. Epub 2022 May 20.

Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.

Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1751-7915.14077DOI Listing
May 2022

First report of green mold disease caused by Penicillium citrinum on Dictyophora rubrovalvata in China.

Plant Dis 2022 May 10. Epub 2022 May 10.

Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12/I, Graz, Austria, 8010;

Dictyophora rubrovolvata is a saprophytic mushroom widely cultivated in China, including Guizhou Province for its high nutritional, medicinal, and economical values (Chen et al. 2021). In May 2021, green mold disease was observed on the fruiting bodies of D. rubrovolvata, causing its death or preventing it from forming a sporocarp, in an indoor-production facility at Asuo village, Baiyun District Guiyang city, Guizhou Province, China (26°73'51" N, 106°72'88" E). The disease incidence was 60%-70% in the affected 1.33-ha growing area, causing a serious economic loss. To identify the causal agent, a total of 15 samples with symptomatic symptoms were collected. Small pieces (5 mm × 5 mm) were cut from the diseased tissues, surface sterilized in 0.4% NaClO for 5 min, washed three times with sterilized water, placed on potato dextrose agar (PDA) medium, and incubated at 24 °C for 7 days. Twenty-one pure cultures were obtained by single-spore isolation method. The colonies were initially white but after seven days as conidia developed they turned green. Hyphae were hyaline and guttulate. Conidiophores were verrucose stipes, triverticulate, and phialides flask shaped. Conidia were smooth and pale green, with subglobose to globose shape measuring 2.0-2.5 × 1.8-2.5 µm (n=50). Based on these morphological characteristics, the isolates matched the description of the genus Penicillium (Visagie et al. 2014). To confirm the identity, DNA of five representative isolates (QS001, QS005, QS008, QS015, QS017) was extracted according to the manufacturer's instructions (Biomiga Fungal DNA Extraction Kit; CA, USA). Afterwards, PCR was performed to amplify ITS region, calmodulin and β-tubulin genes using primer pairs ITS1/ITS4 (White et al. 1990), CMD5/CMD6 (Glass et al. 1995), and Bt2a/Bt2b (Hong et al. 2006), respectively. BLASTN analysis of these sequences showed the best matches with Penicillium citrinum CBS 139.45 (ITS region: 98.60% (493/500 bp) identity to accession MH856132.1; CMD: 99.79% (469/470 bp) identity to accession MN969245.1; β-tubulin:100% (407/407 bp) identity to accession GU944545.1). Representative sequences of the sequenced DNA regions were deposited in GenBank (ITS region: OK446552; CMD: OK492612; β-tubulin: OK482677). Furthermore, a phylogenetic tree was constructed with MEGA 7 based on the concatenated sequences. Koch's postulates were met to confirm the pathogenicity of the representative isolate (QS001) on D. rubrovolvata. Six discs (5mm×5mm) from actively growing P. citrinum QS001 colonies (5-day-old) were placed on six fruiting bodies of D. rubrovolvata (5-month-old). Mock inoculations were performed using PDA discs only without any fungus. The inoculation sites were wrapped with a sterilized 200-μm nylon mesh. All fruiting bodies were incubated at 23°C ± 2°C under a 0-h/24-h photoperiod and 80% relative humidity (RH) after inoculation. After 14 days, green mold was observed on all P. citrinum QS001 inoculated mushrooms. In contrast, no disease was observed in mock inoculated group. The disease assays were repeated three times. P. citrinum QS001 was isolated from all inoculated D. rubrovolvata and verified via the molecular analysis mentioned above. To the best of our knowledge, this is the first report that P. citrinum causes green mold on D. rubrovalvata in China and further studies should focus on managing this disease to prevent any disease outbreaks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-10-21-2291-PDNDOI Listing
May 2022

Implications of carbon catabolite repression for plant-microbe interactions.

Plant Commun 2022 03 28;3(2):100272. Epub 2021 Dec 28.

INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France.

Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xplc.2021.100272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073323PMC
March 2022

Insights into the microbiome assembly during different growth stages and storage of strawberry plants.

Environ Microbiome 2022 Apr 28;17(1):21. Epub 2022 Apr 28.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.

Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10-10 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa.

Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40793-022-00415-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9052558PMC
April 2022

The plant microbiota signature of the Anthropocene as a challenge for microbiome research.

Microbiome 2022 03 26;10(1):54. Epub 2022 Mar 26.

Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.

Background: One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

Results: Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.

Conclusions: Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-021-01224-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8959079PMC
March 2022

Identification of Volatile Organic Compounds Emitted by Two Beneficial Endophytic Strains from Olive Roots.

Plants (Basel) 2022 Jan 25;11(3). Epub 2022 Jan 25.

Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus "Alameda del Obispo", 14004 Cordoba, Spain.

The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. sp. PICF6 and PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Additionally, strain PICF7 is able to promote the growth of barley and , VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens ( spp., , and f.sp. ) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of and . Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of . For example, when co incubated with the defoliating pathotype of the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants11030318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8840531PMC
January 2022

The emergence of disease-preventing bacteria within the plant microbiota.

Environ Microbiol 2022 Jan 9. Epub 2022 Jan 9.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.

Microbiome studies have facilitated the discovery of harmful as well as beneficial microorganisms over the last years. Recently, distinct bacteria were found within the microbiota of crop plants that confer disease resistance to their hosts. Although it is well known that the interplay between microbes and plants can result in improved plant health, the phenomenon of holistically disease-preventing bacteria is new. Here, we put the recent discoveries of disease-preventing bacteria in context with decade-long plant microbiome research that has preceded them. In addition, we provide explanations as to why disease resistance in certain plants, mediated by specific bacteria, has only recently been discovered. We argue that such findings were primarily limited by technological constraints and that analogous findings are very likely to be made with other plant species. The general concept may even be extendable to additional groups of organisms. We, therefore, suggest the introduction of the specific term soterobiont in order to facilitate an unambiguous definition of disease-preventing microorganisms within the microbiota of higher organisms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.15896DOI Listing
January 2022

The Influence of Temperature and Host Gender on Bacterial Communities in the Asian Citrus Psyllid.

Insects 2021 Nov 25;12(12). Epub 2021 Nov 25.

Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.

The Asian citrus psyllid, Kuwayama is the primary vector for (CLas), which causes a destructive disease in citrus plants. Bacterial symbionts are important determinants of insect physiology, and they can be impacted by many external factors. Temperature is an important abiotic factor affecting insect physiology, and it is also known that differences in symbiont proportions may vary in different insect genders. To date, it is unclear how the symbionts of are affected by temperature and gender. This study used high-throughput sequencing of 16S ribosomal RNA amplicons to determine how temperature and gender affect the bacterial communities present in . We identified 27 amplicon sequence variants (ASVs) belonging to 10 orders, seven classes, and five phyla. The dominant phylum was Proteobacteria (99.93%). Other phyla, including Firmicutes, Bacteroidota, Deinococcota, Cyanobacteria, and Actinobacteriota, were less abundant (<0.1%). (71.77-81.59%) and (18.39-28.22%) were the predominant taxa in all samples. Under high-temperature treatment, was more common in females, while had a higher abundance in males. In males, was more abundant under low-temperature treatments than under high-temperature treatments. In contrast, showed a higher abundance under high-temperature treatments than under low-temperature treatments. An RT-qPCR (quantitative real-time PCR) approach confirmed the results obtained with high-throughput DNA sequencing. Our results provide a basis for understanding the co-adaptation of and its symbionts to environmental temperature stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/insects12121054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8704560PMC
November 2021

Fusaricidins, Polymyxins and Volatiles Produced by Strains DSM 32871 and M1.

Pathogens 2021 Nov 15;10(11). Epub 2021 Nov 15.

Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany.

are efficient producers of potent agents against bacterial and fungal pathogens, which are of great interest both for therapeutic applications in medicine as well as in agrobiotechnology. Lipopeptides produced by such organisms play a major role in their potential to inactivate pathogens. In this work we investigated two lipopeptide complexes, the fusaricidins and the polymyxins, produced by strains DSM 32871 and M1 by MALDI-TOF mass spectrometry. The fusaricidins show potent antifungal activities and are distinguished by an unusual variability. For strain DSM 32871 we identified numerous yet unknown variants mass spectrometrically. DSM 32871 produces polymyxins of type E (colistins), while M1 forms polymyxins P. For both strains, novel but not yet completely characterized polymyxin species were detected, which possibly are glycosylated. These compounds may be of interest therapeutically, because polymyxins have gained increasing attention as last-resort antibiotics against multiresistant pathogenic Gram-negative bacteria. In addition, the volatilomes of DSM 32781 and M1 were investigated with a GC-MS approach using different cultivation media. Production of volatile organic compounds (VOCs) was strain and medium dependent. In particular, strain M1 manifested as an efficient VOC-producer that exhibited formation of 25 volatiles in total. A characteristic feature of is the formation of volatile pyrazine derivatives.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/pathogens10111485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621861PMC
November 2021

Arthrobacter is a universal responder to di-n-butyl phthalate (DBP) contamination in soils from various geographical locations.

J Hazard Mater 2022 01 14;422:126914. Epub 2021 Aug 14.

Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria.

Plasticizer phthalic acid esters (PAEs) are commonly found as contaminants in various soils. Previous studies indicated that their natural degradation can substantially differ among soil types; however, potential implications of the soil microbiome remained largely unexplored. Here, we have collected ten soil types from nine different geographical regions of China to investigate the degradation of DBP therein and role of bacteria in this process. Results showed that the degradation rate of DBP was lowest in nutrient-poor red soils from Jiangxi Province, while it was highest in fluvo-aquatic soil from Hebei Province. Bacterial community responses to DBP substantially differed in each of the analyzed soils. Arthrobacter is known for its broad-spectrum activity in terms of DBP degradation in soil and was therefore implemented as bioremediating inoculant in many polluted environments. In the present study, network analyses indicated that synergism between soil bacteria increased following exposure to DBP. Arthrobacter and Sphingomonas were found to expand their positive interactions with other members of the microbiome in DBP-contaminated soils. The overall findings of our study provide a basis for biomarker development for detection of DBP contaminations and an extended basis for future bioremediation approaches based on beneficial bacteria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhazmat.2021.126914DOI Listing
January 2022

Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species.

J Hazard Mater 2022 01 8;422:126836. Epub 2021 Aug 8.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany; Institute for Biochemistry and Biology, University of Postdam, Postdam, Germany. Electronic address:

Multi-species biofilms are more resistant against stress compared to single-species biofilms. However, the mechanisms underlying this common observation remain elusive. Therefore, we studied biofilm formation of well-known opportunistic pathogens (Acinetobacter baumanii, Enterococcus faecium, Escherichia coli, Staphylococcus haemolyticus and Stenotrophomonas maltophilia) in various approaches. Synergistic effects in their multi-species biofilms were observed. Using metatranscriptomics, changes in the gene expression of the involved members became evident, and provided explanations for the improved survivability under nutrient limitation and exposure to disinfectants. Genes encoding proteins for vitamin B6 synthesis and iron uptake were linked to synergism in the multi-species biofilm under nutrient-limited conditions. Our study indicates that sub-lethal concentrations of an alcohol-based disinfectant enhance biofilm yields in multi-species assemblages. A reduction of the dominant taxa in the multi-species biofilm under disinfectant pressure allowed minor taxa to bloom. The findings underline the importance of minor but antimicrobial-resistant species that serve as "protectors" for the whole assemblage due to upregulation of genes involved in defence mechanisms and biofilm formation. This ultimately results in an increase in the total yield of the multi-species biofilm. We conclude that inter-species interactions may be crucial for the survival of opportunistic pathogens; especially under conditions that are typically found under hospital settings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhazmat.2021.126836DOI Listing
January 2022

Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria.

Microbiome 2021 08 11;9(1):170. Epub 2021 Aug 11.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Background: Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem.

Results: Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens.

Conclusions: The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-021-01117-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359052PMC
August 2021

Explorative assessment of coronavirus-like short sequences from host-associated and environmental metagenomes.

Sci Total Environ 2021 Nov 24;793:148494. Epub 2021 Jun 24.

Graz University of Technology, Institute of Environmental Biotechnology, Graz, Austria; BioTechMed-Graz, Graz, Austria. Electronic address:

The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is also an unprecedented challenge for scientists. False-positive virus detection tests not only aggravate the situation in the healthcare sector, but also provide ground for speculations. Previous studies have highlighted the importance of software choice and data interpretation in virome studies. We aimed to further expand theoretical and practical knowledge in bioinformatics-driven virome studies by focusing on short, virus-like DNA sequences in metagenomic data. Analyses of datasets obtained from different sample types (terrestrial, animal and human related samples) and origins showed that coronavirus-like sequences have existed in host-associated and environmental samples before the current COVID-19 pandemic. In the analyzed datasets, various Betacoronavirus-like sequences were detected that also included SARS-CoV-2 matches. Deepening analyses indicated that the detected sequences are not of viral origin and thus should not be considered in virome profiling approaches. Our study confirms the importance of parameter selection, especially in terms of read length, for reliable virome profiling. Natural environments are an important source of coronavirus-like nucleotide sequences that should be taken into account when virome datasets are analyzed and interpreted. We therefore suggest that processing parameters are carefully selected for SARS-CoV-2 profiling in host related as well as environmental samples in order to avoid incorrect identifications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2021.148494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222970PMC
November 2021

Microbiome Structure of the Aphid (Sulzer) Is Shaped by Different Solanaceae Plant Diets.

Front Microbiol 2021 5;12:667257. Epub 2021 Jul 5.

College of Tobacco Science, Guizhou University, Guiyang, China.

(Sulzer) is an important insect pest in agriculture that has a very broad host range. Previous research has shown that the microbiota of insects has implications for their growth, development, and environmental adaptation. So far, there is little detailed knowledge about the factors that influence and shape the microbiota of aphids. In the present study, we aimed to investigate diet-induced changes in the microbiome of using high-throughput sequencing of bacterial 16S ribosomal RNA gene fragments in combination with molecular and microbiological experiments. The transfer of aphids to different plants from the Solanaceae family resulted in a substantial decrease in the abundance of the primary symbiont . In parallel, a substantial increase in the abundance of was observed; it accounted for up to 69.4% of the bacterial community in guts and the attached bacteriocytes. In addition, we observed negative effects on aphid population dynamics when they were transferred to pepper plants ( L.). The microbiome of this treatment group showed a significantly lower increase in the abundance of when compared with the other Solanaceae plant diets, which might be related to the adaptability of the host to this diet. Molecular quantifications of bacterial genera that were substantially affected by the different diets were implemented as an additional verification of the microbiome-based observations. Complementary experiments with bacteria isolated from aphids that were fed with different plants indicated that nicotine-tolerant strains occur in Solanaceae-fed specimens, but they were not restricted to them. Overall, our mechanistic approach conducted under controlled conditions provided strong indications that the aphid microbiome shows responses to different plant diets. This knowledge could be used in the future to develop environmentally friendly methods for the control of insect pests in agriculture.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.667257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8287905PMC
July 2021

First report of passion fruit leaf blight caused by Nigrospora sphaerica in China.

Plant Dis 2021 Jul 2. Epub 2021 Jul 2.

Guizhou University, 71206, College of Tobacco Sciences, 2nd floor of Congde Building, West Campus of Guizhou University, Guiyang, Guizhou, China, 550025;

Passion fruit (Passiflora edulis Sims) is a widely cultivated dicotyledonous perennial plant with woody vines (Asande et al. 2020). In November 2020, leaf blight was observed on leaves of P. edulis (cultivar: 'Panama Red') newly planted in Wangyou, Huishui county, Guizhou province, China (25°82'57" N, 106°50'49" E). The leaf blight occurred on both young and old leaves, starting from the margins, and then extended to the entire leaves. The color of the affected tissue was brown with a yellow hallo in the early period, and then gradually turned to grey. The disease incidence was 60%-70% on a 0.08-ha field. Following isolation of the potential pathogen from 12 diseased leaves, nine isolates were obtained. The colonies were white with a regular round shape at the early stage and became black with fluffy hyphae after eight days on potato dextrose agar (PDA) medium, incubated at 25°C in the dark for 10 days. The single cell conidia were solitary, spherical or slightly ellipsoidal, black, shiny, smooth, aseptate, spherical, and 8.1-13.5 μm (n=50) in diameter. Conidiophores (5.2-9.9 × 4.4-7.2 μm) were mostly reduced to conidiogenous cells and aggregated in clusters on hyphae. Conidiogenous cells were hyaline to pale brown or black, globose to ampulliform or clavate. Morphological characteristics of the isolates matched the description of the genus Nigrospora Mei Wang & L. Cai (Wang et al. 2017). For molecular identification, DNA was extracted, and PCRs were performed with primers ITS1/ITS4 for the ITS region (White et al. 1990), primers Bt2a/Bt2b for the β-tubulin gene (TUB) (Glass and Donaldson 1995), and primers EF1-728F/EF1-986R for the translation elongation factor 1-alpha gene (EF1-α) (Carbone and Kohn 1999). Representative sequences of the ITS region, EF1-α, and TUB sequences (from isolate WYR007) were deposited in GenBank (accession numbers: MW561355; MZ053463; MZ032030) and are included in the supplementary materials. BLAST analysis against sequences from previously published studies showed 99.58% (ITS region), 99.54% (EF1-α), and 99.45% (TUB) identity to Nigrospora sphaerica sequences (accession numbers: MN215808.1; MN864137.1; KY019606.1). In addition, homology was confirmed with a phylogenetic tree using concatenated sequences from ITS, EF1-α and TUB constructed with MEGA 7 for which the maximum likelihood method was used with 1,000 bootstrapping iterations. To complete Koch's postulates, conidia suspensions of isolate WYR007 (prepared from 1-month-old colonies in 0.05% Tween 20 buffer and adjusted to a concentration of 1 × 103 conidia/mL) were sprayed on 15 leaves (200 μL per leaf) of 5 one-year-old healthy P. edulis plants (cultivar: 'Panama Red'). The same number of leaves from control group plants was only treated with 0.05% Tween buffer. All plants were incubated at 26°C ± 2°C under a 16 h/8 h photoperiod and 70%-75% relative humidity (RH) after inoculation. After 14 days, symptomatic blight appeared on all inoculated leaves. In contrast, no symptoms appeared on leaves in the control group. The disease assays were repeated three times. Pure cultures were re-isolated from diseased leaves and confirmed to be N. sphaerica based on the morphological and molecular methods mentioned above (ITS region, the TUB, and the EF1-α sequences). To our knowledge, this study is the first report of N. sphaerica as a pathogen on P. edulis causing leaf blight. The identification of the pathogen could provide relevant background for its future management.s Sims) is a widely cultivated dicotyledonous perennial plant with woody vines (Asande et al. 2020). In November 2020, leaf blight was observed on leaves of P. edulis (cultivar: 'Panama Red') newly planted in Wangyou, Huishui county, Guizhou province, China (25°82'57" N, 106°50'49" E). The leaf blight occurred on both young and old leaves, starting from the margins, and then extended to the entire leaves. The color of the affected tissue was brown with a yellow hallo in the early period, and then gradually turned to grey. The disease incidence was 60%-70% on a 0.08-ha field. Following isolation of the potential pathogen from 12 diseased leaves, nine isolates were obtained. The colonies were white with a regular round shape at the early stage and became black with fluffy hyphae after eight days on potato dextrose agar (PDA) medium, incubated at 25°C in the dark for 10 days. The single cell conidia were solitary, spherical or slightly ellipsoidal, black, shiny, smooth, aseptate, spherical, and 8.1-13.5 μm (n=50) in diameter. Conidiophores (5.2-9.9 × 4.4-7.2 μm) were mostly reduced to conidiogenous cells and aggregated in clusters on hyphae. Conidiogenous cells were hyaline to pale brown or black, globose to ampulliform or clavate. Morphological characteristics of the isolates matched the description of the genus Nigrospora Mei Wang & L. Cai (Wang et al. 2017). For molecular identification, DNA was extracted, and PCRs were performed with primers ITS1/ITS4 for the ITS region (White et al. 1990), primers Bt2a/Bt2b for the β-tubulin gene (TUB) (Glass and Donaldson 1995), and primers EF1-728F/EF1-986R for the translation elongation factor 1-alpha gene (EF1-α) (Carbone and Kohn 1999). Representative sequences of the ITS region, EF1-α, and TUB sequences (from isolate WYR007) were deposited in GenBank (accession numbers: MW561355; MZ053463; MZ032030) and are included in the supplementary materials. BLAST analysis against sequences from previously published studies showed 99.58% (ITS region), 99.54% (EF1-α), and 99.45% (TUB) identity to Nigrospora sphaerica sequences (accession numbers: MN215808.1; MN864137.1; KY019606.1). In addition, homology was confirmed with a phylogenetic tree using concatenated sequences from ITS, EF1-α and TUB constructed with MEGA 7 for which the maximum likelihood method was used with 1,000 bootstrapping iterations. To complete Koch's postulates, conidia suspensions of isolate WYR007 (prepared from 1-month-old colonies in 0.05% Tween 20 buffer and adjusted to a concentration of 1 × 103 conidia/mL) were sprayed on 15 leaves (200 μL per leaf) of 5 one-year-old healthy P. edulis plants (cultivar: 'Panama Red'). The same number of leaves from control group plants was only treated with 0.05% Tween buffer. All plants were incubated at 26°C ± 2°C under a 16 h/8 h photoperiod and 70%-75% relative humidity (RH) after inoculation. After 14 days, symptomatic blight appeared on all inoculated leaves. In contrast, no symptoms appeared on leaves in the control group. The disease assays were repeated three times. Pure cultures were re-isolated from diseased leaves and confirmed to be N. sphaerica based on the morphological and molecular methods mentioned above (ITS region, the TUB, and the EF1-α sequences). To our knowledge, this study is the first report of N. sphaerica as a pathogen on P. edulis causing leaf blight. The identification of the pathogen could provide relevant background for its future management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-05-21-0900-PDNDOI Listing
July 2021

Editorial: Novel Insights Into the Response of the Plant Microbiome to Abiotic Factors.

Front Plant Sci 2021 28;12:607874. Epub 2021 May 28.

Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2021.607874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193938PMC
May 2021

Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens.

Microbiome 2021 06 6;9(1):131. Epub 2021 Jun 6.

State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.

Background: Microbiome interactions are important determinants for ecosystem functioning, stability, and health. In previous studies, it was often observed that bacteria suppress potentially pathogenic fungal species that are part of the same plant microbiota; however, the underlying microbe-microbe interplay remains mostly elusive. Here, we explored antagonistic interactions of the fungus Fusarium graminearum and bacterium Streptomyces hygroscopicus at the molecular level. Both are ubiquitous members of the healthy wheat microbiota; under dysbiosis, the fungus causes devastating diseases.

Results: In co-cultures, we found that Streptomyces alters the fungal acetylome leading to substantial induction of fungal autophagy. The bacterium secrets rapamycin to inactivate the target of rapamycin (TOR), which subsequently promotes the degradation of the fungal histone acetyltransferase Gcn5 through the 26S proteasome. Gcn5 negatively regulates fungal autophagy by acetylating the autophagy-related protein Atg8 at the lysine site K13 and blocking cellular relocalization of Atg8. Thus, degradation of Gcn5 triggered by rapamycin was found to reduce Atg8 acetylation, resulting in autophagy induction in F. graminearum.

Conclusions: Autophagy homeostasis plays an essential role in fungal growth and competition, as well as for virulence. Our work reveals a novel post-translational regulation of autophagy initiated by a bacterial antibiotic. Rapamycin was shown to be a powerful modulator of bacteria-fungi interactions with potential importance in explaining microbial homeostasis in healthy plant microbiomes. The autophagic process provides novel possibilities and targets to biologically control pathogens. Video abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-021-01077-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8182927PMC
June 2021

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato.

Environ Microbiome 2020 Sep 17;15(1):17. Epub 2020 Sep 17.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Background: The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments.

Results: Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (10-10 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed.

Conclusion: Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40793-020-00364-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067393PMC
September 2020

Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants.

Front Microbiol 2021 8;12:650610. Epub 2021 Apr 8.

Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying interactions are well studied. In contrast, effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated the plant.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.650610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060476PMC
April 2021

The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities.

Microb Ecol 2021 Nov 16;82(4):909-918. Epub 2021 Mar 16.

College of Tobacco Science, Guizhou University, Guiyang, 550025, China.

Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-021-01728-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8551121PMC
November 2021

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars.

Front Microbiol 2021 16;12:629852. Epub 2021 Feb 16.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera , , and were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.629852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920960PMC
February 2021

Identification of new eligible indicator organisms for combined sewer overflow via 16S rRNA gene amplicon sequencing in Kanda River, Tokyo.

J Environ Manage 2021 Apr 5;284:112059. Epub 2021 Feb 5.

Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.

Fecal indicator bacteria (FIB) are commonly used to evaluate the pollution impact of combined sewer overflows (CSOs) in urban rivers. Although water quality assessment with FIB has a long tradition, recent studies demonstrated that FIB have a low correlation with pathogens and therefore are not accurate enough for the assessment of potential human hazards in water. Consequently, new eligible and more specific indicators have to be identified, which was done in this study via sequencing of genetic markers from total community DNA. To identify potential microbiome-based indicators, microbial communities in samples from an urban river in Tokyo under different climatic conditions (dry and rainy) were compared with the influent and effluent of three domestic wastewater treatment plants (WWTPs) by analyzing 16 S rRNA gene amplicon libraries. In the first part of this study, physicochemical parameters and FIB quantification with selective culture techniques facilitated the identification of samples contaminated with CSO, sewage, or both. This allowed the grouping of samples into CSO-contaminated and non-contaminated samples, an essential step prior to the microbiome comparison between samples. Increased turbidity, ammonia concentrations, and E. coli [up to (9.37 ± 0.95) × 10 CFU/mL after 11.5 mm of rainfall] were observed in CSO-contaminated river samples. Comparison of dry weather (including WWTP samples) and rainy weather samples showed a reduction in microbial diversity in CSO-contaminated samples. Furthermore, the results of this study suggest Bacteroides spp. as a novel indicator of sewage pollution in surface waters.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jenvman.2021.112059DOI Listing
April 2021

Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.

Microbiome 2021 01 27;9(1):29. Epub 2021 Jan 27.

Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.

Background: Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.

Results: The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 10 16S rRNA gene copies ng DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.

Conclusions: Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-020-00982-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841911PMC
January 2021

Bacterial seed endophyte shapes disease resistance in rice.

Nat Plants 2021 01 4;7(1):60-72. Epub 2021 Jan 4.

Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.

Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-00826-5DOI Listing
January 2021
-->