Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds

Gerna, Davide; Clara, David; Allwardt, Dorothee; Mitter, Birgit; Roach, Thomas

doi:10.1128/spectrum.00172-22

Cited by 10 publications

(10 citation statements)

References 109 publications

(154 reference statements)

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“…The absence of neighbors in pure culture, and consequently the absence of the necessary metabolites, is then one of the reasons behind unculturability ( Pande and Kost, 2017 ). Bacteria living in certain environments, such as endophytes, benefit from the use of highly specialized growth medium containing the environment’s original metabolites ( Gerna et al, 2022 ).…”

Section: A Helping Hand From Your Neighbors – Growth Factorsmentioning

confidence: 99%

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

2023

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In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial “dark matter” hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

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Section: A Helping Hand From Your Neighbors – Growth Factorsmentioning

confidence: 99%

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

2023

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“…Seed‐borne endophytes with antifungal activities have been employed in managing pathogenic infestations on plants (Newcombe et al, 2023 ; Sandhya et al, 2017 ; Yang et al, 2020 ). The characterization of seed‐borne endophytes to determine their functions and application on crops could greatly enrich nutrient‐limited environments and sustain plant health and growth in terms of yield enhancement, pathogen suppression and plant resilience to stresses (Gerna et al, 2022 ; Liu et al, 2023 ). These concepts can bring novel opportunities to help achieve food security.…”

Section: How Do Seed Microbiomes Work and Can Be Manipulated?mentioning

confidence: 99%

The seed microbiomes of staple food crops

Sun,

Adeleke,

Shi

et al. 2023

Microbial Biotechnology

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The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.

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“…Being typical inhabitants of the rhizosphere of many plants, Curtobacterium spp. have been shown to promote seed germination [ 8 , 9 ] and plant growth [ 10 , 11 ], and to suppress the growth of phytopathogens [ 12 , 13 ]. A pathovar, Curtobacterium flaccumfaciens pv.…”

Section: Introductionmentioning

confidence: 99%

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Evseev

Lukianova

Tarakanov

et al. 2023

IJMS

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Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

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Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds

Cited by 10 publications

References 109 publications

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

The seed microbiomes of staple food crops

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

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