TY - JOUR
A1 - Wicaksono, Wisnu Adi
A1 - Braun, Maria
A1 - Bernhardt, Jörg
A1 - Riedel, Katharina
A1 - Cernava, Tomislav
A1 - Berg, Gabriele
T1 - Trade-off for survival
BT - microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity
JF - Environment international : a journal of science, technology, health, monitoring and policy
N2 - The environmental micmbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen as a bioindicator organism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native micmbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.
Y1 - 2022
U6 - https://doi.org/10.1016/j.envint.2022.107474
SN - 1873-6750
VL - 168
PB - Elsevier Science
CY - Amsterdam [u.a.]
ER -
TY - JOUR
A1 - Olimi, Expedito
A1 - Kusstatscher, Peter
A1 - Wicaksono, Wisnu Adi
A1 - Abdelfattah, Ahmed
A1 - Cernava, Tomislav
A1 - Berg, Gabriele
T1 - Insights into the microbiome assembly during different growth stages and storage of strawberry plants
JF - Environmental microbiome
N2 - 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(7)-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.
KW - Fragaria x ananassa
KW - Microbiome assembly
KW - Fruit pathogens
KW - Bacterial
KW - communities
KW - Fungal communities
KW - Amplicon sequencing
KW - CLSM
Y1 - 2022
U6 - https://doi.org/10.1186/s40793-022-00415-3
SN - 2524-6372
VL - 17
IS - 1
PB - BMC
CY - London
ER -
TY - JOUR
A1 - Berg, Gabriele
A1 - Cernava, Tomislav
T1 - The plant microbiota signature of the Anthropocene as a challenge for microbiome research
JF - Microbiome
N2 - 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.
Y1 - 2022
U6 - https://doi.org/10.1186/s40168-021-01224-5
SN - 2049-2618
VL - 10
IS - 1
PB - BMC
CY - London
ER -
TY - JOUR
A1 - Montes-Osuna, Nuria
A1 - Cernava, Tomislav
A1 - Gomez-Lama Cabanas, Carmen
A1 - Berg, Gabriele
A1 - Mercado-Blanco, Jesus
T1 - Identification of volatile organic compounds emitted by two beneficial endophytic pseudomonas strains from olive roots
JF - Plants
N2 - The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens.
Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species.
In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. 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 V. dahliae.
For example, when co incubated with the defoliating pathotype of V. dahliae, 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 in planta.
KW - biological control agents
KW - olive rhizobacteria
KW - Pseudomonas sp
KW - PICF6
KW - Pseudomonas simiae PICF7
KW - root endophytes
KW - Verticillium dahliae
KW - volatilome
Y1 - 2022
U6 - https://doi.org/10.3390/plants11030318
SN - 2223-7747
VL - 11
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Wassermann, Birgit
A1 - Abdelfattah, Ahmed
A1 - Wicaksono, Wisnu Adi
A1 - Kusstatscher, Peter
A1 - Müller, Henry
A1 - Cernava, Tomislav
A1 - Goertz, Simon
A1 - Rietz, Steffen
A1 - Abbadi, Amine
A1 - Berg, Gabriele
T1 - The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines
JF - Microbial biotechnology
N2 - 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.
Y1 - 2022
U6 - https://doi.org/10.1111/1751-7915.14077
SN - 1751-7915
VL - 15
IS - 9
SP - 2379
EP - 2390
PB - Wiley
CY - Hoboken
ER -